Yu J

References (129)

Title : Personalized venlafaxine dose prediction using artificial intelligence technology: a retrospective analysis based on real-world data - Liu_2024_Int.J.Clin.Pharm__
Author(s) : Liu Y , Yu Z , Ye X , Zhang J , Hao X , Gao F , Yu J , Zhou C
Ref : Int J Clin Pharm , : , 2024
Abstract : BACKGROUND: Venlafaxine dose regimens vary considerably between individuals, requiring personalized dosing. AIM: This study aimed to identify dose-related influencing factors of venlafaxine through real-world data analysis and to construct a personalized dose model using advanced artificial intelligence techniques. METHOD: We conducted a retrospective study on patients with depression treated with venlafaxine. Significant variables were selected through a univariate analysis. Subsequently, the predictive performance of seven models (XGBoost, LightGBM, CatBoost, GBDT, ANN, TabNet, and DT) was compared. The algorithm that demonstrated optimal performance was chosen to establish the dose prediction model. Model validation used confusion matrices and ROC analysis. Additionally, a dose subgroup analysis was conducted. RESULTS: A total of 298 patients were included. TabNet was selected to establish the venlafaxine dose prediction model, which exhibited the highest performance with an accuracy of 0.80. The analysis identified seven crucial variables correlated with venlafaxine daily dose, including blood venlafaxine concentration, total protein, lymphocytes, age, globulin, cholinesterase, and blood platelet count. The area under the curve (AUC) for predicting venlafaxine doses of 75 mg, 150 mg, and 225 mg were 0.90, 0.85, and 0.90, respectively. CONCLUSION: We successfully developed a TabNet model to predict venlafaxine doses using real-world data. This model demonstrated substantial predictive accuracy, offering a personalized dosing regimen for venlafaxine. These findings provide valuable guidance for the clinical use of the drug.
ESTHER : Liu_2024_Int.J.Clin.Pharm__
PubMedSearch : Liu_2024_Int.J.Clin.Pharm__
PubMedID: 38733475

Title : Carboxylesterase and Cytochrome P450 Confer Metabolic Resistance Simultaneously to Azoxystrobin and Some Other Fungicides in Botrytis cinerea - Wang_2024_J.Agric.Food.Chem__
Author(s) : Wang Q , Wang X , Cai D , Yu J , Chen X , Niu W , Wang S , Liu X , Zhou D , Yin F , Wang T , Shi X , Wu Z , Zhang J , Hao J , Liu P
Ref : Journal of Agricultural and Food Chemistry , : , 2024
Abstract : Plant pathogens have frequently shown multidrug resistance (MDR) in the field, often linked to efflux and sometimes metabolism of fungicides. To investigate the potential role of metabolic resistance in B. cinerea strains showing MDR, the azoxystrobin-sensitive strain B05.10 and -resistant strain Bc242 were treated with azoxystrobin. The degradation half-life of azoxystrobin in Bc242 (9.63 days) was shorter than that in B05.10 (28.88 days). Azoxystrobin acid, identified as a metabolite, exhibited significantly lower inhibition rates on colony and conidia (9.34 and 11.98%, respectively) than azoxystrobin. Bc242 exhibited higher expression levels of 34 cytochrome P450s (P450s) and 11 carboxylesterase genes (CarEs) compared to B05.10 according to RNA-seq analysis. The expression of P450 genes Bcin_02g01260 and Bcin_12g06380, along with the CarEs Bcin_12g06360 in Saccharomyces cerevisiae, resulted in reduced sensitivity to various fungicides, including azoxystrobin, kresoxim-methyl, pyraclostrobin, trifloxystrobin, iprodione, and carbendazim. Thus, the mechanism of B. cinerea MDR is linked to metabolism mediated by the CarE and P450 genes.
ESTHER : Wang_2024_J.Agric.Food.Chem__
PubMedSearch : Wang_2024_J.Agric.Food.Chem__
PubMedID: 38226868 || 38634420

Title : Comparative study on the enzymatic degradation of phenolic esters: The HPLC-UV quantification of tyrosol and gallic acid liberated from tyrosol acyl esters and alkyl gallates by hydrolytic enzymes - Wang_2024_Food.Chem_442_138529
Author(s) : Wang X , Wang Q , Cai D , Yu J , Chen X , Guo X , Tong P , Liu X , Yin F , Zhou D
Ref : Food Chem , 442 :138529 , 2024
Abstract : HPLC-UV analysis was used to evaluate the enzymatic degradation characteristics of tyrosol acyl esters (TYr-Es) and alkyl gallates (A-GAs). Among various hydrolytic enzymes, TYr-Es can be hydrolyzed by pancrelipase, while A-GAs cannot be hydrolyzed by pancrelipase. Interestingly, carboxylesterase-1b (CES-1b), carboxylesterase-1c (CES-1c) and carboxylesterase-2 (CES-2) are able to hydrolyze TYr-Es and A-GAs, and thus to liberate tyrosol (TYr) and gallic acid (GA). By contrast, the degrees of hydrolysis (DHs) of TYr-Es and A-GAs by CES-1b and CES-1c were significantly higher than those by CES-2. Meanwhile, the DHs of TYr-Es were much higher than those of A-GAs. Especially, the DHs firstly increased and then decreased with the increasing alkyl chain length. Besides, DHs positively correlated with the unsaturation degree at the same chain length. Through regulating carbon length, unsaturation degree and the ester bond structure, controlled-release of phenolic compounds and fatty acids (or fatty alcohols) from phenolic esters will be easily achieved.
ESTHER : Wang_2024_Food.Chem_442_138529
PubMedSearch : Wang_2024_Food.Chem_442_138529
PubMedID: 38271912

Title : Preparation of functional oils rich in phytosterol esters and diacylglycerols by enzymatic transesterification - Shi_2024_Food.Chem_448_139100
Author(s) : Shi W , Li H , Fu Y , Tang X , Yu J , Wang X
Ref : Food Chem , 448 :139100 , 2024
Abstract : Phytosterol esters (PEs) and diacylglycerols (DAGs) have various health benefits in humans. In this study, PEs and DAGs were synthesized by lipase-catalyzed transesterification between a natural oil and phytosterols. First, commercial lipases were screened for transesterification and were further verified using multiple-ligand molecular docking. AYS "Amano" (a lipase from Candida rugosa) was found to be the optimum lipase. Subsequently, the enzymatic transesterification conditions were optimized. The optimized conditions were determined to be a 1:2 M ratio of phytosterols to oil, 100 mmol/L phytosterols, and 9 % AYS "Amano", and 50 degreesC for 24 h in 20 mL n-hexane. Under these conditions, over 70 % of phytosterols were converted to PEs. In this study, an efficient enzymatic process was developed to produce value-added functional oils rich in PEs and DAGs, with PEs content <= 31.6 %, DAGs content <= 11.2 %, acid value >= 0.91 mg KOH/g, and peroxide value >= 2.38 mmol/kg.
ESTHER : Shi_2024_Food.Chem_448_139100
PubMedSearch : Shi_2024_Food.Chem_448_139100
PubMedID: 38552457

Title : Rhynchophylline relieves nonalcoholic fatty liver disease by activating lipase and increasing energy metabolism - Liu_2023_Int.Immunopharmacol_117_109948
Author(s) : Liu K , Liu S , Wu C , Wang Y , Zhang Y , Yu J , Li X , Qi X , Su S , Zhou L , Li Y
Ref : Int Immunopharmacol , 117 :109948 , 2023
Abstract : Hepatic fat metabolism may be altered in the context of overnutrition and obesity, often resulting in the accumulation of triglycerides in hepatocytes and leading to nonalcoholic fatty liver disease (NAFLD). Natural plant alkaloids have demonstrated great potential for the prevention and treatment of NAFLD. However, the role of rhynchophylline (RHY) in lipid metabolism is not clear. We explored the role of RHY in lipid metabolism in cells treated with oleic and palmitic acids to mimic high-fat diet (HFD) conditions. RHY attenuated oleic and palmitic acid-induced increases in triglyceride accumulation in HepG2, AML12, and LMH cells. RHY also increased energy metabolism and reduced oxidative stress. We further investigated the effect of RHY on hepatic lipid metabolism in mice fed an HFD including 40 mg/kg RHY. RHY alleviated hepatic steatosis, reduced fat deposition, promoted energy metabolism, and improved glucose metabolism. We investigated the mechanism responsible for this activity by docking with key proteins of lipid metabolism disorders using Discovery Studio software, which showed that RHY interacted well with lipases. Finally, we found that adding RHY promoted lipase activity and lipolysis. In conclusion, RHY ameliorated HFD-induced NAFLD and its complications by increasing lipase activity.
ESTHER : Liu_2023_Int.Immunopharmacol_117_109948
PubMedSearch : Liu_2023_Int.Immunopharmacol_117_109948
PubMedID: 37012893

Title : Perilipin1 deficiency prompts lipolysis in lipid droplets and aggravates the pathogenesis of persistent immune activation in Drosophila - Wang_2023_J.Innate.Immun__
Author(s) : Wang L , Lin J , Yang K , Wang W , Lv Y , Zeng X , Zhao Y , Yu J , Pan L
Ref : J Innate Immun , : , 2023
Abstract : Lipid droplets (LDs) are highly dynamic intracellular organelles, which are involved in lots of biological processes. However, the dynamic morphogenesis and functions of intracellular LDs during persistent innate immune responses remain obscure. In this study, we induce long-term systemic immune activation in Drosophila through genetic manipulation. Then, the dynamic pattern of LDs is traced in the Drosophila fat body. We find that deficiency of Plin1, a key regulator of LDs' reconfiguration, blocks LDs minimization at the initial stage of immune hyperactivation but enhances LDs breakdown at the later stage of sustained immune activation via recruiting the lipase Brummer (Bmm, homologous to human ATGL). The high wasting in LDs shortens the lifespan of flies with high-energy-cost immune hyperactivation. Therefore, these results suggest a critical function of LDs during long-term immune activation and provide a potential treatment for the resolution of persistent inflammation.
ESTHER : Wang_2023_J.Innate.Immun__
PubMedSearch : Wang_2023_J.Innate.Immun__
PubMedID: 37742619

Title : The potential of hydroxytyrosol fatty acid esters to enhance oral bioavailabilities of hydroxytyrosol and fatty acids: Continuous and slow-release ability in small intestine and blood - Wang_2023_Food.Chem_422_136246
Author(s) : Wang X , Wang Q , Yu J , Guo X , Tong P , Yin F , Liu X , Zhou D
Ref : Food Chem , 422 :136246 , 2023
Abstract : HPLC-UV analysis in rat everted gut sac and in vitro simulated digestion models indicated that hydroxytyrosol fatty acid esters (HTy-Es) could be hydrolyzed by pancreatic lipase to slow-release of free fatty acids (FAs) and HTy. Meanwhile, the HTy-Es, the liberated FAs and the HTy could cross the membrane and were transported into blood circulation. HTy-Es were further hydrolyzed by carboxylesterase in in vitro rat plasma hydrolysis model, which also showed slow-release of FAs (C1-C4) and HTy. Especially, the rates of hydrolysis and transport initially increased and then decreased with the increasing alkyl chain length. Besides, the above rates of the HTy-Es with a straight chain were greater than those of its isomer with a branched chain. Therefore, the above-mentioned continuous and slow-release of FAs and HTy in small intestine and blood clearly demonstrated that HTy-Es would be an effective approach to enhance oral bioavailabilities of free fatty acids and hydroxytyrosol.
ESTHER : Wang_2023_Food.Chem_422_136246
PubMedSearch : Wang_2023_Food.Chem_422_136246
PubMedID: 37126954

Title : Vincamine, from an antioxidant and a cerebral vasodilator to its anticancer potential - Ren_2023_Bioorg.Med.Chem_92_117439
Author(s) : Ren Y , DeRose K , Li L , Gallucci JC , Yu J , Douglas Kinghorn A
Ref : Bioorganic & Medicinal Chemistry , 92 :117439 , 2023
Abstract : Vincamine is a naturally occurring indole alkaloid showing antioxidant activity and has been used clinically for the prevention and treatment of cerebrovascular disorders and insufficiencies. It has been well documented that antioxidants may contribute to cancer treatment, and thus, vincamine has been investigated recently for its potential antitumor activity. Vincamine was found to show cancer cell cytotoxicity and to modulate several important proteins involved in tumor growth, including acetylcholinesterase (AChE), mitogen-activated protein kinase (MAPK), nuclear factor-kappaB (NF-kappaB), nuclear factor erythroid 2-related factor 2 (Nrf2), and T-box 3 (TBX3). Several bisindole alkaloids, including vinblastine and vincristine and their synthetic derivatives, vindesine, vinflunine, and vinorelbine, have been used as clinically effective cancer chemotherapeutic agents. In the present review, the discovery and development of vincamine as a useful therapeutic agent and its antioxidant and antitumor activity are summarized, with its antioxidant-related mechanisms of anticancer potential being described. Also, discussed herein are the design of the potential vincamine-based oncolytic agents, which could contribute to the discovery of further new agents for cancer treatment.
ESTHER : Ren_2023_Bioorg.Med.Chem_92_117439
PubMedSearch : Ren_2023_Bioorg.Med.Chem_92_117439
PubMedID: 37579526

Title : Identification of the first selective bioluminescent probe for real-time monitoring of carboxylesterase 2 in vitro and in vivo - Chen_2023_Analyst__
Author(s) : Chen Z , Yu J , Sun K , Song J , Chen L , Jiang Y , Wang Z , Chen Y , Zhao T , Miao Z , Huang T , Chen M , Zhao Y , Hai A , Qi Q , Feng P , Li M , Ke B
Ref : Analyst , : , 2023
Abstract : Carboxylesterase (CES), a main hydrolysis enzyme family in the human body, plays a crucial role in drug metabolism. Among them, CES1 and CES2 are the primary subtypes, and each exhibits distinct distribution and functions. However, convenient and non-invasive methods for distinguishing them and the real-time monitoring of CES2 are relatively rare, hindering the further understanding of physiological functions and underlying mechanisms. In this study, we have designed, synthesized, and evaluated the first selective bioluminescent probe (CBP 1) for CES2 with high sensitivity, high specificity and rapid reactivity. This probe offers a promising approach for the real-time detection of CES2 and its dynamic fluctuations both in vitro and in vivo.
ESTHER : Chen_2023_Analyst__
PubMedSearch : Chen_2023_Analyst__
PubMedID: 36661088 || 38078792

Title : Plasma membrane association and resistosome formation of plant helper immune receptors - Wang_2023_Proc.Natl.Acad.Sci.U.S.A_120_e2222036120
Author(s) : Wang Z , Liu X , Yu J , Yin S , Cai W , Kim NH , El Kasmi F , Dangl JL , Wan L
Ref : Proc Natl Acad Sci U S A , 120 :e2222036120 , 2023
Abstract : Intracellular plant immune receptors, termed NLRs (Nucleotide-binding Leucine-rich repeat Receptors), confer effector-triggered immunity. Sensor NLRs are responsible for pathogen effector recognition. Helper NLRs function downstream of sensor NLRs to transduce signaling and induce cell death and immunity. Activation of sensor NLRs that contain TIR (Toll/interleukin-1receptor) domains generates small molecules that induce an association between a downstream heterodimer signalosome of EDS1 (EnhancedDisease Susceptibility 1)/SAG101 (Senescence-AssociatedGene 101) and the helper NLR of NRG1 (NRequired Gene 1). Autoactive NRG1s oligomerize and form calcium signaling channels largely localized at the plasma membrane (PM). The molecular mechanisms of helper NLR PM association and effector-induced NRG1 oligomerization are not well characterized. We demonstrate that helper NLRs require positively charged residues in their N-terminal domains for phospholipid binding and PM association before and after activation, despite oligomerization and conformational changes that accompany activation. We demonstrate that effector activation of a TIR-containing sensor NLR induces NRG1 oligomerization at the PM and that the cytoplasmic pool of EDS1/SAG101 is critical for cell death function. EDS1/SAG101 cannot be detected in the oligomerized NRG1 resistosome, suggesting that additional unknown triggers might be required to induce the dissociation of EDS1/SAG101 from the previously described NRG1/EDS1/SAG101 heterotrimer before subsequent NRG1 oligomerization. Alternatively, the conformational changes resulting from NRG1 oligomerization abrogate the interface for EDS1/SAG101 association. Our data provide observations regarding dynamic PM association during helper NLR activation and underpin an updated model for effector-induced NRG1 resistosome formation.
ESTHER : Wang_2023_Proc.Natl.Acad.Sci.U.S.A_120_e2222036120
PubMedSearch : Wang_2023_Proc.Natl.Acad.Sci.U.S.A_120_e2222036120
PubMedID: 37523563

Title : In vitro plasma hydrolysis of phenolic esters and their absorption kinetics in rats: Controlled release of phenolic compounds and enhanced health benefits - Wang_2023_Food.Chem_435_137647
Author(s) : Wang X , Wang Q , Cai D , Yu J , Liu X , Yin F , Zhou D
Ref : Food Chem , 435 :137647 , 2023
Abstract : Phenolic esters are considered as promising functional food ingredients. However, their digestion, absorption and metabolism are still unclear. Tyrosol acyl esters (TYr-Es), hydroxytyrosol acyl esters (HTy-Es) and alkyl gallates (A-GAs) were hydrolyzed by carboxylesterase in plasma and exhibited slow release of polyphenols (phenolic acids). In vitro hydrolysis degrees initially increased and then decreased with the increasing carbon chain length (C2-C16). TYr-Es exhibited higher hydrolysis degrees compared to HTy-Es, and hydrolysis degrees of TYr-Es and HTy-Es were markedly higher than those of A-GAs. Due to the fast hydrolysis rates of TYr-Es and HTy-Es, they were undetectable in all rat plasma samples collected at several times within 24 h after administration. Whereas, A-GAs could be detected in rat plasmas and three absorption peaks were found in the pharmacokinetic profiles. Importantly, the T(1/2), MRT, AUC(0-), AUC(0-t) in octyl gallate group were longer (or stronger) than those in propyl gallate and dodecyl gallate groups.
ESTHER : Wang_2023_Food.Chem_435_137647
PubMedSearch : Wang_2023_Food.Chem_435_137647
PubMedID: 37804730

Title : Functional regulation of Wnt protein through post-translational modifications - Yu_2022_Biochem.Soc.Trans__
Author(s) : Yu J , Virshup DM
Ref : Biochemical Society Transactions , : , 2022
Abstract : Wnts are lipid-modified signaling glycoproteins present in all metazoans that play key roles in development and homeostasis. Post-translational modifications of Wnts regulate their function. Wnts have a unique post-translational modification, O-linked palmitoleation, that is absolutely required for their function. This Wnt-specific modification occurs during Wnt biosynthesis in the endoplasmic reticulum (ER), catalyzed by the O-acyltransferase Porcupine (PORCN). Palmitoleation is required for Wnt to bind to its transporter Wntless (WLS/Evi) as well as to its receptor Frizzled (FZD). Recent structural studies have illustrated how PORCN recognizes its substrates, and how drugs inhibit this. The abundance of WLS is tightly regulated by intracellular recycling and ubiquitylation-mediated degradation in the ER. The function of Wnt glycosylation is less well understood, and the sites and types of glycosylation are not largely conserved among different Wnts. In polarized tissues, the type of glycans can determine whether the route of trafficking is apical or basolateral. In addition, pairing of the 24 highly conserved cysteines in Wnts to form disulfide bonds is critical in maintaining proper structure and activities. Extracellularly, the amino terminus of a subset of Wnts can be cleaved by a dedicated glycosylphosphatidylinositol (GPI)-anchored metalloprotease TIKI, resulting in the inactivation of these Wnt proteins. Additionally, NOTUM is a secreted extracellular carboxylesterase that removes the palmitoleate moiety from Wnt, antagonizing its activity. In summary, Wnt signaling activity is controlled at multiple layers by post-translational modifications.
ESTHER : Yu_2022_Biochem.Soc.Trans__
PubMedSearch : Yu_2022_Biochem.Soc.Trans__
PubMedID: 36484635

Title : Chemical profile, anti-hepatoma activity, anti-acetylcholinesterase and antioxidant activity of aerial part of Aconitum carmichaeli Debx - Yu_2022_Nat.Prod.Res__1
Author(s) : Yu J , Xia J , Xu J , Chen S , Zhang Y , Yin F , Fang J , Cai L , Zhang B , Zhan Y , Zhang X , Zeng Z , Liang Z
Ref : Nat Prod Res , :1 , 2022
Abstract : Five extracts of the aerial parts of Aconitum carmichaeli were obtained by different solvent extraction or macroporous adsorption resin purification: ethyl acetate layer extract (EAE), n-butanol layer extract (BuE), water layer extract (WE), extract eluted by 10% ethanol from macroporous resin (10%EE), extract eluted by 80% ethanol from macroporous resin (80%EE). Antioxidant activities of the five extracts were determined by ABTS, DPPH, FRAP assays, anti-AChE activities by modified Ellman's method, insvitro anti-hepatoma activities by CCK-8 assay, and chemical constituents of 80%EE were identified by UPLC-QE-Orbitrap-MS. The results demonstrated that the 80%EE showed the best insvitro anti-hepatoma activity on Huh-7 cell line with an IC(50) of 103.91 +/- 11.02 microg/mL. 10%EE and 80%EE gave the highest antioxidant activity. Furthermore, current findings demonstrated that the aerial part of Aconitum carmichaeli Debx. has high medicinal value and may be a good natural medicine.
ESTHER : Yu_2022_Nat.Prod.Res__1
PubMedSearch : Yu_2022_Nat.Prod.Res__1
PubMedID: 36503283

Title : Progress in enrichment of n-3 polyunsaturated fatty acid: a review - Xie_2022_Crit.Rev.Food.Sci.Nutr__1
Author(s) : Xie D , Chen Y , Yu J , Yang Z , Wang X
Ref : Crit Rev Food Sci Nutr , :1 , 2022
Abstract : n-3 Polyunsaturated fatty acids (n-3 PUFA) has been widely used in foods, and pharmaceutical products due to its beneficial effects. The content of n-3 PUFA in natural oils is usually low, which decreases its added value. Thus, there is an increasing demand on the market for n-3 PUFA concentrates. This review firstly introduces the differences in bioavailability and oxidative stability between different types of PUFA concentrate (free fatty acid, ethyl ester and acylglycerol), and then provides a comprehensive discussion of different methods for enrichment of lipids with n-3 PUFA including physical-chemical methods and enzymatic methods. Lipases used for catalyzing esterification, transesterification and hydrolysis reactions play an important role in the production of highly enriched various types of n-3 PUFA concentrates. Lipase-catalyzed alcoholysis or hydrolysis reactions are the mostly employed method to prepare high-quality n-3 PUFA of structural acylglycerols. Although many important advantages offered by lipases in enrichment of n-3 PUFA, the high cost of enzyme limits its industrial-scale production. Further research should focus on looking for biological enzymes with extraordinary catalytic ability and clear selectivity. Other novel technologies such as protein engineering and immobilization may be needed to modify lipases to improve its selectivity, catalytic ability and reuse.
ESTHER : Xie_2022_Crit.Rev.Food.Sci.Nutr__1
PubMedSearch : Xie_2022_Crit.Rev.Food.Sci.Nutr__1
PubMedID: 35699651

Title : Phytochemical profiling and antioxidant, enzyme-inhibitory, and toxic activities of extracts from Adonis ramosa Franch - Guo_2022_Nat.Prod.Res__1
Author(s) : Guo X , Chen M , He X , Zhao Y , Yu J , Zhu J , Li L , Xia G , Zang H
Ref : Nat Prod Res , :1 , 2022
Abstract : This study investigated the content and biological activity of three solvent extracts of Adonis ramosa Franch (AR), which contains 12 types of phytochemicals. The overall yield and total protein content of the aqueous extract were the highest, and it exhibited the highest hydroxyl and superoxide radical-scavenging abilities, copper chelating abilities, and cupric reducing antioxidant capacity. Ethanol extract had the highest total phenolic, flavonoid, and carbohydrate contents, and it showed the highest iron chelating activity, and HClO- and nitrite-scavenging abilities. Methanol AR extract contained the highest total steroid and tannin contents; it also demonstrated high radical- and reactive oxygen species-scavenging abilities and had the best ferric reducing antioxidant power, which allowed it to effectively prevent beta-carotene bleaching. Methanol extract also showed good stability and low toxicity. All tested solvent extracts of AR exhibited weak enzyme-inhibitory activities for four enzymes (alpha-glucosidase, alpha-amylase, acetylcholinesterase and butyrylcholinesterase). Overall, AR can serve as a natural antioxidant.
ESTHER : Guo_2022_Nat.Prod.Res__1
PubMedSearch : Guo_2022_Nat.Prod.Res__1
PubMedID: 35045779

Title : Lipase-catalyzed esterification in water enabled by nanomicelles. Applications to 1-pot multi-step sequences - Singhania_2022_Chem.Sci_13_1440
Author(s) : Singhania V , Cortes-Clerget M , Dussart-Gautheret J , Akkachairin B , Yu J , Akporji N , Gallou F , Lipshutz BH
Ref : Chem Sci , 13 :1440 , 2022
Abstract : Esterification in an aqueous micellar medium is catalyzed by a commercially available lipase in the absence of any co-factors. The presence of only 2 wt% designer surfactant, TPGS-750-M, assists in a 100% selective enzymatic process in which only primary alcohols participate (in a 1 : 1 ratio with carboxylic acid). An unexpected finding is also disclosed where the simple additive, PhCF(3) (1 equiv. vs. substrate), appears to significantly extend the scope of usable acid/alcohol combinations. Taken together, several chemo- and bio-catalyzed 1-pot, multi-step reactions can now be performed in water.
ESTHER : Singhania_2022_Chem.Sci_13_1440
PubMedSearch : Singhania_2022_Chem.Sci_13_1440
PubMedID: 35222928

Title : LIPG is a novel prognostic biomarker and correlated with immune infiltrates in lung adenocarcinoma - Wang_2022_J.Clin.Lab.Anal__e24824
Author(s) : Wang S , Chen Z , Lv H , Wang C , Wei H , Yu J
Ref : J Clin Lab Anal , :e24824 , 2022
Abstract : BACKGROUND: Although many biomarkers for lung adenocarcinoma (LUAD) have been identified, their specificity and sensitivity remain unsatisfactory. Endothelial lipase gene (LIPG) plays an important role in a variety of cancers, but its role in lung adenocarcinoma remains unclear. METHODS: TCGA, GEO, K-M plotter, CIBERSORT, GSEA, HPA, and GDSC were used to analyze LIPG in LUAD. Data analysis was mainly achieved by R 4.0.3. RESULTS: The expression of LIPG in LUAD tissues was higher than that in adjacent normal tissues, especially in women, patients aged >65 years, and those with lymph node metastasis. High expression predicted a poor prognosis. The results of enrichment analysis suggest that LIPG may exert profound effects on the development of LUAD through multiple stages of lipid metabolism and immune system regulation. In addition, LIPG expression was significantly correlated with the expression levels of multiple immune checkpoint genes and the abundance of multiple immune infiltrates, including the activated memory CD4 T cell, M1 macrophage, neutrophil, plasma cells, and T follicular helper (Tfh) cells in the LUAD microenvironment content. At the same time, patients with high LIPG expression respond well to a variety of antitumor drugs and have a low rate of drug resistance. CONCLUSIONS: LIPG is a prognostic marker and is associated with lipid metabolism and immune infiltration in LUAD.
ESTHER : Wang_2022_J.Clin.Lab.Anal__e24824
PubMedSearch : Wang_2022_J.Clin.Lab.Anal__e24824
PubMedID: 36572999
Gene_locus related to this paper: human-LIPG

Title : Isolation and Mechanistic Characterization of a Novel Zearalenone-Degrading Enzyme - Ji_2022_Foods_11_
Author(s) : Ji J , Yu J , Xu W , Zheng Y , Zhang Y , Sun X
Ref : Foods , 11 : , 2022
Abstract : Zearalenone (ZEN) and its derivatives pose a serious threat to global food quality and animal health. The use of enzymes to degrade mycotoxins has become a popular method to counter this threat. In this study, Aspergillus niger ZEN-S-FS10 extracellular enzyme solution with ZEN-degrading effect was separated and purified to prepare the biological enzyme, FSZ, that can degrade ZEN. The degradation rate of FSZ to ZEN was 7580% (pH = 7.0, 28 degreesC). FSZ can function in a temperature range of 2838 degreesC and pH range of 2.07.0 and can also degrade ZEN derivatives (alpha-ZAL, beta-ZOL, and ZAN). According to the enzyme kinetics fitting, ZEN has a high degradation rate. FSZ can degrade ZEN in real samples of corn flour. FSZ can be obtained stably and repeatedly from the original strain. One ZEN degradation product was isolated: FSZP(C18H26O4), with a relative molecular weight of 306.18 g/mol. Amino-acid-sequencing analysis revealed that FSZ is a novel enzyme (homology < 10%). According to the results of molecular docking, ZEN and ZAN can utilize their end-terminal carbonyl groups to bind FSZ residues PHE307, THR55, and GLU129 for a high-degradation rate. However, alpha-ZAL and beta-ZOL instead contain hydroxyl groups that would prevent binding to GLU129; thus, the degradation rate is low for these derivatives.
ESTHER : Ji_2022_Foods_11_
PubMedSearch : Ji_2022_Foods_11_
PubMedID: 36141036

Title : Parallel pathways for serotonin biosynthesis and metabolism in C. elegans - Yu_2022_Nat.Chem.Biol__
Author(s) : Yu J , Vogt MC , Fox BW , Wrobel CJJ , Fajardo Palomino D , Curtis BJ , Zhang B , Le HH , Tauffenberger A , Hobert O , Schroeder FC
Ref : Nat Chemical Biology , : , 2022
Abstract : The neurotransmitter serotonin plays a central role in animal behavior and physiology, and many of its functions are regulated via evolutionarily conserved biosynthesis and degradation pathways. Here we show that in Caenorhabditis elegans, serotonin is abundantly produced in nonneuronal tissues via phenylalanine hydroxylase, in addition to canonical biosynthesis via tryptophan hydroxylase in neurons. Combining CRISPR-Cas9 genome editing, comparative metabolomics and synthesis, we demonstrate that most serotonin in C. elegans is incorporated into N-acetylserotonin-derived glucosides, which are retained in the worm body and further modified via the carboxylesterase CEST-4. Expression patterns of CEST-4 suggest that serotonin or serotonin derivatives are transported between different tissues. Last, we show that bacterial indole production interacts with serotonin metabolism via CEST-4. Our results reveal a parallel pathway for serotonin biosynthesis in nonneuronal cell types and further indicate that serotonin-derived metabolites may serve distinct signaling functions and contribute to previously described serotonin-dependent phenotypes.
ESTHER : Yu_2022_Nat.Chem.Biol__
PubMedSearch : Yu_2022_Nat.Chem.Biol__
PubMedID: 36216995

Title : Hesperidin methyl chalcone ameliorates lipid metabolic disorders by activating lipase activity and increasing energy metabolism - Liu_2022_Biochim.Biophys.Acta.Mol.Basis.Dis__166620
Author(s) : Liu S , Liu K , Wang Y , Wu C , Xiao Y , Yu J , Ma Z , Liang H , Li X , Li Y , Zhou L
Ref : Biochimica & Biophysica Acta Mol Basis Dis , :166620 , 2022
Abstract : Obesity has become an increasingly serious health issue with the continuous improvement in living standards. Its prevalence has become an economic burden on health care systems worldwide. Flavonoids have been shown to be beneficial in the prevention and treatment of obesity. Here, we evaluated the therapeutic potential of the flavonoid hesperidin methyl chalcone (HMC) on mice with high-fat diet (HFD)-induced hepatic steatosis in vivo and in vitro. Treatment with HMC reduced oleic and palmitic acid-induced increases in intracellular triglyceride accumulation in HepG2, AML12 and LMH cells. HMC also enhanced energy metabolism and lowered oxidative stress. We used Discovery studio to dock key proteins associated with lipid metabolism disorders to HMC, and found that HMC interacted with lipase. Furthermore, we demonstrated that HMC improved lipase activity and lipolysis. In addition, we found that HMC promoted glucose absorption, alleviated lipid metabolic disorders, improved HFD-induced liver injury, and regulated HFD-induced changes in energy metabolism. In conclusion, our study demonstrated that HMC ameliorated HFD-induced obesity and its complications by promoting lipase activity, and provides a novel approach for the prevention and treatment of obesity and related diseases.
ESTHER : Liu_2022_Biochim.Biophys.Acta.Mol.Basis.Dis__166620
PubMedSearch : Liu_2022_Biochim.Biophys.Acta.Mol.Basis.Dis__166620
PubMedID: 36494040

Title : Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis - Yu_2021_ACS.Catalysis_11_11733
Author(s) : Yu J , Juan S , Chi C , Liu T , Geng T , Cai Z , Dong W , Shi C , Ma X , Zhang Z , Xing B , Jin H , Zhang L , Dong S , Yang D , Ma M
Ref : ACS Catal , 11 :11733 , 2021
Abstract : The d-amino acid residues are hallmark building blocks of nonribosomal peptides. Here, we report the bifunctional thioesterase domain (TE domain) Skyxy-TE that catalyzes both epimerization and cyclization in skyllamycin biosynthesis. Skyxy-TE specifically catalyzes the epimerization of the C-terminal l-amino acid residue of the linear substrate, then catalyzes regioselective intramolecular cyclization. The crystal structure of Skyxy-TE was solved at 2.25 and site-directed mutagenesis was performed, revealing key residues involved in the epimerization and cyclization. This study expands the understanding of the versatile TE domains and facilitates chemoenzymatic synthesis or combinatorial biosynthesis in the future.
ESTHER : Yu_2021_ACS.Catalysis_11_11733
PubMedSearch : Yu_2021_ACS.Catalysis_11_11733
Gene_locus related to this paper: strsq-a0a1j0r317

Title : Combinatorial Assembly of Modular Glucosides via Carboxylesterases Regulates C. elegans Starvation Survival - Wrobel_2021_J.Am.Chem.Soc__
Author(s) : Wrobel CJJ , Yu J , Rodrigues PR , Ludewig AH , Curtis BJ , Cohen SM , Fox BW , O'Donnell MP , Sternberg PW , Schroeder FC
Ref : Journal of the American Chemical Society , : , 2021
Abstract : The recently discovered modular glucosides (MOGLs) form a large metabolite library derived from combinatorial assembly of moieties from amino acid, neurotransmitter, and lipid metabolism in the model organism C. elegans. Combining CRISPR-Cas9 genome editing, comparative metabolomics, and synthesis, we show that the carboxylesterase homologue Cel-CEST-1.2 is responsible for specific 2-O-acylation of diverse glucose scaffolds with a wide variety of building blocks, resulting in more than 150 different MOGLs. We further show that this biosynthetic role is conserved for the closest homologue of Cel-CEST-1.2 in the related nematode species C. briggsae, Cbr-CEST-2. Expression of Cel-cest-1.2 and MOGL biosynthesis are strongly induced by starvation conditions in C. elegans, one of the premier model systems for mechanisms connecting nutrition and physiology. Cel-cest-1.2-deletion results in early death of adult animals under starvation conditions, providing first insights into the biological functions of MOGLs.
ESTHER : Wrobel_2021_J.Am.Chem.Soc__
PubMedSearch : Wrobel_2021_J.Am.Chem.Soc__
PubMedID: 34460264
Gene_locus related to this paper: caebr-a8wyd4 , caeel-t02b5.1 , caeel-t02b5.3

Title : [Experimental study on liver injury induced by intraperitoneal hypertension under mechanical ventilation] - Zhang_2021_Zhonghua.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_33_740
Author(s) : Zhang S , Wang H , Yu J
Ref : Zhonghua Wei Zhong Bing Ji Jiu Yi Xue , 33 :740 , 2021
Abstract : OBJECTIVE: To investigate the effects of mechanical ventilation on liver cytological and enzymatic indexes in abdominal compartment syndrome (ACS) by establishing a porcine model of abdominal hypertension. METHODS: Six healthy adult pigs were selected. After general anesthesia, they were intubated and given ventilator assisted breathing. The breathing mode was volume controlled ventilation (VCV), tidal volume (VT) 10 mL/kg, respiratory rate (RR) 16 time/min, fraction of inspiration oxygen (FiO(2)) 0.40, positive end expiratory pressure (PEEP) 5 cmH(2)O (1 cmH(2)O = 0.098 kPa). Intraperitoneal pressure was simulated by injecting normal saline into the pressurized water sac, and the pressure was measured once every 50 mL of normal saline. 5 mL of blood was collected from ear vein every 1 hour before and 4 hours after operation for liver enzyme examination. 4 hours after operation, the animals were sacrificed and the liver was collected to observe pathological changes under light microscope. RESULTS: Six pigs were successfully modeled. The RR and heart rate (HR) of the animals remained stable. No one suffered from barotrauma or death during the experiment. There was a positive correlation between abdominal pressure and abdominal volume increase (r(2) = 0.839 6, P = 0.003 7). There were no significant differences in the levels of alanine aminotransferase (ALT), alkaline phosphatase (ALP) and cholinesterase (ChE) preoperative and 1, 2, 3, 4 hours after operation. As time went on, aspartate aminotransferase (AST) increased first and then decreased, and increased significantly at 1 hour after operation (U/L: 46.84+/-8.57 vs. 23.35+/-5.14, P < 0.05), and decreased significantly 2, 3, 4 hours after operation (U/L: 16.33+/-3.58, 14.54+/-3.35, 15.44+/-3.21 vs. 23.35+/-5.14, all P < 0.05). The level of gamma-glutamyltranspeptidase (GGT) increased and then decreased, but there was significant difference only at 1 hour after operation, compared with baseline (U/L: 101.20+/-17.79 vs. 51.34+/-9.13, P < 0.05). Under the light microscope, there were dilation and congestion of interlobular vein, dilation of interlobular bile duct, hyperplasia of small bile duct, hyperplasia of connective tissue in portal area, infiltration of a large number of acute and chronic inflammatory cells, swelling of hepatocytes, light staining of cytoplasm, balloon like transformation of some cells, and punctate necrosis. CONCLUSIONS: Abdominal hypertension under mechanical ventilation can cause obvious enzyme changes and cytological damage of liver.
ESTHER : Zhang_2021_Zhonghua.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_33_740
PubMedSearch : Zhang_2021_Zhonghua.Wei.Zhong.Bing.Ji.Jiu.Yi.Xue_33_740
PubMedID: 34296697

Title : A photoelectrochemical sensor based on an acetylcholinesterase-CdS\/ZnO-modified extended-gate field-effect transistor for glyphosate detection - Yu_2021_Analyst__
Author(s) : Yu J , Lin J , Li J
Ref : Analyst , : , 2021
Abstract : A new photoelectrochemical enzyme biosensor based on an extended-gate field-effect transistor (EGFET) was constructed for the highly sensitive detection of glyphosate based on the inhibition of acetylcholinesterase (AChE) activity by glyphosate. First, a two-step hydrothermal method was used to introduce ZnO and CdS onto an activated indium tin oxide (ITO) electrode to prepare a CdS/ZnO/ITO electrode. Then, AChE was immobilized on CdS/ZnO/ITO with chitosan to obtain an AChE/CdS/ZnO EGFET sensor. Under optimal experimental conditions, the logarithmic value of glyphosate in the range of 1.0 x 10-15-1.0 x 10-11 mol L-1 exhibited a good linear relationship with the photo-drain current response. The detection limit was 3.8 x 10-16 mol L-1 (signal-to-noise ratio = 3). The results show that the AChE/CdS/ZnO EGFET sensor has extremely high sensitivity and good selectivity. Moreover, the sensor was used for the determination of glyphosate in vegetables, demonstrating its application for the real-time detection of samples.
ESTHER : Yu_2021_Analyst__
PubMedSearch : Yu_2021_Analyst__
PubMedID: 34160494

Title : BCL6B hypermethylation predicts metastasis and poor prognosis in early-stage hepatocellular carcinoma after thermal ablation - Li_2021_J.Cancer.Res.Ther_17_644
Author(s) : Li X , Guo M , Yang L , Cheng Z , Yu X , Han Z , Liu F , Sun Q , Han X , Yu J , Liang P
Ref : J Cancer Research Ther , 17 :644 , 2021
Abstract : AIMS: The aim of this study was to evaluate the role of BCL6B methylation in the progression of early-stage hepatocellular carcinoma (HCC) after thermal ablation. SETTINGS AND DESIGN: This is a retrospective study and written informed consent was obtained from all patients or their legal guardians. SUBJECTS AND METHODS: Between October 2008 and December 2013, 73 patients with early-stage HCC within the Milan criteria, who received thermal ablation, were recruited. STATISTICAL ANALYSIS USED: Based on methylation-specific polymerase chain reaction, the relationship between BCL6B methylation and patient characteristics and prognosis was analyzed using univariate, multivariate, and Kaplan-Meier analysis. RESULTS: The median follow-up period was 56 (8-110) months. For the BCL6B unmethylated group, the 1-, 3- and 5-year metastasis and overall survival (OS) rates after thermal ablation were 10.0%, 10.0%, and 40.0% and 100%, 100% and 90.0%, respectively. The 1-, 3-, and 5-year metastasis and OS rates of the methylated group were 23.8%, 66.7% and 88.9% and 66.2%, 71.4% and 41.3%, respectively. Levels of absolute count lymphocyte, serum cholinesterase and albumin in the BCL6B unmethylated group were higher than those in the methylated group (P = 0.020, 0.000, and 0.009, respectively). Kaplan-Meier analysis revealed that BCL6B methylation was related to metastasis and poor prognosis (P = 0.001 and 0.018, respectively). Univariate analysis revealed that BCL6B methylation was a risk factor for metastasis and poor prognosis (odds ratio [OR]: 5.663; 95% confidence interval [CI], 1.745-18.375, P = 0.004 and OR: 3.734; 95% CI, 1.151-12.110, P = 0.028, respectively). Multivariate analysis revealed that BCL6B methylation was an independent risk factor for metastasis (OR: 3.736; 95% CI, 1.000-13.963,P = 0.05) and not for prognosis (OR: 2.780; 95% CI, 0.835-9.250,P = 0.096). CONCLUSIONS: BCL6B methylation could be a valuable prognostic factor for metastasis and poor prognosis in early-stage HCC after thermal ablation, which is an independent risk factor for metastasis. Our findings provide insights for combining ablation and epigenetic therapy for patients with HCC.
ESTHER : Li_2021_J.Cancer.Res.Ther_17_644
PubMedSearch : Li_2021_J.Cancer.Res.Ther_17_644
PubMedID: 34269294

Title : [Proteolytic cleavage of neuroligins and functions of their cleavage products] - Yu_2020_Zhejiang.Da.Xue.Xue.Bao.Yi.Xue.Ban_49_514
Author(s) : Yu J , Xu J
Ref : Zhejiang Da Xue Xue Bao Yi Xue Ban , 49 :514 , 2020
Abstract : Neuroligin is a key protein that mediates synaptic development and maturation, and is closely related to neurodevelopmental diseases such as autism. In recent years, researchers have found that neuroligin can be hydrolyzed by various proteases at different stages of development, neuronal activities or pathological states of some neuropsychiatric diseases, thus affecting synaptic activity and participating in the occurrence and development of neurological diseases. The hydrolysates may have different physiological functions from the whole protein, and play different functions in neural activities, such as regulating synaptic plasticity, increasing synaptic strength and number, affecting amyloid-beta polymerization, promoting glioma proliferation and growth, activating related signaling pathways, and so on. In this article, on the basis of elaborating the structure and function of neuroligin as a whole protein, the conditions and products of its hydrolysis are summarized and analyzed, and the functional consequences and physiological significance of its hydrolysis are discussed.
ESTHER : Yu_2020_Zhejiang.Da.Xue.Xue.Bao.Yi.Xue.Ban_49_514
PubMedSearch : Yu_2020_Zhejiang.Da.Xue.Xue.Bao.Yi.Xue.Ban_49_514
PubMedID: 32985166

Title : sEH Inhibitor Tppu Ameliorates Cecal Ligation and Puncture-Induced Sepsis by Regulating Macrophage Functions - Chen_2020_Shock_53_761
Author(s) : Chen Z , Tang Y , Yu J , Dong R , Yang Y , Fu M , Luo J , Hu S , Wang DW , Tu L , Xu X
Ref : Shock , 53 :761 , 2020
Abstract : BACKGROUND: Sepsis is a life-threatening organ dysfunction initiated by a dysregulated response to infection, with imbalanced inflammation and immune homeostasis. Macrophages play a pivotal role in sepsis. N-[1-(1-oxopropyl)-4-piperidinyl]-N'-[4-(trifluoromethoxy)phenyl)-urea (TPPU) is an inhibitor of soluble epoxide hydrolase (sEH), which can rapidly hydrolyze epoxyeicosatrienoic acids (EETs) to the bio-inactive dihydroxyeicosatrienoic acids. TPPU was linked with the regulation of macrophages and inflammation. Here, we hypothesized that sEH inhibitor TPPU ameliorates cecal ligation and puncture (CLP)-induced sepsis by regulating macrophage functions. METHODS: A polymicrobial sepsis model induced by CLP was used in our study. C57BL/6 mice were divided into four groups: sham+ phosphate buffer saline (PBS), sham+TPPU, CLP+PBS, CLP+TPPU. Mice were observed 48h after surgery to assess the survival rate. For other histological examinations, mice were sacrificed 6h after surgery. Macrophage cell line RAW264.7 was used for in vitro studies. RESULTS: TPPU treatment, accompanied with increased EETs levels, markedly improved the survival of septic mice induced by CLP surgery, which was associated with alleviated organ damage and dysfunction triggered by systemic inflammatory response. Moreover, TPPU treatment significantly inhibited systemic inflammatory response via EETs-induced inactivation of mitogen-activated protein kinase signaling due to enhanced macrophage phagocytic ability and subsequently reduced bacterial proliferation and dissemination, and decreased inflammatory factors release. CONCLUSION: sEH inhibitor TPPU ameliorates cecal ligation and puncture-induced sepsis by regulating macrophage functions, including improved phagocytosis and reduced inflammatory response. Our data indicate that sEH inhibition has potential therapeutic effects on polymicrobial-induced sepsis.
ESTHER : Chen_2020_Shock_53_761
PubMedSearch : Chen_2020_Shock_53_761
PubMedID: 31318834

Title : Modular metabolite assembly in C. elegans depends on carboxylesterases and formation of lysosome-related organelles - Le_2020_Elife_9_
Author(s) : Le HH , Wrobel CJ , Cohen SM , Yu J , Park H , Helf MJ , Curtis BJ , Kruempel JC , Rodrigues PR , Hu PJ , Sternberg PW , Schroeder FC
Ref : Elife , 9 : , 2020
Abstract : Signaling molecules derived from attachment of diverse metabolic building blocks to ascarosides play a central role in the life history of C. elegans and other nematodes; however, many aspects of their biogenesis remain unclear. Using comparative metabolomics, we show that a pathway mediating formation of intestinal lysosome-related organelles (LROs) is required for biosynthesis of most modular ascarosides as well as previously undescribed modular glucosides. Similar to modular ascarosides, the modular glucosides are derived from highly selective assembly of moieties from nucleoside, amino acid, neurotransmitter, and lipid metabolism, suggesting that modular glucosides, like the ascarosides, may serve signaling functions. We further show that carboxylesterases that localize to intestinal organelles are required for the assembly of both modular ascarosides and glucosides via ester and amide linkages. Further exploration of LRO function and carboxylesterase homologs in C. elegans and other animals may reveal additional new compound families and signaling paradigms.
ESTHER : Le_2020_Elife_9_
PubMedSearch : Le_2020_Elife_9_
PubMedID: 33063667

Title : Molecular Basis for the Biosynthesis of an Unusual Chain-Fused Polyketide Gregatin A - Wang_2020_J.Am.Chem.Soc_142_8464
Author(s) : Wang WG , Wang H , Du LQ , Li M , Chen L , Yu J , Cheng GG , Zhan MT , Hu QF , Zhang L , Yao M , Matsuda Y
Ref : Journal of the American Chemical Society , 142 :8464 , 2020
Abstract : Gregatin A (1) is a fungal polyketide featuring an alkylated furanone core, but the biosynthetic mechanism to furnish the intri-guing molecular skeleton has yet to be elucidated. Herein, we have identified the biosynthetic gene cluster of gregatin A (1) in Penicillium sp. sh18, and investigated the mechanism that produces the intriguing structure of 1 by in vivo and in vitro recon-stitution of its biosynthesis. Our study established the biosynthetic route leading to 1, and illuminated that 1 is generated by the fusion of two different polyketide chains, which are, amazingly, synthesized by a single PKS GrgA with the aid of a trans-acting enoylreductase GrgB. Chain fusion, as well as chain hydrolysis, is catalyzed by an alpha/beta hydrolase GrgF, hybridizing the C11 and C4 carbon chains by Claisen condensation. Finally, structural analysis and mutational experiments using GrgF provided insight into how the enzyme facilitates the unusual chain-fusing reaction. In unraveling a new biosynthetic strategy involving a bifunc-tional PKS and a polyketide fusing enzyme, our study expands our knowledge concerning fungal polyketide biosynthesis.
ESTHER : Wang_2020_J.Am.Chem.Soc_142_8464
PubMedSearch : Wang_2020_J.Am.Chem.Soc_142_8464
PubMedID: 32275405
Gene_locus related to this paper: pensq-GrgF

Title : HEV-LFS : A novel scoring model for patients with hepatitis E virus-related liver failure - Wu_2019_J.Viral.Hepat_26_1334
Author(s) : Wu J , Guo N , Zhang X , Xiong C , Liu J , Xu Y , Fan J , Yu J , Zhao X , Liu B , Wang W , Zhang J , Cao H , Li L
Ref : J Viral Hepat , 26 :1334 , 2019
Abstract : A noninvasive assessment method for acute or acute-on-chronic liver failure in patients with hepatitis E virus (HEV) infection is urgently needed. We aimed to develop a scoring model for diagnosing HEV patients who developed liver failure (HEV-LF) at different stages. A cross-sectional set of 350 HEV-LF patients were identified and enrolled, and the Guidelines for Diagnosis and Treatment of Liver Failure in China and the Asian Pacific Association for the Study of the Liver were adopted as references. HEV-LFS , a novel scoring model that incorporates data on cholinesterase (CHE), urea nitrogen (UREA), platelets and international normalized ratio was developed using a derived dataset. For diagnosing HEV-LF stages F1 to F3, the HEV-LFS scoring model (F1: 0.87; F2: 0.90; F3: 0.92) had a significantly higher AUROC than did the CLIF-C-ACLFs (F1: 0.65; F2: 0.56; F3: 0.51) and iMELD (F1: 0.70; F2: 0.57; F3: 0.51) scoring models, of which the HEV-LFS scoring model had the best sensitivity and specificity. In addition, the HEV-LFS scoring model was correlated with mortality, length of hospitalization and ICU stay. As the GDTLF score increased, the CHE level decreased and the UREA increased gradually. Encouragingly, a calibration curve showed good agreement between the derivation and validation sets. Notably, we also established a nomogram to facilitate the practical operability of the HEV-LFS scoring model in clinical settings. In conclusion, both CHE and UREA may be indicators for HEV-LF patients. The HEV-LFS scoring model is an efficient and accessible model for classifying HEV-LF at different stages.
ESTHER : Wu_2019_J.Viral.Hepat_26_1334
PubMedSearch : Wu_2019_J.Viral.Hepat_26_1334
PubMedID: 31294523

Title : Congenital hypothyroidism due to thyroglobulin deficiency: a case report with a novel mutation in TG gene - Heo_2019_Ann.Pediatr.Endocrinol.Metab_24_199
Author(s) : Heo S , Jang JH , Yu J
Ref : Ann Pediatr Endocrinol Metab , 24 :199 , 2019
Abstract : Congenital hypothyroidism (CH) is the most common endocrine disorder in neonates and infants with an incidence of one in 2,000 to one in 4,000 newborns. Primary CH can be caused by thyroid dysgenesis and thyroid dyshormonogenesis. CH due to a TG gene mutation is one cause of thyroid dyshormonogenesis and can be characterized by goitrous CH with absent or low levels of serum thyroglobulin (Tg). In the present case, a 15-day-old neonate was referred to us with elevated thyroid stimulating hormone detected during a neonatal screening test. At the age of 34 months, extensive genetic testing was performed, including targeted exome sequencing for hypothyroidism, and revealed compound heterozygous mutations in the TG gene. Sanger sequencing of both parents' DNA samples revealed a c.3790T> C (p.Cys1264Arg) mutation located at exon 17 inherited from the mother, and a c.4057C> T (p.Gln1353*) mutation located at exon 19 was inherited from the father. The c.4057C> T (p.Gln1353*) mutation located at exon 19 has never been reported and, therefore, is a new discovery. We report a case of primary permanent CH with compound heterozygous mutations of the TG gene, including a novel mutation.
ESTHER : Heo_2019_Ann.Pediatr.Endocrinol.Metab_24_199
PubMedSearch : Heo_2019_Ann.Pediatr.Endocrinol.Metab_24_199
PubMedID: 31607114

Title : SNHG20\/miR-140-5p\/NDRG3 axis contributes to 5-fluorouracil resistance in gastric cancer - Yu_2019_Oncol.Lett_18_1337
Author(s) : Yu J , Shen J , Qiao X , Cao L , Yang Z , Ye H , Xi C , Zhou Q , Wang P , Gong Z
Ref : Oncol Lett , 18 :1337 , 2019
Abstract : 5-fluorouracil (5-FU)-based chemotherapy is the first line treatment for advanced gastric cancer. However, the effectiveness of 5-FU is limited by drug resistance. The N-myc downstream-regulated gene, family member 3 (NDRG3) is a member of the NDRG family and has been implicated in numerous types of cancer. However, the role of NDRG3 in gastric cancer remains unclear. In the present study, NDRG3 mRNA expression in gastric cancer and adjacent normal tissues was analyzed using the Gene Expression Profiling Interactive Analysis web tool. NDRG3 expression was silenced using short hairpin RNAs to examine the effect of NDRG3 on the growth of gastric cancer cells. Potential regulators of NDRG3 were identified using the TargetScan and MicroRNA tools and verified by a luciferase assay and reverse transcription-quantitative PCR analysis. The current study demonstrated that NDRG3 was upregulated in gastric cancer specimens and promoted cell proliferation in gastric cancer cell lines. Furthermore, the present study revealed that the small nucleolar RNA host gene 20 (SNHG20)/microRNA (miR)-140-5p signaling pathway may regulate the expression of NDRG3. SNHG20 was revealed to be involved in mediating resistance to 5-FU in gastric cancer cell lines via NDRG3. In conclusion, the results of the present study suggest that the SNHG20/miR-140-5p/NDRG3 axis may be involved in mediating resistance to 5-FU in gastric cancer.
ESTHER : Yu_2019_Oncol.Lett_18_1337
PubMedSearch : Yu_2019_Oncol.Lett_18_1337
PubMedID: 31423195
Gene_locus related to this paper: human-NDRG3

Title : The effect on congenital heart diseases of maternal EPHX1 polymorphisms modified by polycyclic aromatic hydrocarbons exposure - Tao_2019_Medicine.(Baltimore)_98_e16556
Author(s) : Tao J , Li N , Liu Z , Deng Y , Li X , Chen M , Yu J , Zhu J , Yu P , Wang Y
Ref : Medicine (Baltimore) , 98 :e16556 , 2019
Abstract : Polycyclic aromatic hydrocarbons (PAHs) may be 1 of etiologic factors responsible for congenital heart diseases (CHDs). Variations of the microsomal epoxide hydrolase (EPHX1) gene, as well as their possible interactions with PAHs exposure, may increase susceptibility to CHDs.This case-control study investigated the risk of CHDs in relation to the EPHX1 polymorphisms and assessed the interactions between these polymorphisms and PAHs exposure in 357 mothers of CHDs fetuses and 270 control mothers. Logistic regression models for the risk of CHDs were applied to determine the effect of genetic polymorphisms using additive, recessive, and dominant genetic models, as well as gene-exposure interactions. Multiple testing was adjusted by applying the false discovery rate (FDR).None of the maternal genetic polymorphisms of EPHX1 was associated with CHDs occurrence. Only the single nucleotide polymorphism rs1051740 was associated with an increased risk of right-sided obstructive malformations under the recessive model (adjusted odds ratio [aOR] = 1.852, 95% confidence interval [CI]: 1.065, 3.22) before FDR correction. A possible modifying effect of PAHs exposure on genetic polymorphisms of EPHX1 was found in susceptibility to CHDs, though no multiplicative-scale interactions between maternal exposure to PAHs and polymorphisms of EPHX1 gene were seento affect the risk of CHDs.The role of EPHX1 gene polymorphisms for CHDs need to be further evaluated, in particularly by interacting with PAHs exposure.
ESTHER : Tao_2019_Medicine.(Baltimore)_98_e16556
PubMedSearch : Tao_2019_Medicine.(Baltimore)_98_e16556
PubMedID: 31348278

Title : Oncogenic role of ABHD5 in endometrial cancer - Zhou_2019_Cancer.Manag.Res_11_2139
Author(s) : Zhou Q , Wang F , Zhou K , Huang K , Zhu Q , Luo X , Yu J , Shi Z
Ref : Cancer Manag Res , 11 :2139 , 2019
Abstract : Background: Abhydrolase domain containing 5 (ABHD5) functions as a tumor suppressor in colorectal and prostate cancers. The aim of this study was to investigate the roles of ABHD5 in endometrial cancer. Materials and methods: ABHD5 expression was detected in clinical samples by immunohistochemical staining. Cell proliferation and invasion were evaluated with the Cell Counting Kit-8 and Transwell assay, respectively. Western blotting was performed to analyze protein expression. Glucose uptake was assessed by 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxyglucose. Lactate production was detected by a lactate assay kit. Results: In the present study, ABHD5 was overexpressed in endometrial cancer tissues, and its expression was closely correlated with the International Federation of Gynecology and Obstetrics (FIGO) stage and lymph node metastasis. In addition, we observed that the knockdown of ABHD5 inhibited cell proliferation, invasion, glucose uptake and lactate production in HEC-1A cells, which expressed high levels of ABHD5. Conversely, the opposite effects were observed when ABHD5 was ectopically expressed in Ishikawa cells, which had low levels of ABHD5. Furthermore, the changes in glycolysis regulators (enolase 1 [ENO1], glucose transporter 1 [GLUT1] and lactate dehydrogenase A [LDHA]) and epithelial-to-mesenchymal transition-related proteins (E-cadherin and Snail) in HEC-1A cells with ABHD5 knockdown were consistent with the effects of ABHD5 on glycolysis and cell invasion. Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) was increased, while the phosphorylated AKT (p-AKT) was decreased when ABHD5 was downregulated. Notably, treatment with the allosteric AKT inhibitor MK-2206 completely abolished the effects caused by ABHD5 overexpression in Ishikawa cells. Finally, ABHD5 knockdown potently suppressed tumor growth in vivo. Conclusion: Overall, these results suggest that ABHD5 may play an oncogenic role in endometrial cancer via the AKT pathway.
ESTHER : Zhou_2019_Cancer.Manag.Res_11_2139
PubMedSearch : Zhou_2019_Cancer.Manag.Res_11_2139
PubMedID: 30936746
Gene_locus related to this paper: human-ABHD5

Title : Pharmacological activities of dihydrotanshinone I, a natural product from Salvia miltiorrhiza Bunge - Chen_2019_Pharmacol.Res_145_104254
Author(s) : Chen X , Yu J , Zhong B , Lu J , Lu JJ , Li S , Lu Y
Ref : Pharmacol Res , 145 :104254 , 2019
Abstract : Salvia miltiorrhiza Bunge (Danshen), a famous traditional Chinese herb, has been used clinically for the treatment of various diseases for centuries. Document data showed that tanshinones, a class of lipophilic abietane diterpenes rich in this herb, possess multiple biological effects in vitro and in vivo models. Among which, 15,16-dihydrotanshinone I (DHT) has received much attention in recent years. In this systematical review, we carefully selected, analyzed, and summarized high-quality publications related to pharmacological effects and the underlying mechanisms of DHT. DHT has anti-cancer, cardiovascular protective, anti-inflammation, anti-Alzheimer's disease, and other effects. Furthermore, several molecules such as hypoxia-inducible factor (HIF-1alpha), human antigen R (HuR), acetylcholinesterase (AchE), etc. have been identified as the potential targets for DHT. The diverse pharmacological activities of DHT provide scientific evidence for the local and traditional uses of Salvia miltiorrhiza Bunge. We concluded that DHT might serve as a lead compound for drug discovery in related diseases while further in-depth investigations are still needed.
ESTHER : Chen_2019_Pharmacol.Res_145_104254
PubMedSearch : Chen_2019_Pharmacol.Res_145_104254
PubMedID: 31054311

Title : Neuroligins Differentially Mediate Subtype-Specific Synapse Formation in Pyramidal Neurons and Interneurons - Xia_2019_Neurosci.Bull_35_497
Author(s) : Xia QQ , Xu J , Liao TL , Yu J , Shi L , Xia J , Luo JH
Ref : Neurosci Bull , 35 :497 , 2019
Abstract : Neuroligins (NLs) are postsynaptic cell-adhesion proteins that play important roles in synapse formation and the excitatory-inhibitory balance. They have been associated with autism in both human genetic and animal model studies, and affect synaptic connections and synaptic plasticity in several brain regions. Yet current research mainly focuses on pyramidal neurons, while the function of NLs in interneurons remains to be understood. To explore the functional difference among NLs in the subtype-specific synapse formation of both pyramidal neurons and interneurons, we performed viral-mediated shRNA knockdown of NLs in cultured rat cortical neurons and examined the synapses in the two major types of neurons. Our results showed that in both types of neurons, NL1 and NL3 were involved in excitatory synapse formation, and NL2 in GABAergic synapse formation. Interestingly, NL1 affected GABAergic synapse formation more specifically than NL3, and NL2 affected excitatory synapse density preferentially in pyramidal neurons. In summary, our results demonstrated that different NLs play distinct roles in regulating the development and balance of excitatory and inhibitory synapses in pyramidal neurons and interneurons.
ESTHER : Xia_2019_Neurosci.Bull_35_497
PubMedSearch : Xia_2019_Neurosci.Bull_35_497
PubMedID: 30790215

Title : Pesticide Residues Identification by Optical Spectrum in the Time-Sequence of Enzyme Inhibitors Performed on Microfluidic Paper-Based Analytical Devices (microPADs) - Yang_2019_Molecules_24_
Author(s) : Yang N , Shaheen N , Xie L , Yu J , Ahmad H , Mao H
Ref : Molecules , 24 : , 2019
Abstract : Pesticides vary in the level of poisonousness, while a conventional rapid test card only provides a general "absence or not" solution, which cannot identify the various genera of pesticides. In order to solve this problem, we proposed a seven-layer paper-based microfluidic chip, integrating the enzyme acetylcholinesterase (AChE) and chromogenic reaction. It enables on-chip pesticide identification via a reflected light intensity spectrum in time-sequence according to the different reaction efficiencies of pesticide molecules and assures the optimum temperature for enzyme activity. After pretreatment of figures of reflected light intensity during the 15 min period, the figures mainly focused on the reflected light variations aroused by the enzyme inhibition assay, and thus, the linear discriminant analysis showed satisfying discrimination of imidacloprid (Y = -1.6525X - 139.7500), phorate (Y = -3.9689X - 483.0526), and avermectin (Y = -2.3617X - 28.3082). The correlation coefficients for these linearity curves were 0.9635, 0.8093, and 0.9094, respectively, with a 95% limit of agreement. Then, the avermectin class chemicals and real-world samples (i.e., lettuce and rice) were tested, which all showed feasible graphic results to distinguish all the chemicals. Therefore, it is feasible to distinguish the three tested kinds of pesticides by the changes in the reflected light spectrum in each min (15 min) via the proposed chip with a high level of automation and integration.
ESTHER : Yang_2019_Molecules_24_
PubMedSearch : Yang_2019_Molecules_24_
PubMedID: 31269660

Title : The effects of pinoresinol on cholinergic dysfunction-induced memory impairments and synaptic plasticity in mice - Yu_2019_Food.Chem.Toxicol_125_376
Author(s) : Yu J , Kwon H , Cho E , Jeon J , Kang RH , Youn K , Jun M , Lee YC , Ryu JH , Kim DH
Ref : Food & Chemical Toxicology , 125 :376 , 2019
Abstract : Dementia is a category of brain diseases that cause a decrease in cognitive functions. Alzheimer's disease (AD) is the most frequently mentioned neurodegenerative disease showing dementia. Although many useful drugs for dementia were developed, we still need better and safer drugs. Here, we tested pinoresinol, a lignan found in sesame seed and olive oil, whether it could be a candidate for this purpose. Pinoresinol (25mg/kg, p.o.) ameliorated memory impairment in dementia model induced by cholinergic blockade in the passive avoidance test in a dose-dependent manner. Moreover, pinoresinol (50muM) facilitated induction of hippocampal long-term potentiation, a cellular model of learning and memory. Pinoresinol blocked acetylcholinesterase (AchE), an acetylcholine-degrading enzyme, activity in a concentration-dependent manner. Moreover, pinoresinol (50muM) facilitated calcium influx into neuro2a cell. These results suggest that pinoresinol improves memory impairment and facilitates hippocampal LTP induction and these results might be related to the effect of pinoresinol on AChE and calcium influx.
ESTHER : Yu_2019_Food.Chem.Toxicol_125_376
PubMedSearch : Yu_2019_Food.Chem.Toxicol_125_376
PubMedID: 30685474

Title : Protective effects of enzyme degradation extract from Porphyra yezoensis against oxidative stress and brain injury in D-galactose-induced aging mice - Wang_2019_Br.J.Nutr__1
Author(s) : Wang C , Shen Z , Yu J , Yang J , Meng F , Jiang X , Zhu C
Ref : British Journal of Nutrition , :1 , 2019
Abstract : This study investigated the effects of Porphyra yezoensis enzyme degradation extract (PYEDE) on the brain injuries and neurodegenerative diseases due to oxidative stress. We used in vitro antioxidant systems to verify the antioxidant potential of PYEDE. The results indicated that PYEDE alleviated weight loss and organ atrophy, reduced the levels of lipid peroxidation and protein carbonylation, and elevated glutathione (GSH) content in the serum and brains of the D-gal-induced aging model mice. PYEDE also renewed the glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), and total anti-oxidant capability (T-AOC) activities, downregulated the inducible nitric oxide synthase (iNOS) activity and nitric oxide (NO) levels, normalized the hippocampal neurons, and modulated multiple neurotransmitter systems by inhibiting the activities of acetylcholinesterase (AchE) and monoamine oxidase (MAO) in the upregulation of acetylcholine (Ach), dopamine (DA) and norepinephrine (NE) levels. Overall, PYEDE is a promising supplement for the alleviation of oxidative stress and age-associated brain diseases.
ESTHER : Wang_2019_Br.J.Nutr__1
PubMedSearch : Wang_2019_Br.J.Nutr__1
PubMedID: 31787131

Title : Glioblastoma stem cell-derived exosomes induce M2 macrophages and PD-L1 expression on human monocytes - Gabrusiewicz_2018_Oncoimmunology_7_e1412909
Author(s) : Gabrusiewicz K , Li X , Wei J , Hashimoto Y , Marisetty AL , Ott M , Wang F , Hawke D , Yu J , Healy LM , Hossain A , Akers JC , Maiti SN , Yamashita S , Shimizu Y , Dunner K , Zal MA , Burks JK , Gumin J , Nwajei F , Rezavanian A , Zhou S , Rao G , Sawaya R , Fuller GN , Huse JT , Antel JP , Li S , Cooper L , Sulman EP , Chen C , Geula C , Kalluri R , Zal T , Heimberger AB
Ref : Oncoimmunology , 7 :e1412909 , 2018
Abstract : Exosomes can mediate a dynamic method of communication between malignancies, including those sequestered in the central nervous system and the immune system. We sought to determine whether exosomes from glioblastoma (GBM)-derived stem cells (GSCs) can induce immunosuppression. We report that GSC-derived exosomes (GDEs) have a predilection for monocytes, the precursor to macrophages. The GDEs traverse the monocyte cytoplasm, cause a reorganization of the actin cytoskeleton, and skew monocytes toward the immune suppresive M2 phenotype, including programmed death-ligand 1 (PD-L1) expression. Mass spectrometry analysis demonstrated that the GDEs contain a variety of components, including members of the signal transducer and activator of transcription 3 (STAT3) pathway that functionally mediate this immune suppressive switch. Western blot analysis revealed that upregulation of PD-L1 in GSC exosome-treated monocytes and GBM-patient-infiltrating CD14(+) cells predominantly correlates with increased phosphorylation of STAT3, and in some cases, with phosphorylated p70S6 kinase and Erk1/2. Cumulatively, these data indicate that GDEs are secreted GBM-released factors that are potent modulators of the GBM-associated immunosuppressive microenvironment.
ESTHER : Gabrusiewicz_2018_Oncoimmunology_7_e1412909
PubMedSearch : Gabrusiewicz_2018_Oncoimmunology_7_e1412909
PubMedID: 29632728

Title : Mutations in the pancreatic secretory enzymes CPA1 and CPB1 are associated with pancreatic cancer - Tamura_2018_Proc.Natl.Acad.Sci.U.S.A_115_4767
Author(s) : Tamura K , Yu J , Hata T , Suenaga M , Shindo K , Abe T , MacGregor-Das A , Borges M , Wolfgang CL , Weiss MJ , He J , Canto MI , Petersen GM , Gallinger S , Syngal S , Brand RE , Rustgi A , Olson SH , Stoffel E , Cote ML , Zogopoulos G , Potash JB , Goes FS , McCombie RW , Zandi PP , Pirooznia M , Kramer M , Parla J , Eshleman JR , Roberts NJ , Hruban RH , Klein AP , Goggins M
Ref : Proc Natl Acad Sci U S A , 115 :4767 , 2018
Abstract : To evaluate whether germline variants in genes encoding pancreatic secretory enzymes contribute to pancreatic cancer susceptibility, we sequenced the coding regions of CPB1 and other genes encoding pancreatic secretory enzymes and known pancreatitis susceptibility genes (PRSS1, CPA1, CTRC, and SPINK1) in a hospital series of pancreatic cancer cases and controls. Variants in CPB1, CPA1 (encoding carboxypeptidase B1 and A1), and CTRC were evaluated in a second set of cases with familial pancreatic cancer and controls. More deleterious CPB1 variants, defined as having impaired protein secretion and induction of endoplasmic reticulum (ER) stress in transfected HEK 293T cells, were found in the hospital series of pancreatic cancer cases (5/986, 0.5%) than in controls (0/1,045, P = 0.027). Among familial pancreatic cancer cases, ER stress-inducing CPB1 variants were found in 4 of 593 (0.67%) vs. 0 of 967 additional controls (P = 0.020), with a combined prevalence in pancreatic cancer cases of 9/1,579 vs. 0/2,012 controls (P < 0.01). More ER stress-inducing CPA1 variants were also found in the combined set of hospital and familial cases with pancreatic cancer than in controls [7/1,546 vs. 1/2,012; P = 0.025; odds ratio, 9.36 (95% CI, 1.15-76.02)]. Overall, 16 (1%) of 1,579 pancreatic cancer cases had an ER stress-inducing CPA1 or CPB1 variant, compared with 1 of 2,068 controls (P < 0.00001). No other candidate genes had statistically significant differences in variant prevalence between cases and controls. Our study indicates ER stress-inducing variants in CPB1 and CPA1 are associated with pancreatic cancer susceptibility and implicate ER stress in pancreatic acinar cells in pancreatic cancer development.
ESTHER : Tamura_2018_Proc.Natl.Acad.Sci.U.S.A_115_4767
PubMedSearch : Tamura_2018_Proc.Natl.Acad.Sci.U.S.A_115_4767
PubMedID: 29669919

Title : The enhancing effect of Aubang Gahl Soo on the hippocampal synaptic plasticity and memory through enhancing cholinergic system in mice - Lee_2018_J.Ethnopharmacol_224_91
Author(s) : Lee J , Kwon H , Yu J , Cho E , Jeon J , Lee S , Ryu JH , Lee YC , Kim DH , Jung JW
Ref : J Ethnopharmacol , 224 :91 , 2018
Abstract : ETHNOPHARMACOLOGICAL RELEVANCE: Aubang Gahl Soo (AGS) is a Korean traditional drink manufactured from medicinal plants and fruits using sugar or honey. Although traditional old book stated its effects on body, there is no scientific evidence yet. Therefore, in the present study, we tested AGS on brain functions. AIM OF THIS STUDY: In this study, we tried to uncover the effect of on brain functions. To do this we examined the action of AGS on the hippocampal synaptic function and memory in mice. MATERIALS AND METHODS: To examine the effect of AGS on synaptic plasticity, we observed input-output curves (I/O curve), paired-pulse facilitation (PPF), and long-term potentiation (LTP) using mouse hippocampal slices. Moreover, to investigate the functional relevance of the effect of AGS on synaptic plasticity, we conducted passive avoidance, Y-maze and Morris water maze tests. To examine relevant mechanism, acetylcholinesterase (AChE) activity and acetylcholine (ACh) level assay were also conducted. RESULTS: In the basal synaptic transmission study, we found that AGS did not affect I/O curves and PPF. However, AGS facilitated hippocampal LTP in a concentration-dependent manner. Moreover, AGS blocked AChE activity (IC50 = 485mug/ml). Moreover, ACh level was increased by AGS (100mug/ml) treatment. Along with this, facilitating effect of AGS on hippocampal LTP also blocked by scopolamine, a muscarinic acetylcholine receptor antagonist. Moreover, AGS also ameliorated memory impairments induced by scopolamine in passive avoidance, Y-maze, and Morris water maze tests. CONCLUSIONS: These results suggest that AGS facilitates hippocampal LTP through activating cholinergic system and ameliorates cholinergic dysfunction-induced memory deficit.
ESTHER : Lee_2018_J.Ethnopharmacol_224_91
PubMedSearch : Lee_2018_J.Ethnopharmacol_224_91
PubMedID: 29842961

Title : Clinical diagnostic significance of prealbumin, cholinesterase and retinol binding protein in liver cirrhosis combined with encephalopathy - Tan_2018_Br.J.Biomed.Sci__1
Author(s) : Tan L , Meng Y , Zeng T , Wang Q , Long T , Wu S , Guan X , Fu H , Zheng W , Tian Y , Chen J , Yu J , Wu Y , Li H , Cao L
Ref : Br J Biomed Sci , :1 , 2018
Abstract : OBJECTIVE: Hepatic encephalopathy is a common consequence of liver cirrhosis, but diagnosis can be difficult as it is based on clinical criteria alone. We hypothesised that serum prealbumin, cholinesterase and retinol binding protein (RBP) can help support the diagnosis of hepatic encephalopathy. METHODS: We enrolled 306 cirrhotic patients (110 with encephalopathy), 100 chronic hepatitis B patients and 50 healthy controls, measuring routine liver function tests (ALT, AST, GGT, ALP, and bilirubin), albumin, prothrombin time, prealbumin, cholinesterase and RBP by routine methods. Logistic regression analysis and areas under the receiver operating characteristic curves (AUCs) were used to find predictive factors for hepatic encephalopathy. RESULTS: There were differences in all laboratory indices between the three groups (all p < 0.001). In univariate analysis, albumin, prothrombin time, prealbumin, cholinesterase and RBP were significantly altered in those with encephalopathy (p < 0.01), but only prealbumin, cholinesterase and RBP levels were significant predictors in multivariate analysis, and each was linked to the severity of liver fibrosis defined by the Child-Pugh score (all p < 0.001). The AUCs (95% CI) of prealbumin, cholinesterase and RBP for diagnosing liver cirrhosis with hepatic encephalopathy were comparable at 0.85 (81-90), 0.81 (0.76-0.85) and 0.81 (0.76-0.86), respectively (all p < 0.01). CONCLUSIONS: Serum prealbumin, cholinesterase and RBP levels are of potential clinical value in diagnosis of liver cirrhosis complicated by encephalopathy.
ESTHER : Tan_2018_Br.J.Biomed.Sci__1
PubMedSearch : Tan_2018_Br.J.Biomed.Sci__1
PubMedID: 30392460

Title : Expression and purification of biologically active recombinant human paraoxonase 1 from a Drosophila S2 stable cell line - Yun_2016_Protein.Expr.Purif_131_34
Author(s) : Yun H , Yu J , Kim S , Lee N , Lee J , Lee S , Kim ND , Yu C , Rho J
Ref : Protein Expr Purif , 131 :34 , 2016
Abstract : Many pesticides and chemical warfare nerve agents are highly toxic organophosphorus compounds (OPs), which inhibit acetylcholinesterase activity. Human paraoxonase 1 (PON1) has demonstrated significant potential for use as a catalytic bioscavenger capable of hydrolyzing a broad range of OPs. However, there are several limitations to the use of human PON1 as a catalytic bioscavenger, including the relatively difficult purification of PON1 from human plasma and its dependence on the presence of hydrophobic binding partners to maintain stability. Therefore, research efforts to efficiently produce recombinant human PON1 are necessary. In this study, we developed a Drosophila S2 stable cell line expressing recombinant human PON1. The recombinant human PON1 was fused with the human immunoglobulin Fc domain (PON1-hFc) to improve protein stability and purification efficiency. We purified the recombinant human PON1-hFc from the S2 stable cell line and characterized its enzymatic properties for OP hydrolysis. We purified the recombinant human PON1-hFc from the S2 stable cell line and characterized its enzymatic properties for OP hydrolysis compared with those of the recombinant human PON1 derived from E. coli. We observed that the recombinant human PON1-hFc is functionally more stable for OP hydrolyzing activities compared to the recombinant human PON1. The catalytic efficiency of the recombinant PON1-hFc towards diisopropyl fluorophosphate (DFP, 0.26 x 106 M-1 min-1) and paraoxon hydrolysis (0.015 x 106 M-1 min-1) was 1.63- and 1.24-fold higher, respectively, than the recombinant human PON1. Thus, we report that the recombinant PON1-hFc exerts hydrolytic activity against paraoxon and DFP.
ESTHER : Yun_2016_Protein.Expr.Purif_131_34
PubMedSearch : Yun_2016_Protein.Expr.Purif_131_34
PubMedID: 27838376

Title : Fucoxanthin, a Marine Carotenoid, Reverses Scopolamine-Induced Cognitive Impairments in Mice and Inhibits Acetylcholinesterase in Vitro - Lin_2016_Mar.Drugs_14_
Author(s) : Lin J , Huang L , Yu J , Xiang S , Wang J , Zhang J , Yan X , Cui W , He S , Wang Q
Ref : Mar Drugs , 14 : , 2016
Abstract : Fucoxanthin, a natural carotenoid abundant in edible brown seaweeds, has been shown to possess anti-cancer, anti-oxidant, anti-obesity and anti-diabetic effects. In this study, we report for the first time that fucoxanthin effectively protects against scopolamine-induced cognitive impairments in mice. In addition, fucoxanthin significantly reversed the scopolamine-induced increase of acetylcholinesterase (AChE) activity and decreased both choline acetyltransferase activity and brain-derived neurotrophic factor (BDNF) expression. Using an in vitro AChE activity assay, we discovered that fucoxanthin directly inhibits AChE with an IC50 value of 81.2 muM. Molecular docking analysis suggests that fucoxanthin likely interacts with the peripheral anionic site within AChE, which is in accordance with enzymatic activity results showing that fucoxanthin inhibits AChE in a non-competitive manner. Based on our current findings, we anticipate that fucoxanthin might exhibit great therapeutic efficacy for the treatment of Alzheimer's disease by acting on multiple targets, including inhibiting AChE and increasing BDNF expression.
ESTHER : Lin_2016_Mar.Drugs_14_
PubMedSearch : Lin_2016_Mar.Drugs_14_
PubMedID: 27023569

Title : High-throughput proteomics integrated with gene microarray for discovery of colorectal cancer potential biomarkers - Yu_2016_Oncotarget_7_75279
Author(s) : Yu J , Li X , Zhong C , Li D , Zhai X , Hu W , Guo C , Yuan Y , Zheng S
Ref : Oncotarget , 7 :75279 , 2016
Abstract : Proteins, as executives of genes' instructions, are responsible for cellular phenotypes. Integratingproteomics with gene microarray, we conducted this study to identify potential protein biomarkers of colorectal cancer (CRC). Isobaric tags with related and absolute quantitation (iTRAQ) labeling mass spectrometry (MS) was applied to screen and identify differentially expressed proteins between paired CRC and adjacent normal mucosa. Meanwhile, Affymetrix U133plus2.0 microarrays were used to perform gene microarray analysis. Verification experiments included immunohistochemistry (IHC), western blot and enzyme-linked immunosorbent assay (ELISA) of selected proteins. Overall, 5469 differentially expressed proteins were detected with iTRAQ-MS from 24 matched CRC and adjacent normal tissues. And gene microarray identified 39859 differential genes from 52 patients. Of these, 3083 differential proteins had corresponding differentially expressed genes, with 245 proteins and their genes showed >1.5-fold change in expression level. Gene ontology enrichment analysis revealed that up-regulated proteins were more involved in cell adhesion and motion than down-regulated proteins. In addition, up-regulated proteins were more likely to be located in nucleus and vesicles. Further verification experiments with IHC confirmed differential expression levels of 5 proteins (S100 calcium-binding protein A9, annexin A3, nicotinamide phosphoribosyltransferase, carboxylesterase 2 and calcium activated chloride channel A1) between CRC and normal tissues. Besides, western blot showed a stepwise increase of annexin A3 abundance in normal colorectal mucosa, adenoma and CRC tissues. ELISAresults revealed significantly higher serum levels of S100 calcium-binding protein A9 and annexin A3 in CRC patients than healthy controls, validating diagnostic value of these proteins. Cell experiments showed that inhibition of annexin A3 could suppress CRC cell proliferation and aggressiveness. S100 calcium-binding protein A9, annexin A3, nicotinamide phosphoribosyltransferase, carboxylesterase 2 and calcium activated chloride channel A1 were probably potential biomarkers of colorectal cancer. Annexin A3 was a potentially valuable therapeutic target of CRC.
ESTHER : Yu_2016_Oncotarget_7_75279
PubMedSearch : Yu_2016_Oncotarget_7_75279
PubMedID: 27661117

Title : FAM172A is a tumor suppressor in colorectal carcinoma - Cui_2016_Tumour.Biol_37_6501
Author(s) : Cui C , Ye L , Huang Z , Huang S , Liu H , Yu J
Ref : Tumour Biol , 37 :6501 , 2016
Abstract : The present study was designed to elucidate the regulatory role of a novel protein FAM172A in carcinogenesis of colorectal carcinoma (CRC). Investigation of clinical samples using Western blotting showed that expression of FAM172A is significantly lower in cancerous tissues than in adjacent tissues. Furthermore, we constructed in vitro model for continuous overexpression and silencing of FAM172A with a retroviral vector system. FAM172A suppressed the proliferative and invasive potentials of LOVO cells as shown in MTT test, transwell migration assay, wound healing assay, 3D-culture morphologic study, and xenograft experiment. RT-PCR and Western blotting showed that FAM172A overexpression inhibited expressions of Cyclin D1, CDK2, MMP-2, MMP-9, PERK, elF2alpha, ATF6, XBP1, and GRP78, while FAM172A silencing induced their expressions. FAM172A might regulate ERS through PERK-elF2alpha, ATF6-XBP1-GRP78 signal pathway. The results implicated that FAM172A functioned as a tumor suppressor in colorectal carcinoma.
ESTHER : Cui_2016_Tumour.Biol_37_6501
PubMedSearch : Cui_2016_Tumour.Biol_37_6501
PubMedID: 26637224
Gene_locus related to this paper: human-f172a

Title : Identification and Characterization of a New Alkaline SGNH Hydrolase from a Thermophilic Bacterium Bacillus sp. K91 - Yu_2016_J.Microbiol.Biotechnol_26_730
Author(s) : Yu T , Ding J , Zheng Q , Han N , Yu J , Yang Y , Li J , Mu Y , Wu Q , Huang Z
Ref : J Microbiol Biotechnol , 26 :730 , 2016
Abstract : est19 is a gene from Bacillus sp. K91 that encodes a new esterase. A comparison of the amino acid sequence showed that Est19 has typical Ser-Gly-Asn-His (SGNH) family motifs and could be grouped into the SGNH hydrolase family. The Est19 protein was functionally cloned, and expressed and purified from Escherichia coli BL21(DE3). The enzyme activity was optimal at 60 degrees C and pH 9.0, and displayed esterase activity towards esters with short-chain acyl esters (C(2)-C(6)). A structural model of Est19 was constructed using phospholipase A1 from Streptomyces albidoflavus NA297 as a template. The structure showed an alpha/beta-hydrolase fold and indicated the presence of the typical catalytic triad Ser49-Asp227-His230, which were further investigated by site-directed mutagenesis. To the best of our knowledge, Est19 is a new member of the SGNH hydrolase family identified from thermophiles, which may be applicable in the industrial production of semisynthetic beta-lactam antibiotics after modification.
ESTHER : Yu_2016_J.Microbiol.Biotechnol_26_730
PubMedSearch : Yu_2016_J.Microbiol.Biotechnol_26_730
PubMedID: 26699742

Title : Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5) - Yu_2016_Antonie.Van.Leeuwenhoek_109_1337
Author(s) : Yu J , Guan X , Liu C , Xiang W , Yu Z , Liu X , Wang G
Ref : Antonie Van Leeuwenhoek , 109 :1337 , 2016
Abstract : A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4alpha L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)).
ESTHER : Yu_2016_Antonie.Van.Leeuwenhoek_109_1337
PubMedSearch : Yu_2016_Antonie.Van.Leeuwenhoek_109_1337
PubMedID: 27401830
Gene_locus related to this paper: 9baci-a0a494yt46

Title : Sequence Assembly of Yarrowia lipolytica Strain W29\/CLIB89 Shows Transposable Element Diversity - Magnan_2016_PLoS.One_11_e0162363
Author(s) : Magnan C , Yu J , Chang I , Jahn E , Kanomata Y , Wu J , Zeller M , Oakes M , Baldi P , Sandmeyer S
Ref : PLoS ONE , 11 :e0162363 , 2016
Abstract : Yarrowia lipolytica, an oleaginous yeast, is capable of accumulating significant cellular mass in lipid making it an important source of biosustainable hydrocarbon-based chemicals. In spite of a similar number of protein-coding genes to that in other Hemiascomycetes, the Y. lipolytica genome is almost double that of model yeasts. Despite its economic importance and several distinct strains in common use, an independent genome assembly exists for only one strain. We report here a de novo annotated assembly of the chromosomal genome of an industrially-relevant strain, W29/CLIB89, determined by hybrid next-generation sequencing. For the first time, each Y. lipolytica chromosome is represented by a single contig. The telomeric rDNA repeats were localized by Irys long-range genome mapping and one complete copy of the rDNA sequence is reported. Two large structural variants and retroelement differences with reference strain CLIB122 including a full-length, novel Ty3/Gypsy long terminal repeat (LTR) retrotransposon and multiple LTR-like sequences are described. Strikingly, several of these are adjacent to RNA polymerase III-transcribed genes, which are almost double in number in Y. lipolytica compared to other Hemiascomycetes. In addition to previously-reported dimeric RNA polymerase III-transcribed genes, tRNA pseudogenes were identified. Multiple full-length and truncated LINE elements are also present. Therefore, although identified transposons do not constitute a significant fraction of the Y. lipolytica genome, they could have played an active role in its evolution. Differences between the sequence of this strain and of the existing reference strain underscore the utility of an additional independent genome assembly for this economically important organism.
ESTHER : Magnan_2016_PLoS.One_11_e0162363
PubMedSearch : Magnan_2016_PLoS.One_11_e0162363
PubMedID: 27603307
Gene_locus related to this paper: yarli-q6c4p0

Title : Sunitinib, a Clinically Used Anticancer Drug, Is a Potent AChE Inhibitor and Attenuates Cognitive Impairments in Mice - Huang_2016_ACS.Chem.Neurosci_7_1047
Author(s) : Huang L , Lin J , Xiang S , Zhao K , Yu J , Zheng J , Xu D , Mak SH , Hu S , Nirasha S , Wang C , Chen X , Zhang J , Xu S , Wei X , Zhang Z , Zhou D , Zhou W , Cui W , Han YF , Hu Z , Wang Q
Ref : ACS Chem Neurosci , 7 :1047 , 2016
Abstract : Sunitinib, a tyrosine kinase inhibitor, is clinically used for the treatment of cancer. In this study, we found for the first time that sunitinib inhibits acetylcholinesterase (AChE) at submicromolar concentrations in vitro. In addition, sunitinib dramatically decreased the hippocampal and cortical activity of AChE in a time-dependent manner in mice. Molecular docking analysis further demonstrates that sunitinib might interact with both the catalytic anion and peripheral anionic sites within AChE, which is in accordance with enzymatic activity results showing that sunitinib inhibits AChE in a mixed pattern. Most importantly, we evaluated the effects of sunitinib on scopolamine-induced cognitive impairments in mice by using novel object recognition and Morris water maze tests. Surprisingly, sunitinib could attenuate cognitive impairments to a similar extent as donepezil, a marketed AChE inhibitor used for the treatment of Alzheimer's disease. In summary, our results have shown that sunitinib could potently inhibit AChE and attenuate cognitive impairments in mice.
ESTHER : Huang_2016_ACS.Chem.Neurosci_7_1047
PubMedSearch : Huang_2016_ACS.Chem.Neurosci_7_1047
PubMedID: 27046396

Title : Differential expression of lipid metabolism-related genes and myosin heavy chain isoform genes in pig muscle tissue leading to different meat quality - Zhang_2015_Animal_9_1073
Author(s) : Zhang C , Luo JQ , Zheng P , Yu B , Huang ZQ , Mao XB , He J , Yu J , Chen JL , Chen DW
Ref : Animal , 9 :1073 , 2015
Abstract : The aim of this study was to investigate the variations in meat quality, lipid metabolism-related genes, myosin heavy chain (MyHC) isoform genes and peroxisome proliferator-activated receptor gamma coactivator-1alpha (PGC-1alpha) gene mRNA expressions in longissimus dorsi muscle (LM) of two different pig breeds. Six Rongchang and six Landrace barrows were slaughtered at 161 days of age. Subsequently, meat quality traits and gene expression levels in LM were observed. Results showed that Rongchang pigs not only exhibited greater pH, CIE a*24 h and intramuscular fat content but also exhibited lower body weight, carcass weight, dressing percentage, LM area and CIE b*24 h compared with Landrace pigs (P<0.05). Meanwhile, the mRNA expression levels of the lipogenesis (peroxisome proliferator-activated receptor gamma, acetyl-CoA carboxylase and fatty acid synthase) and fatty acid uptake (lipoprotein lipase)-related genes were greater in the Rongchang (P<0.05), whereas the lipolysis (adipose triglyceride lipase and hormone sensitive lipase) and fatty acid oxidation (carnitine palmitoyltransferase-1B)-related genes were better expressed in the Landrace. Moreover, compared with the Landrace, the mRNA expression levels of MyHCI, MyHCIIa and MyHCIIx were greater, whereas the mRNA expression levels of MyHCIIb were lower in the Rongchang pigs (P<0.05). In addition, the mRNA expression levels of PGC-1alpha were greater in Rongchang pigs than in the Landrace (P<0.05), which can partly explain the differences in MyHC isoform gene expressions between Rongchang and Landrace pigs. Although the small number of samples does not allow to obtain a definitive conclusion, we can suggest that Rongchang pigs possess better meat quality, and the underlying molecular mechanisms responsible for the better meat quality in fatty pigs may be partly due to the higher mRNA expression levels of lipogenesis and fatty acid uptake-related genes, as well as the oxidative and intermediate muscle fibers, and due to the lower mRNA expression levels of lipolysis and fatty acid oxidation-related genes, as well as the glycolytic muscle fibers.
ESTHER : Zhang_2015_Animal_9_1073
PubMedSearch : Zhang_2015_Animal_9_1073
PubMedID: 25716066

Title : Genome Sequence of Aspergillus flavus NRRL 3357, a Strain That Causes Aflatoxin Contamination of Food and Feed - Nierman_2015_Genome.Announc_3_e00168
Author(s) : Nierman WC , Yu J , Fedorova-Abrams ND , Losada L , Cleveland TE , Bhatnagar D , Bennett JW , Dean R , Payne GA
Ref : Genome Announc , 3 : , 2015
Abstract : Aflatoxin contamination of food and livestock feed results in significant annual crop losses internationally. Aspergillus flavus is the major fungus responsible for this loss. Additionally, A. flavus is the second leading cause of aspergillosis in immunocompromised human patients. Here, we report the genome sequence of strain NRRL 3357.
ESTHER : Nierman_2015_Genome.Announc_3_e00168
PubMedSearch : Nierman_2015_Genome.Announc_3_e00168
PubMedID: 25883274
Gene_locus related to this paper: aspfa-a0a0d9n0w1 , aspfn-b8nid9 , aspor-q2uj83 , aspoz-a0a1s9dwr5 , aspoz-a0a1s9d9g3 , aspfn-imqb , aspfn-agia

Title : Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites - Zhou_2014_BMC.Genomics_15_42
Author(s) : Zhou D , Zhang D , Ding G , Shi L , Hou Q , Ye Y , Xu Y , Zhou H , Xiong C , Li S , Yu J , Hong S , Yu X , Zou P , Chen C , Chang X , Wang W , Lv Y , Sun Y , Ma L , Shen B , Zhu C
Ref : BMC Genomics , 15 :42 , 2014
Abstract : BACKGROUND: Anopheles sinensis is an important mosquito vector of Plasmodium vivax, which is the most frequent and widely distributed cause of recurring malaria throughout Asia, and particularly in China, Korea, and Japan.
RESULTS: We performed 454 next-generation sequencing and obtained a draft sequence of A. sinensis assembled into scaffolds spanning 220.8 million base pairs. Analysis of this genome sequence, we observed expansion and contraction of several immune-related gene families in anopheline relative to culicine mosquito species. These differences suggest that species-specific immune responses to Plasmodium invasion underpin the biological differences in susceptibility to Plasmodium infection that characterize these two mosquito subfamilies.
CONCLUSIONS: The A. sinensis genome produced in this study, provides an important resource for analyzing the genetic basis of susceptibility and resistance of mosquitoes to Plasmodium parasites research which will ultimately facilitate the design of urgently needed interventions against this debilitating mosquito-borne disease.
ESTHER : Zhou_2014_BMC.Genomics_15_42
PubMedSearch : Zhou_2014_BMC.Genomics_15_42
PubMedID: 24438588
Gene_locus related to this paper: anoga-Q7PVF9 , 9dipt-a0a084vlt1 , 9dipt-a0a084vdq2 , 9dipt-sime3xf.a , 9dipt-sime3xf.b , 9dipt-a0a084vbj8 , 9dipt-a0a084wan7 , 9dipt-a0a084wik4 , 9dipt-a0a084wk64 , 9dipt-a0a084wez8 , 9dipt-a0a084vji7 , 9dipt-a0a084vlc2 , 9dipt-a0a084vsa5 , 9dipt-a0a084wlk0 , 9dipt-a0a084wah8 , 9dipt-a0a084wln4 , 9dipt-a0a084we78 , 9dipt-a0a084wjm6 , 9dipt-a0a084wjm7 , 9dipt-a0a084we77 , 9dipt-a0a084wlk1 , 9dipt-a0a084we80 , 9dipt-a0a084wjm4 , 9dipt-a0a084w1n7 , 9dipt-a0a084we79 , 9dipt-a0a084wev9 , 9dipt-a0a084vlc3 , 9dipt-a0a084vdq4 , 9dipt-a0a084vdq5 , 9dipt-a0a084vdq1 , 9dipt-a0a084wah9 , 9dipt-a0a084wan6 , 9dipt-a0a084wlj8 , 9dipt-a0a084wk45 , 9dipt-a0a084wk46 , 9dipt-a0a084wlj9 , 9dipt-a0a084vsa4 , 9dipt-a0a084vs93 , 9dipt-a0a084wl93 , anosi-a0a0f7kyf5 , anosi-a0a0f7l1f2 , anosi-a0a084wum0 , anost-a0a182xxz0 , anosi-a0a084vn28 , anosi-a0a084vpt0 , anoga-q7q887

Title : Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis - Wang_2014_Genome.Biol_15_R39
Author(s) : Wang L , Yu S , Tong C , Zhao Y , Liu Y , Song C , Zhang Y , Zhang X , Wang Y , Hua W , Li D , Li F , Yu J , Xu C , Han X , Huang S , Tai S , Wang J , Xu X , Li Y , Liu S , Varshney RK
Ref : Genome Biol , 15 :R39 , 2014
Abstract : BACKGROUND: Sesame, Sesamum indicum L., is considered the queen of oilseeds for its high oil content and quality, and is grown widely in tropical and subtropical areas as an important source of oil and protein. However, the molecular biology of sesame is largely unexplored. RESULTS: Here, we report a high-quality genome sequence of sesame assembled de novo with a contig N50 of 52.2 kb and a scaffold N50 of 2.1 Mb, containing an estimated 27,148 genes. The results reveal novel, independent whole genome duplication and the absence of the Toll/interleukin-1 receptor domain in resistance genes. Candidate genes and oil biosynthetic pathways contributing to high oil content were discovered by comparative genomic and transcriptomic analyses. These revealed the expansion of type 1 lipid transfer genes by tandem duplication, the contraction of lipid degradation genes, and the differential expression of essential genes in the triacylglycerol biosynthesis pathway, particularly in the early stage of seed development. Resequencing data in 29 sesame accessions from 12 countries suggested that the high genetic diversity of lipid-related genes might be associated with the wide variation in oil content. Additionally, the results shed light on the pivotal stage of seed development, oil accumulation and potential key genes for sesamin production, an important pharmacological constituent of sesame. CONCLUSIONS: As an important species from the order Lamiales and a high oil crop, the sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame.
ESTHER : Wang_2014_Genome.Biol_15_R39
PubMedSearch : Wang_2014_Genome.Biol_15_R39
PubMedID: 24576357
Gene_locus related to this paper: sesin-a0a6i9snr9

Title : Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization - Qin_2014_Proc.Natl.Acad.Sci.U.S.A_111_5135
Author(s) : Qin C , Yu C , Shen Y , Fang X , Chen L , Min J , Cheng J , Zhao S , Xu M , Luo Y , Yang Y , Wu Z , Mao L , Wu H , Ling-Hu C , Zhou H , Lin H , Gonzalez-Morales S , Trejo-Saavedra DL , Tian H , Tang X , Zhao M , Huang Z , Zhou A , Yao X , Cui J , Li W , Chen Z , Feng Y , Niu Y , Bi S , Yang X , Cai H , Luo X , Montes-Hernandez S , Leyva-Gonzalez MA , Xiong Z , He X , Bai L , Tan S , Liu D , Liu J , Zhang S , Chen M , Zhang L , Zhang Y , Liao W , Wang M , Lv X , Wen B , Liu H , Luan H , Yang S , Wang X , Xu J , Li X , Li S , Wang J , Palloix A , Bosland PW , Li Y , Krogh A , Rivera-Bustamante RF , Herrera-Estrella L , Yin Y , Yu J , Hu K , Zhang Z
Ref : Proc Natl Acad Sci U S A , 111 :5135 , 2014
Abstract : As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded approximately 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of approximately 81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.
ESTHER : Qin_2014_Proc.Natl.Acad.Sci.U.S.A_111_5135
PubMedSearch : Qin_2014_Proc.Natl.Acad.Sci.U.S.A_111_5135
PubMedID: 24591624
Gene_locus related to this paper: capch-q75qh4 , capan-a0a1u8fuf5 , capan-a0a1u8gmz3 , capan-a0a1u8f879 , capan-a0a1u8ftr2 , capan-a0a1u8g8s6

Title : Seasonally variable intestinal metagenomes of the red palm weevil (Rhynchophorus ferrugineus) - Jia_2013_Environ.Microbiol_15_3020
Author(s) : Jia S , Zhang X , Zhang G , Yin A , Zhang S , Li F , Wang L , Zhao D , Yun Q , Tala , Wang J , Sun G , Baabdullah M , Yu X , Hu S , Al-Mssallem IS , Yu J
Ref : Environ Microbiol , 15 :3020 , 2013
Abstract : The intestinal microbes residing in the red palm weevil (RPW, Rhynchophorus ferrugineus) larva consume tender interior fibrous tissues of date palm trunks. The understanding of such microbiota at molecular level provides vital clues for the biological control of this devastating pest. Using pyrosequencing and shotgun strategy, we first study taxonomic profiles of the microbiota sampled at different months (March, July and November), and then confirm the impact of high-temperature stress on the microbial populations based on data from 16S rRNA amplicons using both field and laboratory samples. We further identify Klebsiella pneumoniae in November and Lactococcus lactis in July as the dominant species of the microbiota. We find that the RPW gut microbiota degrades polysaccharides and sucrose with hydrolases and that different active bacterial species in November and July are responsible for the symbiotic relationship between the microbiota and the host. Our results provide vital information for pest control and cellulolytic bacterial species characterization.
ESTHER : Jia_2013_Environ.Microbiol_15_3020
PubMedSearch : Jia_2013_Environ.Microbiol_15_3020
PubMedID: 24102776

Title : Genome Sequences of Avian Pathogenic Escherichia coli Strains Isolated from Brazilian Commercial Poultry - Rojas_2013_Genome.Announc_1_e0011013
Author(s) : Rojas TC , Maluta RP , Parizzi LP , Koenigkan LV , Yang J , Yu J , Pereira GA , Dias da Silveira W
Ref : Genome Announc , 1 :e0011013 , 2013
Abstract : Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. The disease might present as different local infections or as septicemia. Here, we present the draft genome sequences of three Brazilian APEC strains isolated from different kinds of infections. The availability of these APEC genome sequences is important for gaining a thorough understanding of the genomic features of E. coli, particularly those of this pathotype.
ESTHER : Rojas_2013_Genome.Announc_1_e0011013
PubMedSearch : Rojas_2013_Genome.Announc_1_e0011013
PubMedID: 23516222
Gene_locus related to this paper: ecoli-d7xp23 , ecoli-IROD , ecoli-IROE , ecoli-estX , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-yiel , ecoli-ypt1 , ecoli-yqia , ecoli-Z1930 , ecoli-YfhR

Title : Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation - Fookes_2013_Genome.Announc_1_e00027
Author(s) : Fookes M , Yu J , De Majumdar S , Thomson N , Schneiders T
Ref : Genome Announc , 1 : , 2013
Abstract : We report the genome sequence of Klebsiella pneumoniae subsp. pneumoniae Ecl8, a spontaneous streptomycin-resistant mutant of strain ECL4, derived from NCIB 418. K. pneumoniae Ecl8 has been shown to be genetically tractable for targeted gene deletion strategies and so provides a platform for in-depth analyses of this species.
ESTHER : Fookes_2013_Genome.Announc_1_e00027
PubMedSearch : Fookes_2013_Genome.Announc_1_e00027
PubMedID: 23405357
Gene_locus related to this paper: klep7-a6t9v6 , klep7-y1077 , klepn-w8uta0

Title : Genome sequence of the date palm Phoenix dactylifera L - Al-Mssallem_2013_Nat.Commun_4_2274
Author(s) : Al-Mssallem IS , Hu S , Zhang X , Lin Q , Liu W , Tan J , Yu X , Liu J , Pan L , Zhang T , Yin Y , Xin C , Wu H , Zhang G , Ba Abdullah MM , Huang D , Fang Y , Alnakhli YO , Jia S , Yin A , Alhuzimi EM , Alsaihati BA , Al-Owayyed SA , Zhao D , Zhang S , Al-Otaibi NA , Sun G , Majrashi MA , Li F , Tala , Wang J , Yun Q , Alnassar NA , Wang L , Yang M , Al-Jelaify RF , Liu K , Gao S , Chen K , Alkhaldi SR , Liu G , Zhang M , Guo H , Yu J
Ref : Nat Commun , 4 :2274 , 2013
Abstract : Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (~671 Mb) and >96% of its genes (~41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm's unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.
ESTHER : Al-Mssallem_2013_Nat.Commun_4_2274
PubMedSearch : Al-Mssallem_2013_Nat.Commun_4_2274
PubMedID: 23917264
Gene_locus related to this paper: phodc-a0a2h3y3d5 , phodc-a0a2h3z529 , phodc-a0a2h3y147 , phodc-a0a2h3xrz4 , phodc-a0a3q0ic37 , phodc-a0a2h3yxf0 , phodc-a0a2h3zh01 , phodc-a0a3q0hs32

Title : Endothelial lipase mediates HDL levels in normal and hyperlipidemic rabbits - Zhang_2012_J.Atheroscler.Thromb_19_213
Author(s) : Zhang J , Yu Y , Nakamura K , Koike T , Waqar AB , Zhang X , Liu E , Nishijima K , Kitajima S , Shiomi M , Qi Z , Yu J , Graham MJ , Crooke RM , Ishida T , Hirata K , Hurt-Camejo E , Chen YE , Fan J
Ref : J Atheroscler Thromb , 19 :213 , 2012
Abstract : AIM: Existing evidence suggests that endothelial lipase (EL) plays an important role in high-densitylipoprotein (HDL) metabolism. Because rabbits are a useful animal model for the study of human lipid metabolism and atherosclerosis, we characterized rabbit EL (rEL) expression and investigated its relationship with plasma HDL levels in normal and hyperlipidemic rabbits. METHODS: We cloned the rEL cDNA and analyzed the EL tissue expression using Northern blotting, real-time RT-PCR, Western blotting, and in situ hybridization. We evaluated the effects of rEL antisense on plasma HDL levels. RESULTS: We found that rEL mRNA was highly expressed in cholesterol synthesis-related organs, including the liver, testis, and adrenal along with its expression in the lung, kidney, bone marrow, and small intestine. Interestingly, Watanabe heritable hyperlipidemic (WHHL) rabbits, a model of human familial hypercholesterolemia, had lower plasma levels of HDLs than normal rabbits. The plasma HDL levels in WHHL rabbits were inversely associated with high levels of plasma rEL proteins and hepatic expression of rEL mRNA. Injection of rEL-specific antisense oligonucleotides into rabbits resulted in the elevation of plasma large HDLs. Furthermore, we demonstrated that rEL mRNA was expressed by both endothelial cells and macrophages in the lesions of aortic atherosclerosis of WHHL rabbits. CONCLUSIONS: rEL is expressed in multiple tissues and may have many physiological and pathophysiological functions, such as in the regulation of cholesterol metabolism and atherosclerosis. Our results suggest that EL is an important regulator of plasma HDL levels in rabbits.
ESTHER : Zhang_2012_J.Atheroscler.Thromb_19_213
PubMedSearch : Zhang_2012_J.Atheroscler.Thromb_19_213
PubMedID: 22240910

Title : Draft genome of a Brazilian avian-pathogenic Escherichia coli strain and in silico characterization of virulence-related genes - Rojas_2012_J.Bacteriol_194_3023
Author(s) : Rojas TC , Parizzi LP , Tiba MR , Chen L , Pereira GA , Sangal V , Yang J , Yu J , Dias da Silveira W
Ref : Journal of Bacteriology , 194 :3023 , 2012
Abstract : Avian-pathogenic Escherichia coli (APEC) strains cause extraintestinal diseases in avian species. Here, we present the draft genome of an APEC strain (SCI-07) from Brazil that was isolated from skin lesions (gelatinous edema) on the head and periorbital tissues of a laying hen with swollen head syndrome.
ESTHER : Rojas_2012_J.Bacteriol_194_3023
PubMedSearch : Rojas_2012_J.Bacteriol_194_3023
PubMedID: 22582380
Gene_locus related to this paper: ecoli-IROD , ecoli-IROE , ecoli-ycfp , ecoli-YFBB , ecoli-ypt1 , ecoli-YfhR

Title : Design, synthesis and pharmacological evaluation of novel tacrine-caffeic acid hybrids as multi-targeted compounds against Alzheimer's disease - Chao_2012_Bioorg.Med.Chem.Lett_22_6498
Author(s) : Chao X , He X , Yang Y , Zhou X , Jin M , Liu S , Cheng Z , Liu P , Wang Y , Yu J , Tan Y , Huang Y , Qin J , Rapposelli S , Pi R
Ref : Bioorganic & Medicinal Chemistry Lett , 22 :6498 , 2012
Abstract : A novel series of tacrine-caffeic acid hybrids (5a-f) were designed and synthesized by combining caffeic acid (CA) with tacrine. The antioxidant study revealed that all the hybrids have much more antioxidant capacities compared to CA. Among these compounds, 5e showed the highest selectivity in inhibiting acetylcholinesterase (AChE) over butyrylcholinesterase (BuChE). Enzyme kinetic study had suggested that 5e binds to both catalytic (CAS) and peripheral anionic sites (PAS) of AChE. Moreover, compound 5e also inhibited self- or AChE-induced beta-amyloid(1-40) aggregation, as well as had potent neuroprotective effects against H(2)O(2)- and glutamate- induced cell death with low toxicity in HT22 cells.
ESTHER : Chao_2012_Bioorg.Med.Chem.Lett_22_6498
PubMedSearch : Chao_2012_Bioorg.Med.Chem.Lett_22_6498
PubMedID: 22981331

Title : Increased NDRG1 expression is associated with advanced T stages and poor vascularization in non-small cell lung cancer - Fan_2012_Pathol.Oncol.Res_18_549
Author(s) : Fan C , Yu J , Liu Y , Xu H , Wang E
Ref : Pathol Oncol Res , 18 :549 , 2012
Abstract : N-myc downstream regulated gene 1 (NDRG1) is a member of the N-myc downstream regulated gene family which belongs to the alpha/beta hydrolase superfamily. Earlier studies have shown its association with inhibition of tumor metastasis. However, its function in malignant tumors is not fully enunciated. Recently there was increasing evidence that NDRG1 is involved in stress responses. In the current study, we examined the expression of NDRG1 and its correlation with clinicopathological factors and microvessel density (MVD) in non-small cell lung cancer (NSCLC) using immunohistochemistry (IHC). NDRG1 expression in NSCLC (71/115, 61.7%) was higher than that in normal lung tissues (32/115, 27.8%) (p < 0.05). NDRG1 expression in NSCLC cells was found in cytoplasm (63/115, 54.8%), nuclear (24/115, 20.9%) and cell membrane (13/115, 11.3%). NDRG1 expression in NSCLC with advanced T stages (T2-4) (63/84, 75.0%) was significantly higher than that with T1 stage (8/31, 25.8%) (P < 0.05). No other clinicopathological factors including lymph node metastasis were found to be associated with NDRG1 expression (p > 0.05). Moreover increased NDRG1 expression was associated with lower MVD in NSCLC (P < 0.05). MVD in adenocarcinoma (33.4 +/- 8.4/HP) was significantly higher than that in squamous cell carcinoma (SCC) (19.3 +/- 8.1/HP) (P < 0.05). No other clinicopathological factors were associated with MVD in NSCLC (p > 0.05). The present findings indicate an increase of NDRG1 expression with the progress of tumour extent which may be due to unbalanced tumor oxygenation on account of poor vascularization in NSCLC.
ESTHER : Fan_2012_Pathol.Oncol.Res_18_549
PubMedSearch : Fan_2012_Pathol.Oncol.Res_18_549
PubMedID: 20853080

Title : Implication of lipid metabolism disturbance and Alzheimer's disease: focus on the lipoprotein lipase plays an important role in learning and memory function PMCID: PMC3287633 -
Author(s) : Chui D , Zhou T , Zhou L , Yang H , Liu X , Liu T , Yu J , Liu Y , Wu XF , Zhang H , Fan D
Ref : Mol Neurodegener , 7 Suppl 1 :O9 , 2012

Title : Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A - Liang_2012_PLoS.One_7_e45346
Author(s) : Liang W , Zhao Y , Chen C , Cui X , Yu J , Xiao J , Kan B
Ref : PLoS ONE , 7 :e45346 , 2012
Abstract : Salmonella Paratyphi A (S. Paratyphi A) is a highly adapted, human-specific pathogen that causes paratyphoid fever. Cases of paratyphoid fever have recently been increasing, and the disease is becoming a major public health concern, especially in Eastern and Southern Asia. To investigate the genomic variation and evolution of S. Paratyphi A, a pan-genomic analysis was performed on five newly sequenced S. Paratyphi A strains and two other reference strains. A whole genome comparison revealed that the seven genomes are collinear and that their organization is highly conserved. The high rate of substitutions in part of the core genome indicates that there are frequent homologous recombination events. Based on the changes in the pan-genome size and cluster number (both in the core functional genes and core pseudogenes), it can be inferred that the sharply increasing number of pseudogene clusters may have strong correlation with the inactivation of functional genes, and indicates that the S. Paratyphi A genome is being degraded.
ESTHER : Liang_2012_PLoS.One_7_e45346
PubMedSearch : Liang_2012_PLoS.One_7_e45346
PubMedID: 23028950

Title : [Effects of radiofrequency thermocoagulation on trigeminal ganglions in rabbits] - Yin_2011_Zhonghua.Yi.Xue.Za.Zhi_91_1718
Author(s) : Yin HM , Li AB , Yu J
Ref : Zhonghua Yi Xue Za Zhi , 91 :1718 , 2011
Abstract : OBJECTIVE: To study the histological effects of different temperatures and durations of radiofrequency on the trigeminal ganglions in rabbits. METHODS: Trigeminal ganglions of 80 rabbits were treated by R-2000B RF thermocoagulation at 60, 70, 80 degrees C respectively and the thermal electrode of 50 mm long and 0.4 mm in diameter. The treaded trigeminal ganglions were removed for HE (hematoxylin & eosin) dying at Days 1, 7, 14 and 28. And the expressions of neurofilament protein (NF200), acetylcholinesterase (ACHE) and muscarinic receptors (M-receptor) were observed after an immunohistochemical detection of HE positive samples. RESULTS: The positive manifestations of HE were degeneration of trigeminal ganglionic cells, the distribution of nerve fibers and a loss of myelinic membrane. The positive features of immunohistochemistry were as follows: NF200: dark yellow-brown particles within cytoplasm of ganglionic cells and nerve fibers cells; ACHE: deep yellow-brown particles within cytoplasm of ganglion cells and nerve fibers cells; M-receptor: yellow-brown particles within cytoplasm of ganglionic cells and nerve fibers cells. The expressions of NF200, ACHE and M-receptor increased while the temperature and radio frequency time remained constant. There was no significant difference between the expression rates of NF200, ACHE, M receptor at the same temperature for 1 and 3 minutes (P > 0.05). When treated for the same time, the expressions of NF200, ACHE and M receptor decreased more significantly at 70 degrees C versus 60 degrees C (P < 0.05). However, there was no significant difference between 70 degrees C and 80 degrees C (P > 0.05). CONCLUSION: 70 degrees C may be a suitable temperature at which radiofrequency causes the greatest harm to trigeminal ganglions so that nerve activity decreases significantly.
ESTHER : Yin_2011_Zhonghua.Yi.Xue.Za.Zhi_91_1718
PubMedSearch : Yin_2011_Zhonghua.Yi.Xue.Za.Zhi_91_1718
PubMedID: 21914325

Title : A sex-specific association of common variants of neuroligin genes (NLGN3 and NLGN4X) with autism spectrum disorders in a Chinese Han cohort - Yu_2011_Behav.Brain.Funct_7_13
Author(s) : Yu J , He X , Yao D , Li Z , Li H , Zhao Z
Ref : Behav Brain Funct , 7 :13 , 2011
Abstract : BACKGROUND: Synaptic genes, NLGN3 and NLGN4X, two homologous members of the neuroligin family, have been supposed as predisposition loci for autism spectrum disorders (ASDs), and defects of these two genes have been identified in a small fraction of individuals with ASDs. But no such rare variant in these two genes has as yet been adequately replicated in Chinese population and no common variant has been further investigated to be associated with ASDs. METHODS: 7 known ASDs-related rare variants in NLGN3 and NLGN4X genes were screened for replication of the initial findings and 12 intronic tagging single nucleotide polymorphisms (SNPs) were genotyped for case-control association analysis in a total of 229 ASDs cases and 184 control individuals in a Chinese Han cohort, using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. RESULTS: We found that a common intronic variant, SNP rs4844285 in NLGN3 gene, and a specific 3-marker haplotype XA-XG-XT (rs11795613-rs4844285-rs4844286) containing this individual SNP were associated with ASDs and showed a male bias, even after correction for multiple testing (SNP allele: P = 0.048, haplotype:P = 0.032). Simultaneously, none of these 7 known rare mutation of NLGN3 and NLGN4X genes was identified, neither in our patients with ASDs nor controls, giving further evidence that these known rare variants might be not enriched in Chinese Han cohort. CONCLUSION: The present study provides initial evidence that a common variant in NLGN3 gene may play a role in the etiology of ASDs among affected males in Chinese Han population, and further supports the hypothesis that defect of synapse might involvement in the pathophysiology of ASDs.
ESTHER : Yu_2011_Behav.Brain.Funct_7_13
PubMedSearch : Yu_2011_Behav.Brain.Funct_7_13
PubMedID: 21569590

Title : Acetylthiocholine (ATC)--cleaving cholinesterase (ChE) activity as a potential biomarker of pesticide exposure in the Manila clam, Ruditapes philippinarum, of Korea - Choi_2011_Mar.Environ.Res_71_162
Author(s) : Choi JY , Yu J , Yang DB , Ra K , Kim KT , Hong GH , Shin KH
Ref : Mar Environ Research , 71 :162 , 2011
Abstract : The acetylthiocholine (ATC) - cleaving cholinesterase (ChE) activity in Manila clam, which is widely distributed throughout the coastal environment of Korea, was assayed as a potentially useful biomarker of organophosphorous pesticides (OPs). A clear dose-response relationship was determined between inhibited ChE in adductor muscle of clams and four OPs (methidathion, chlorpyrifos, diazinon, IBP) which are heavily used OPs in Korea. The measured EC(50)-24 h values of methidathion, chlorpyrifos, diazinon, and IBP for Ruditapes philippinarum were 7.16 mug l(-1), 0.34 mg l(-1), 3.01 mg l(-1), and 3.41 mg l(-1), respectively. In field studies, ChE activity in Manila clams collected from 23 stations in the mid-western coastal region demonstrated spatial variation with statistical differences. These results suggest that ChE activity in R. philippinarum is a potential biomarker for assessing organophosphorous pesticide contamination in coastal environments.
ESTHER : Choi_2011_Mar.Environ.Res_71_162
PubMedSearch : Choi_2011_Mar.Environ.Res_71_162
PubMedID: 21262527

Title : Complete genome sequence of Streptococcus suis serotype 14 strain JS14 - Hu_2011_J.Bacteriol_193_2375
Author(s) : Hu P , Yang M , Zhang A , Wu J , Chen B , Hua Y , Yu J , Xiao J , Jin M
Ref : Journal of Bacteriology , 193 :2375 , 2011
Abstract : Streptococcus suis is an important zoonotic agent leading to a variety of diseases in swine and can be transmitted to human beings upon close contact. Here, we report the complete genome sequence of S. suis serotype 14 strain JS14 which was isolated from a diseased pig in Jiangsu Province, China.
ESTHER : Hu_2011_J.Bacteriol_193_2375
PubMedSearch : Hu_2011_J.Bacteriol_193_2375
PubMedID: 21398551
Gene_locus related to this paper: strej-e8uk64 , strsu-a4vws4 , strsu-q673u2 , strsy-a4vus4

Title : The genome of the mesopolyploid crop species Brassica rapa - Wang_2011_Nat.Genet_43_1035
Author(s) : Wang X , Wang H , Wang J , Sun R , Wu J , Liu S , Bai Y , Mun JH , Bancroft I , Cheng F , Huang S , Li X , Hua W , Freeling M , Pires JC , Paterson AH , Chalhoub B , Wang B , Hayward A , Sharpe AG , Park BS , Weisshaar B , Liu B , Li B , Tong C , Song C , Duran C , Peng C , Geng C , Koh C , Lin C , Edwards D , Mu D , Shen D , Soumpourou E , Li F , Fraser F , Conant G , Lassalle G , King GJ , Bonnema G , Tang H , Belcram H , Zhou H , Hirakawa H , Abe H , Guo H , Jin H , Parkin IA , Batley J , Kim JS , Just J , Li J , Xu J , Deng J , Kim JA , Yu J , Meng J , Min J , Poulain J , Hatakeyama K , Wu K , Wang L , Fang L , Trick M , Links MG , Zhao M , Jin M , Ramchiary N , Drou N , Berkman PJ , Cai Q , Huang Q , Li R , Tabata S , Cheng S , Zhang S , Sato S , Sun S , Kwon SJ , Choi SR , Lee TH , Fan W , Zhao X , Tan X , Xu X , Wang Y , Qiu Y , Yin Y , Li Y , Du Y , Liao Y , Lim Y , Narusaka Y , Wang Z , Li Z , Xiong Z , Zhang Z
Ref : Nat Genet , 43 :1035 , 2011
Abstract : We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
ESTHER : Wang_2011_Nat.Genet_43_1035
PubMedSearch : Wang_2011_Nat.Genet_43_1035
PubMedID: 21873998
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brarp-m4ei94 , brarp-m4c988 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brarp-m4dwa6 , brana-a0a078j4f0 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078dfa9 , brana-a0a078ic91 , brarp-m4ctw3 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078jx23 , brarp-m4da84 , brarp-m4dwr7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , brarp-m4cwq4 , brarp-m4dcj8 , brarp-m4eh17 , brarp-m4eey4 , brarp-m4dnj8 , brarp-m4ey83 , brarp-m4ey84

Title : Complete genome sequence of Streptococcus suis serotype 3 strain ST3 - Hu_2011_J.Bacteriol_193_3428
Author(s) : Hu P , Yang M , Zhang A , Wu J , Chen B , Hua Y , Yu J , Chen H , Xiao J , Jin M
Ref : Journal of Bacteriology , 193 :3428 , 2011
Abstract : Streptococcus suis is a zoonotic pathogen causing economic loss in the swine industry and is also a threat to human health. To date, the mechanism of pathogenesis is not fully understood. Here, we report the complete genome sequence of S. suis strain ST3 of serotype 3, which provides opportunities to reveal genetic basis of infection of S. suis non-serotype 2 strains.
ESTHER : Hu_2011_J.Bacteriol_193_3428
PubMedSearch : Hu_2011_J.Bacteriol_193_3428
PubMedID: 21572001
Gene_locus related to this paper: strsu-b9wvz1

Title : Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes - Zhang_2011_BMC.Genomics_12_523
Author(s) : Zhang A , Yang M , Hu P , Wu J , Chen B , Hua Y , Yu J , Chen H , Xiao J , Jin M
Ref : BMC Genomics , 12 :523 , 2011
Abstract : BACKGROUND: Streptococcus suis (S. suis) is a major swine pathogen and an emerging zoonotic agent. Serotypes 1, 2, 3, 7, 9, 14 and 1/2 are the most prevalent serotypes of this pathogen. However, almost all studies were carried out on serotype 2 strains. Therefore, characterization of genomic features of other serotypes will be required to better understand their virulence potential and phylogenetic relationships among different serotypes.
RESULTS: Four Chinese S. suis strains belonging to serotypes 1, 7, 9 and 1/2 were sequenced using a rapid, high-throughput approach. Based on the 13 corresponding serotype strains, including 9 previously completed genomes of this bacterium, a full comparative genomic analysis was performed. The results provide evidence that (i) the pan-genome of this species is open and the size increases with addition of new sequenced genomes, (ii) strains of serotypes 1, 3, 7 and 9 are phylogenetically distinct from serotype 2 strains, but all serotype 2 strains, plus the serotype 1/2 and 14 strains, are very closely related. (iii) all these strains, except for the serotype 1 strain, could harbor a recombinant site for a pathogenic island (89 K) mediated by conjugal transfer, and may have the ability to gain the 89 K sequence.
CONCLUSIONS: There is significant genomic diversity among different strains in S. suis, and the gain and loss of large amount of genes are involved in shaping their genomes. This is indicated by (i) pairwise gene content comparisons between every pair of these strains, (ii) the open pan-genome of this species, (iii) the observed indels, invertions and rearrangements in the collinearity analysis. Phylogenetic relationships may be associated with serotype, as serotype 2 strains are closely related and distinct from other serotypes like 1, 3, 7 and 9, but more strains need to be sequenced to confirm this.
ESTHER : Zhang_2011_BMC.Genomics_12_523
PubMedSearch : Zhang_2011_BMC.Genomics_12_523
PubMedID: 22026465
Gene_locus related to this paper: strsu-b9wvz1

Title : Genetic and dietary regulation of lipid droplet expansion in Caenorhabditis elegans - Zhang_2010_Proc.Natl.Acad.Sci.U.S.A_107_4640
Author(s) : Zhang SO , Box AC , Xu N , Le Men J , Yu J , Guo F , Trimble R , Mak HY
Ref : Proc Natl Acad Sci U S A , 107 :4640 , 2010
Abstract : Dietary fat accumulates in lipid droplets or endolysosomal compartments that undergo selective expansion under normal or pathophysiological conditions. We find that genetic defects in a peroxisomal beta-oxidation pathway cause size expansion in lipid droplets that are distinct from the lysosome-related organelles in Caenorhabditis elegans. Expansion of lipid droplets is accompanied by an increase in triglycerides (TAG) that are resistant to fasting- or TAG lipase-triggered lipolysis. Nevertheless, in mutant animals, a diet poor in vaccenic acid reduced the TAG level and lipid droplet size. Our results implicate peroxisomal dysfunction in pathologic lipid droplet expansion in animals and illustrate how dietary factors modulate the phenotype of such genetic defects.
ESTHER : Zhang_2010_Proc.Natl.Acad.Sci.U.S.A_107_4640
PubMedSearch : Zhang_2010_Proc.Natl.Acad.Sci.U.S.A_107_4640
PubMedID: 20176933

Title : The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation - Qin_2010_BMC.Genomics_11_247
Author(s) : Qin QL , Zhang XY , Wang XM , Liu GM , Chen XL , Xie BB , Dang HY , Zhou BC , Yu J , Zhang YZ
Ref : BMC Genomics , 11 :247 , 2010
Abstract : BACKGROUND: Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes.
RESULTS: The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. CONCLUSION: Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.
ESTHER : Qin_2010_BMC.Genomics_11_247
PubMedSearch : Qin_2010_BMC.Genomics_11_247
PubMedID: 20398413
Gene_locus related to this paper: zunps-d5bb86 , zunps-d5bdi3 , zunps-d5bdw4 , zunps-d5bdx7 , zunps-d5bfq8 , zunps-d5bhe6 , zunps-d5bju1 , zunps-d5bk35 , zunps-d5bk43

Title : Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14 - Ding_2009_BMC.Genomics_10_158
Author(s) : Ding F , Tang P , Hsu MH , Cui P , Hu S , Yu J , Chiu CH
Ref : BMC Genomics , 10 :158 , 2009
Abstract : BACKGROUND: Streptococcus pneumoniae serotype 14 is one of the most common pneumococcal serotypes that cause invasive pneumococcal diseases worldwide. Serotype 14 often expresses resistance to a variety of antimicrobial agents, resulting in difficulties in treatment. To gain insight into the evolution of virulence and antimicrobial resistance traits in S. pneumoniae from the genome level, we sequenced the entire genome of a serotype 14 isolate (CGSP14), and carried out comprehensive comparison with other pneumococcal genomes. Multiple serotype 14 clinical isolates were also genotyped by multilocus sequence typing (MLST). RESULTS: Comparative genomic analysis revealed that the CGSP14 acquired a number of new genes by horizontal gene transfer (HGT), most of which were associated with virulence and antimicrobial resistance and clustered in mobile genetic elements. The most remarkable feature is the acquisition of two conjugative transposons and one resistance island encoding eight resistance genes. Results of MLST suggested that the major driving force for the genome evolution is the environmental drug pressure. CONCLUSION: The genome sequence of S. pneumoniae serotype 14 shows a bacterium with rapid adaptations to its lifecycle in human community. These include a versatile genome content, with a wide range of mobile elements, and chromosomal rearrangement; the latter re-balanced the genome after events of HGT.
ESTHER : Ding_2009_BMC.Genomics_10_158
PubMedSearch : Ding_2009_BMC.Genomics_10_158
PubMedID: 19361343
Gene_locus related to this paper: strpi-pepx , strpj-b8zns7 , strpn-AXE1 , strpn-b2dz20 , strpn-SP0614

Title : Amyloid-beta expression in retrosplenial cortex of triple transgenic mice: relationship to cholinergic axonal afferents from medial septum - Robertson_2009_Neurosci_164_1334
Author(s) : Robertson RT , Baratta J , Yu J , LaFerla FM
Ref : Neuroscience , 164 :1334 , 2009
Abstract : Triple transgenic (3xTg-AD) mice harboring the presenilin 1, amyloid precursor protein, and tau transgenes (Oddo et al., 2003b) display prominent levels of amyloid-beta (Abeta) immunoreactivity in forebrain regions. The Abeta immunoreactivity is first seen intracellularly in neurons and later as extracellular plaque deposits. The present study examined Abeta immunoreactivity that occurs in layer III of the granular division of retrosplenial cortex (RSg). This pattern of Abeta immunoreactivity in layer III of RSg develops relatively late, and is seen in animals older than 14 months. The appearance of the Abeta immunoreactivity is similar to an axonal terminal field and thus may offer a unique opportunity to study the relationship between afferent projections and the formation of Abeta deposits. Axonal tract tracing techniques demonstrated that the pattern of axon terminal labeling in layer III of RSg, following placement of DiI in medial septum, is remarkably similar to the pattern of cholinergic axons in RSg, as detected by acetylcholinesterase histochemical staining, choline acetyltransferase immunoreactivity, or p75 receptor immunoreactivity; this pattern also is strikingly similar to the band of Abeta immunoreactivity. In animals sustaining early damage to the medial septal nucleus (prior to the advent of Abeta immunoreactivity), the band of Abeta in layer III of RSg does not develop; the corresponding band of cholinergic markers also is eliminated. In older animals (after the appearance of the Abeta immunoreactivity) damage to cholinergic afferents by electrolytic lesions, immunotoxin lesions, or cutting the cingulate bundle, result in a rapid loss of the cholinergic markers and a slower reduction of Abeta immunoreactivity. These results suggest that the septal cholinergic axonal projections transport Abeta or amyloid precursor protein (APP) to layer III of RSg.
ESTHER : Robertson_2009_Neurosci_164_1334
PubMedSearch : Robertson_2009_Neurosci_164_1334
PubMedID: 19772895

Title : Cooperation and functional diversification of two closely related galactolipase genes for jasmonate biosynthesis - Hyun_2008_Dev.Cell_14_183
Author(s) : Hyun Y , Choi S , Hwang HJ , Yu J , Nam SJ , Ko J , Park JY , Seo YS , Kim EY , Ryu SB , Kim WT , Lee YH , Kang H , Lee I
Ref : Dev Cell , 14 :183 , 2008
Abstract : Jasmonic acid (JA) plays pivotal roles in diverse plant biological processes, including wound response. Chloroplast lipid hydrolysis is a critical step for JA biosynthesis, but the mechanism of this process remains elusive. We report here that DONGLE (DGL), a homolog of DEFECTIVE IN ANTHER DEHISCENCE1 (DAD1), encodes a chloroplast-targeted lipase with strong galactolipase and weak phospholipase A(1) activity. DGL is expressed in the leaves and has a specific role in maintaining basal JA content under normal conditions, and this expression regulates vegetative growth and is required for a rapid JA burst after wounding. During wounding, DGL and DAD1 have partially redundant functions for JA production, but they show different induction kinetics, indicating temporally separated roles: DGL plays a role in the early phase of JA production, and DAD1 plays a role in the late phase of JA production. Whereas DGL and DAD1 are necessary and sufficient for JA production, phospholipase D appears to modulate wound response by stimulating DGL and DAD1 expression.
ESTHER : Hyun_2008_Dev.Cell_14_183
PubMedSearch : Hyun_2008_Dev.Cell_14_183
PubMedID: 18267087
Gene_locus related to this paper: arath-AT4G16820 , arath-PLA11 , arath-PLA12 , arath-PLA13 , arath-PLA15 , arath-PLA16 , arath-PLA17

Title : Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3 - Wang_2008_PLoS.One_3_e1937
Author(s) : Wang F , Wang J , Jian H , Zhang B , Li S , Zeng X , Gao L , Bartlett DH , Yu J , Hu S , Xiao X
Ref : PLoS ONE , 3 :e1937 , 2008
Abstract : Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as genes for two sets of flagellum systems, structural RNA modification, eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and synthesis. And WP3 contains 55 open reading frames encoding putative c-type cytochromes which are substantial to its wide environmental adaptation ability. The mtr-omc gene cluster involved in the insoluble metal reduction in the Shewanella genus was identified and compared. The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature.
ESTHER : Wang_2008_PLoS.One_3_e1937
PubMedSearch : Wang_2008_PLoS.One_3_e1937
PubMedID: 18398463
Gene_locus related to this paper: shepw-b8ci75 , shepw-b8cib3 , shepw-b8ciu7 , shepw-b8cld5 , shepw-b8cll2 , shepw-b8clm3 , shepw-b8cls4 , shepw-b8ct86 , shepw-b8ctf0 , shepw-b8ctt3 , shepw-b8cuq7 , shepw-b8cuu6 , shepw-b8cuz1 , shepw-b8cvm0 , shepw-b8cqh1 , shepw-b8cgv9 , shepw-b8chj5 , shepw-b8cpv3 , shepw-b8civ4 , shepw-b8cn18

Title : Lipoprotein lipase activator ameliorates the severity of dietary steatohepatitis - Yu_2007_Biochem.Biophys.Res.Commun_356_53
Author(s) : Yu J , Chu ES , Hui AY , Cheung KF , Chan HL , Leung WK , Farrell GC , Sung JJ
Ref : Biochemical & Biophysical Research Communications , 356 :53 , 2007
Abstract : Dietary model of steatohepatitis was established by feeding mice a methionine choline deficient (MCD) diet. Mice on MCD or control diet for 3 weeks were treated with or without NO-1886, a newly synthetic lipoprotein lipase (LPL) activator. In a separate experiment, NO-1886 was given after pre-treatment with 3 weeks of MCD diet. NO-1886 significantly reduced MCD-induced inflammation by repressing levels of hepatic lipid peroxides and pro-inflammatory tumor necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), and cyclooxygenase-2 (COX-2). In addition, NO-1886 dampened hepatic steatosis via accelerating fatty acid oxidation caused by enhanced expression of PPARalpha, cytochrome P450-10 (Cyp4a10), and Acyl-CoA oxidase (ACO). It failed to regulate genes of fatty acid uptake and synthesis pathways. In conclusion, NO-1886 ameliorated and induced regression of experimental steatohepatitis via increasing endogenous LPL activation resulting in suppression on pro-inflammatory factors and reduction of hepatic fatty acids. These findings indicate that NO-1886 is a potential therapeutic agent for steatohepatitis.
ESTHER : Yu_2007_Biochem.Biophys.Res.Commun_356_53
PubMedSearch : Yu_2007_Biochem.Biophys.Res.Commun_356_53
PubMedID: 17350593

Title : A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates - Chen_2007_PLoS.One_2_e315
Author(s) : Chen C , Tang J , Dong W , Wang C , Feng Y , Wang J , Zheng F , Pan X , Liu D , Li M , Song Y , Zhu X , Sun H , Feng T , Guo Z , Ju A , Ge J , Dong Y , Sun W , Jiang Y , Yan J , Yang H , Wang X , Gao GF , Yang R , Yu J
Ref : PLoS ONE , 2 :e315 , 2007
Abstract : BACKGROUND: Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen, causing more than 200 cases of severe human infection worldwide, with the hallmarks of meningitis, septicemia, arthritis, etc. Very recently, SS2 has been recognized as an etiological agent for streptococcal toxic shock syndrome (STSS), which was originally associated with Streptococcus pyogenes (GAS) in Streptococci. However, the molecular mechanisms underlying STSS are poorly understood. METHODS AND FINDINGS: To elucidate the genetic determinants of STSS caused by SS2, whole genome sequencing of 3 different Chinese SS2 strains was undertaken. Comparative genomics accompanied by several lines of experiments, including experimental animal infection, PCR assay, and expression analysis, were utilized to further dissect a candidate pathogenicity island (PAI). Here we show, for the first time, a novel molecular insight into Chinese isolates of highly invasive SS2, which caused two large-scale human STSS outbreaks in China. A candidate PAI of approximately 89 kb in length, which is designated 89K and specific for Chinese SS2 virulent isolates, was investigated at the genomic level. It shares the universal properties of PAIs such as distinct GC content, consistent with its pivotal role in STSS and high virulence. CONCLUSIONS: To our knowledge, this is the first PAI candidate from S. suis worldwide. Our finding thus sheds light on STSS triggered by SS2 at the genomic level, facilitates further understanding of its pathogenesis and points to directions of development on some effective strategies to combat highly pathogenic SS2 infections.
ESTHER : Chen_2007_PLoS.One_2_e315
PubMedSearch : Chen_2007_PLoS.One_2_e315
PubMedID: 17375201
Gene_locus related to this paper: strsu-a4vws4 , strsu-q302y4 , strsy-a4vus4 , strsy-a4vwf6

Title : The DNA sequence, annotation and analysis of human chromosome 3 - Muzny_2006_Nature_440_1194
Author(s) : Muzny DM , Scherer SE , Kaul R , Wang J , Yu J , Sudbrak R , Buhay CJ , Chen R , Cree A , Ding Y , Dugan-Rocha S , Gill R , Gunaratne P , Harris RA , Hawes AC , Hernandez J , Hodgson AV , Hume J , Jackson A , Khan ZM , Kovar-Smith C , Lewis LR , Lozado RJ , Metzker ML , Milosavljevic A , Miner GR , Morgan MB , Nazareth LV , Scott G , Sodergren E , Song XZ , Steffen D , Wei S , Wheeler DA , Wright MW , Worley KC , Yuan Y , Zhang Z , Adams CQ , Ansari-Lari MA , Ayele M , Brown MJ , Chen G , Chen Z , Clendenning J , Clerc-Blankenburg KP , Davis C , Delgado O , Dinh HH , Dong W , Draper H , Ernst S , Fu G , Gonzalez-Garay ML , Garcia DK , Gillett W , Gu J , Hao B , Haugen E , Havlak P , He X , Hennig S , Hu S , Huang W , Jackson LR , Jacob LS , Kelly SH , Kube M , Levy R , Li Z , Liu B , Liu J , Liu W , Lu J , Maheshwari M , Nguyen BV , Okwuonu GO , Palmeiri A , Pasternak S , Perez LM , Phelps KA , Plopper FJ , Qiang B , Raymond C , Rodriguez R , Saenphimmachak C , Santibanez J , Shen H , Shen Y , Subramanian S , Tabor PE , Verduzco D , Waldron L , Wang Q , Williams GA , Wong GK , Yao Z , Zhang J , Zhang X , Zhao G , Zhou J , Zhou Y , Nelson D , Lehrach H , Reinhardt R , Naylor SL , Yang H , Olson M , Weinstock G , Gibbs RA
Ref : Nature , 440 :1194 , 2006
Abstract : After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
ESTHER : Muzny_2006_Nature_440_1194
PubMedSearch : Muzny_2006_Nature_440_1194
PubMedID: 16641997
Gene_locus related to this paper: human-AADAC , human-AADACL2 , human-ABHD5 , human-ABHD6 , human-ABHD10 , human-ABHD14A , human-APEH , human-BCHE , human-CIB , human-LIPH , human-MGLL , human-NLGN1 , human-PLA1A

Title : A role for neurotrophin-3 in targeting developing cholinergic axon projections to cerebral cortex - Robertson_2006_Neurosci_143_523
Author(s) : Robertson RT , Baratta J , Yu J , Guthrie KM
Ref : Neuroscience , 143 :523 , 2006
Abstract : This study examined the relationship between expression of neurotrophin-3 (NT-3) and the ingrowth of cholinergic axonal projections in cerebral cortex. Patterns of expression of NT-3 (defined by beta-galactosidase reporter expression in heterozygous offspring of transgenic NT-3(lacZneo/+) mice) revealed that limbic cortical regions (including frontal, cingulate, and insular cortex, as well as the dentate gyrus) express NT-3 and that these cortical regions receive early and relatively dense cholinergic axons (stained for acetylcholinesterase, AChE). Using the dentate gyrus as a model system, studies revealed that expression of the NT-3 reporter parallels, and precedes by approximately 2 days, the ingrowth of AChE positive cholinergic axons. Studies of forebrain organotypic slice cultures demonstrate that basal forebrain-derived cholinergic axons extend into cortical regions in a pattern that mimics the pattern of expression of the NT-3 reporter. Similarly, chimeric co-cultures, combining wild type septum with a slice of hippocampus from heterozygous NT-3(lacZneo/+) mice, demonstrate that cholinergic axons grow into regions of the dentate gyrus that express the NT-3 reporter. Hemisphere slice cultures made from NT-3 knockout mice reveal cholinergic axonal growth into cortex, but these axons do not form the regional pattern characteristic of slice cultures made from wild type or heterozygous NT-3(lacZneo/+) mice. Further, chimeric co-cultures made using slices of wild type septum combined with slices of hippocampus from NT-3 knockout mice demonstrate robust cholinergic axonal growth into the hippocampus, but the cholinergic axons do not form the characteristic preterminal pattern associated with the dentate gyrus. Slice cultures from limbic cortical tissue from the NT-3 null mice do not display exaggerated levels of cell death. In aggregate, these data support the hypothesis that expression of NT-3 by cortical neurons serves to attract basal forebrain cholinergic projections to their target cells in cerebral cortex.
ESTHER : Robertson_2006_Neurosci_143_523
PubMedSearch : Robertson_2006_Neurosci_143_523
PubMedID: 17049175

Title : Patterns of afferent projections to the dentate gyrus studied in organotypic co-cultures - Guthrie_2005_Brain.Res.Dev.Brain.Res_157_162
Author(s) : Guthrie KM , Tran A , Baratta J , Yu J , Robertson RT
Ref : Brain Research Developmental Brain Research , 157 :162 , 2005
Abstract : Cholinergic axons originating from the septum form a characteristic layer of preterminal axons and apparent termination in the molecular layer of the hippocampal dentate gyrus. The present study explored the specificity of this characteristic axonal pattern, through the use of organotypic slice co-cultures. Slices of hippocampus were co-cultured with a slice from one of a variety of other potential sources of afferents, and the afferent axons were labeled histochemically or immunocytochemically to determine which afferents distribute within the dentate molecular layer in a pattern similar to that formed by septal cholinergic projections. Acetylcholinesterase (AChE) histochemistry demonstrated that cholinergic axons from septum, substantia innominata, and striatum all consistently targeted the inner molecular layer of the dentate gyrus. AChE-labeled cholinergic axons from dorsal lateral pontine tegmentum and from spinal cord sometimes formed this pattern, while axons from the habenula failed to extend into the dentate gyrus. Immunocytochemically identified monoaminergic axons from the substantia nigra, locus coeruleus, and raphe extended into co-cultured hippocampus; each of these afferent systems displayed a prominent axonal plexus within the hilus of the dentate, but only the raphe axons projected prominently to the molecular layer. These data demonstrate that the molecular layer of the dentate gyrus provides an attractive target zone for some cholinergic and monoaminergic afferents, but not all. Commonalities between neuronal populations that preferentially project to the molecular layer in vitro may offer clues regarding the axon guidance mechanisms that normally direct cholinergic axons to target sites in the dentate gyrus molecular layer.
ESTHER : Guthrie_2005_Brain.Res.Dev.Brain.Res_157_162
PubMedSearch : Guthrie_2005_Brain.Res.Dev.Brain.Res_157_162
PubMedID: 15882910

Title : Genome sequencing and analysis of Aspergillus oryzae - Machida_2005_Nature_438_1157
Author(s) : Machida M , Asai K , Sano M , Tanaka T , Kumagai T , Terai G , Kusumoto K , Arima T , Akita O , Kashiwagi Y , Abe K , Gomi K , Horiuchi H , Kitamoto K , Kobayashi T , Takeuchi M , Denning DW , Galagan JE , Nierman WC , Yu J , Archer DB , Bennett JW , Bhatnagar D , Cleveland TE , Fedorova ND , Gotoh O , Horikawa H , Hosoyama A , Ichinomiya M , Igarashi R , Iwashita K , Juvvadi PR , Kato M , Kato Y , Kin T , Kokubun A , Maeda H , Maeyama N , Maruyama J , Nagasaki H , Nakajima T , Oda K , Okada K , Paulsen I , Sakamoto K , Sawano T , Takahashi M , Takase K , Terabayashi Y , Wortman JR , Yamada O , Yamagata Y , Anazawa H , Hata Y , Koide Y , Komori T , Koyama Y , Minetoki T , Suharnan S , Tanaka A , Isono K , Kuhara S , Ogasawara N , Kikuchi H
Ref : Nature , 438 :1157 , 2005
Abstract : The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
ESTHER : Machida_2005_Nature_438_1157
PubMedSearch : Machida_2005_Nature_438_1157
PubMedID: 16372010
Gene_locus related to this paper: aspor-Q2U722 , aspfn-b8mvx2 , aspfn-b8mwk1 , aspfn-b8n1a4 , aspfn-b8n5l3 , aspfn-b8n7y0 , aspfn-b8n829 , aspfn-b8ncj5 , aspfn-b8nhj9 , aspfn-b8njx6 , aspfn-b8nsk2 , aspfu-q4wj61 , aspor-axe1 , aspor-CPI , aspor-cutas , aspor-cuti2 , aspor-DPPIV , aspor-faec , aspor-MDLB , aspor-ppme1 , aspor-q2tw11 , aspor-q2tw16 , aspor-q2tw28 , aspor-q2twc4 , aspor-q2twg0 , aspor-q2twj3 , aspor-q2twv2 , aspor-q2twv4 , aspor-q2tx21 , aspor-q2txq8 , aspor-q2tya1 , aspor-q2tyh6 , aspor-q2tyn9 , aspor-q2typ0 , aspor-q2tyq4 , aspor-q2tyv8 , aspor-q2tz03 , aspor-q2tzh3 , aspor-q2tzr5 , aspor-q2tzv9 , aspor-q2u0k7 , aspor-q2u0q2 , aspor-q2u0r6 , aspor-q2u1a5 , aspor-q2u1a6 , aspor-q2u1k0 , aspor-q2u1k8 , aspor-q2u1m8 , aspor-q2u2a1 , aspor-q2u2a4 , aspor-q2u3a3 , aspor-q2u3a6 , aspor-q2u3k5 , aspor-q2u3l6 , aspor-q2u4a0 , aspor-q2u4e0 , aspor-q2u4f6 , aspor-q2u4g6 , aspor-q2u4h9 , aspor-q2u4w9 , aspor-q2u4y8 , aspor-q2u5f5 , aspor-q2u5n3 , aspor-q2u5y8 , aspor-q2u6h7 , aspor-q2u6j5 , aspor-q2u6m8 , aspor-q2u6m9 , aspor-q2u6n6 , aspor-q2u7i2 , aspor-q2u7v0 , aspor-q2u8j8 , aspor-q2u8r1 , aspor-q2u8r4 , aspor-q2u8t5 , aspor-q2u8z3 , aspor-q2u9a1 , aspor-q2u9n5 , aspor-q2u144 , aspor-q2u161 , aspor-q2u185 , aspor-q2u199 , aspor-q2u212 , aspor-q2u331 , aspor-q2u348 , aspor-q2u400 , aspor-q2u453 , aspor-q2u489 , aspor-q2u704 , aspor-q2u728 , aspor-q2u798 , aspor-q2u822 , aspor-q2u854 , aspor-q2u875 , aspor-q2u908 , aspor-q2ua10 , aspor-q2ua48 , aspor-q2uab6 , aspor-q2uak9 , aspor-q2uaq4 , aspor-q2ub32 , aspor-q2ub76 , aspor-q2uba1 , aspor-q2ubd6 , aspor-q2ubm2 , aspor-q2ubr2 , aspor-q2uc28 , aspor-q2uc65 , aspor-q2uc77 , aspor-q2uc98 , aspor-q2uck0 , aspor-q2ucy7 , aspor-q2ud03 , aspor-q2ud06 , aspor-q2ud08 , aspor-q2ud23 , aspor-q2udn5 , aspor-q2udr0 , aspor-q2uec1 , aspor-q2uef3 , aspor-q2uf10 , aspor-q2uf27 , aspor-q2uf48 , aspor-q2ufd8 , aspor-q2ufe5 , aspor-q2ufm4 , aspor-q2ufr3 , aspor-q2ufz8 , aspor-q2ug78 , aspor-q2ugd6 , aspor-q2uge1 , aspor-q2ugg7 , aspor-q2ugi2 , aspor-q2ugl2 , aspor-q2ugy9 , aspor-q2uh24 , aspor-q2uh73 , aspor-q2uhe4 , aspor-q2uhf0 , aspor-q2uhj6 , aspor-q2uhn1 , aspor-q2uhq0 , aspor-q2ui56 , aspor-q2uib2 , aspor-q2uib5 , aspor-q2uie9 , aspor-q2uih1 , aspor-q2uii1 , aspor-q2uik9 , aspor-q2uiq0 , aspor-q2uiu1 , aspor-q2uix9 , aspor-q2uiy5 , aspor-q2uiz4 , aspor-q2uj89 , aspor-q2uja2 , aspor-q2uju3 , aspor-q2uk31 , aspor-q2uk42 , aspor-q2ukb6 , aspor-q2ukq7 , aspor-q2ul81 , aspor-q2uli9 , aspor-q2ulr2 , aspor-q2ulv7 , aspor-q2umf3 , aspor-q2umv2 , aspor-q2umx6 , aspor-q2unw5 , aspor-q2up23 , aspor-q2up89 , aspor-q2upe6 , aspor-q2upi1 , aspor-q2upl1 , aspor-q2upw4 , aspor-q2uq56 , aspor-q2uqb4 , aspor-q2uqm7 , aspor-q2ur58 , aspor-q2ur64 , aspor-q2ur80 , aspor-q2ur83 , aspor-q2ure7 , aspor-q2urf3 , aspor-q2urg5 , aspor-q2urq0 , aspor-q2urt4 , aspor-q2uru5 , aspor-q2usi0 , aspor-q2usp7 , aspor-q2usq8 , aspor-q2usv6 , aspor-q2uta5 , aspor-q2uu89 , aspor-q2uub4 , aspor-q2uux8 , aspor-q2uv29 , aspor-TGLA , aspor-q2ue03 , aspor-q2uj83 , aspno-a0a0l1j1c9

Title : The Genomes of Oryza sativa: a history of duplications - Yu_2005_PLoS.Biol_3_e38
Author(s) : Yu J , Wang J , Lin W , Li S , Li H , Zhou J , Ni P , Dong W , Hu S , Zeng C , Zhang J , Zhang Y , Li R , Xu Z , Li X , Zheng H , Cong L , Lin L , Yin J , Geng J , Li G , Shi J , Liu J , Lv H , Li J , Deng Y , Ran L , Shi X , Wang X , Wu Q , Li C , Ren X , Li D , Liu D , Zhang X , Ji Z , Zhao W , Sun Y , Zhang Z , Bao J , Han Y , Dong L , Ji J , Chen P , Wu S , Xiao Y , Bu D , Tan J , Yang L , Ye C , Xu J , Zhou Y , Yu Y , Zhang B , Zhuang S , Wei H , Liu B , Lei M , Yu H , Li Y , Xu H , Wei S , He X , Fang L , Huang X , Su Z , Tong W , Tong Z , Ye J , Wang L , Lei T , Chen C , Chen H , Huang H , Zhang F , Li N , Zhao C , Huang Y , Li L , Xi Y , Qi Q , Li W , Hu W , Tian X , Jiao Y , Liang X , Jin J , Gao L , Zheng W , Hao B , Liu S , Wang W , Yuan L , Cao M , McDermott J , Samudrala R , Wong GK , Yang H
Ref : PLoS Biol , 3 :e38 , 2005
Abstract : We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
ESTHER : Yu_2005_PLoS.Biol_3_e38
PubMedSearch : Yu_2005_PLoS.Biol_3_e38
PubMedID: 15685292
Gene_locus related to this paper: orysa-Q7XTC5 , orysa-Q852M6 , orysa-Q8GSE8 , orysa-Q9S7P1 , orysa-Q9FYP7 , orysa-Q5ZBH3 , orysa-Q5ZA26 , orysa-Q5JLP6 , orysa-Q8H5P9 , orysa-Q8H5P5 , orysa-Q7F1Y5 , orysa-Q949C9 , orysa-cbp1 , orysa-cbp3 , orysa-cbpx , orysa-Q33B71 , orysa-Q8GSJ3 , orysa-LPL1 , orysa-Q6YSZ8 , orysa-Q8S5X5 , orysa-Q8LIG3 , orysa-Q6K7F5 , orysa-Q7F1B1 , orysa-Q8H4S9 , orysa-Q69UB1 , orysa-Q9FW17 , orysa-Q337C3 , orysa-Q7F959 , orysa-Q84QZ6 , orysa-Q84QY7 , orysa-Q851E3 , orysa-Q6YTH5 , orysa-Q0JK71 , orysa-Q8S1D9 , orysa-Q5N8V4 , orysa-Q0JCY4 , orysa-Q8GTK2 , orysa-B9EWJ8 , orysa-Q8H3K6 , orysa-Q6ZDG8 , orysa-Q6ZDG6 , orysa-Q6ZDG5 , orysa-Q6ZDG4 , orysa-Q5NAI4 , orysa-Q658B2 , orysa-Q5JMQ8 , orysa-Q5QMD9 , orysa-Q5N7L1 , orysa-Q8RYV9 , orysa-Q8H3R3 , orysa-Q5SNH3 , orysa-Q8W0F0 , orysa-pir7a , orysa-pir7b , orysa-q2qlm4 , orysa-q2qm78 , orysa-q2qm82 , orysa-q2qn31 , orysa-q2qnj4 , orysa-q2qnt9 , orysa-q2qur1 , orysa-q2qx94 , orysa-q2qyi1 , orysa-q2qyj1 , orysa-q2r051 , orysa-q2r077 , orysa-q2ram0 , orysa-q2rat1 , orysa-q2rbb3 , orysa-Q4VWY7 , orysa-q5na00 , orysa-q5nbu1 , orysa-Q5QLC0 , orysa-q5smv5 , orysa-Q5VP27 , orysa-q5vrt2 , orysa-q5w6c5 , orysa-q5z5a3 , orysa-q5z9i2 , orysa-q5z417 , orysa-q5z901 , orysa-Q5ZAM8 , orysa-Q5ZBI5 , orysa-Q5ZCR3 , orysa-q6atz0 , orysa-q6ave2 , orysa-q6f358 , orysa-q6h6s1 , orysa-q6h7i6 , orysa-q6i5q3 , orysa-q6i5u7 , orysa-q6j657 , orysa-q6k3d9 , orysa-q6k4q2 , orysa-q6k880 , orysa-q6l5b6 , orysa-Q6L5F5 , orysa-q6l556 , orysj-q6yse8 , orysa-q6yy42 , orysa-q6yzk1 , orysa-q6z8b1 , orysa-q6z995 , orysa-q6zc62 , orysa-q6zia4 , orysa-q6zjq6 , orysa-q7x7y5 , orysa-Q7XC50 , orysa-q7xej4 , orysa-q7xem8 , orysa-q7xkj9 , orysa-q7xr62 , orysa-q7xr63 , orysa-q7xr64 , orysa-q7xsg1 , orysa-q7xsq2 , orysa-q7xts6 , orysa-q7xv53 , orysa-Q7XVB5 , orysa-Q8L562 , orysa-Q8LQS5 , orysa-Q8RZ40 , orysa-Q8RZ79 , orysa-Q8S0U8 , orysa-Q8S0V0 , orysa-Q8S125 , orysa-Q8SAY7 , orysa-Q8SAY9 , orysa-Q8W3C6 , orysa-Q8W3F2 , orysa-Q8W3F4 , orysa-Q8W3F6 , orysa-Q9LHX5 , orysa-q33aq0 , orysa-q53lh1 , orysa-q53m20 , orysa-q53nd8 , orysa-q60e79 , orysa-q60ew8 , orysa-q67iz2 , orysa-q67iz3 , orysa-q67iz7 , orysa-q67iz8 , orysa-q67j02 , orysa-q67j05 , orysa-q67j07 , orysa-q67j09 , orysa-q67j10 , orysa-q67tr6 , orysa-q67tv0 , orysa-q67uz1 , orysa-q67v34 , orysa-q67wz5 , orysa-q69j38 , orysa-q69k08 , orysa-q69md7 , orysa-q69me0 , orysa-q69pf3 , orysa-q69ti3 , orysa-q69xr2 , orysa-q69y12 , orysa-q69y21 , orysa-q75hy2 , orysa-q75i01 , orysa-Q94JD7 , orysa-Q0J0A4 , orysa-q651a8 , orysa-q651z3 , orysa-q652g4 , orysa-q688m0 , orysa-q688m8 , orysa-q688m9 , orysa-Q6H8G1 , orysi-a2wn01 , orysi-a2xc83 , orysi-a2yh83 , orysi-a2z179 , orysi-a2zef2 , orysi-b8a7e6 , orysi-b8a7e7 , orysi-b8bfe5 , orysi-b8bhp9 , orysj-a3b9l8 , orysj-b9eub8 , orysj-b9eya5 , orysj-b9fi05 , orysj-b9fkb0 , orysj-b9fn42 , orysj-b9gbb7 , orysj-cgep , orysj-PLA7 , orysj-q0d4u5 , orysj-q0djj0 , orysj-q0jaf0 , orysj-q5jl22 , orysj-q5jlw7 , orysj-q5z419 , orysj-q6h7q9 , orysj-q6yvk6 , orysj-q6z6i1 , orysj-q7f8x1 , orysj-q7xcx3 , orysj-q9fwm6 , orysj-q10j20 , orysj-q10ss2 , orysj-q69uw6 , orysj-q94d71 , orysj-q338c0 , orysi-b8bly4 , orysj-b9gbs4 , orysi-a2zb88 , orysj-b9gbs1 , orysi-b8b698 , orysj-pla4 , orysj-pla1

Title : Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae - Galagan_2005_Nature_438_1105
Author(s) : Galagan JE , Calvo SE , Cuomo C , Ma LJ , Wortman JR , Batzoglou S , Lee SI , Basturkmen M , Spevak CC , Clutterbuck J , Kapitonov V , Jurka J , Scazzocchio C , Farman M , Butler J , Purcell S , Harris S , Braus GH , Draht O , Busch S , d'Enfert C , Bouchier C , Goldman GH , Bell-Pedersen D , Griffiths-Jones S , Doonan JH , Yu J , Vienken K , Pain A , Freitag M , Selker EU , Archer DB , Penalva MA , Oakley BR , Momany M , Tanaka T , Kumagai T , Asai K , Machida M , Nierman WC , Denning DW , Caddick M , Hynes M , Paoletti M , Fischer R , Miller B , Dyer P , Sachs MS , Osmani SA , Birren BW
Ref : Nature , 438 :1105 , 2005
Abstract : The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.
ESTHER : Galagan_2005_Nature_438_1105
PubMedSearch : Galagan_2005_Nature_438_1105
PubMedID: 16372000
Gene_locus related to this paper: emeni-axe1 , emeni-BST1 , emeni-c8vrl3 , emeni-CUTI3 , emeni-faec , emeni-ppme1 , emeni-q5aqv0 , emeni-q5ara9 , emeni-q5av79 , emeni-q5avd3 , emeni-q5awc7 , emeni-q5awq3 , emeni-q5awu9 , emeni-q5aww7 , emeni-q5ax50 , emeni-q5ay37 , emeni-q5ay57 , emeni-q5ayk9 , emeni-q5az32 , emeni-q5azl2 , emeni-q5azp1 , emeni-q5b1v2 , emeni-q5b2c1 , emeni-q5b3d2 , emeni-q5b5j7 , emeni-q5b7i6 , emeni-q5b8p6 , emeni-q5b9e7 , emeni-q5b246 , emeni-q5b446 , emeni-q5b602 , emeni-q5b938 , emeni-q5ba78 , emeni-q5bad3 , emeni-q5bar0 , emeni-q5bcd1 , emeni-q5bcd2 , emeni-q5bcf8 , emeni-q5bdr0 , emeni-q5beh9 , emeni-q5bgk7 , emeni-q7si80 , emeni-q5bdv9 , emeni-c8vu15 , 9euro-a0a3d8t644 , emeni-q5b719 , emeni-q5ax97 , emeni-tdia , emeni-afoc , emeni-dbae

Title : Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery - Yang_2005_Nucleic.Acids.Res_33_6445
Author(s) : Yang F , Yang J , Zhang X , Chen L , Jiang Y , Yan Y , Tang X , Wang J , Xiong Z , Dong J , Xue Y , Zhu Y , Xu X , Sun L , Chen S , Nie H , Peng J , Xu J , Wang Y , Yuan Z , Wen Y , Yao Z , Shen Y , Qiang B , Hou Y , Yu J , Jin Q
Ref : Nucleic Acids Research , 33 :6445 , 2005
Abstract : The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.
ESTHER : Yang_2005_Nucleic.Acids.Res_33_6445
PubMedSearch : Yang_2005_Nucleic.Acids.Res_33_6445
PubMedID: 16275786
Gene_locus related to this paper: ecoli-yeiG , shidy-IROD , shidy-q67dv1 , shifl-AES , shifl-BIOH , shifl-entf , shifl-FES , shifl-PLDB , shifl-PTRB , shifl-S2753 , shifl-SF1334 , shifl-SF1808 , shifl-SF3046 , shifl-SF3908 , shifl-yafa , shifl-YBFF , shifl-YCDJ , shifl-ycfp , shifl-YCJY , shifl-YFBB , shifl-YHET , shifl-YJFP , shifl-YPFH , shiss-yaim , shiss-yeiG , shiss-yqia

Title : The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen - Chiu_2005_Nucleic.Acids.Res_33_1690
Author(s) : Chiu CH , Tang P , Chu C , Hu S , Bao Q , Yu J , Chou YY , Wang HS , Lee YS
Ref : Nucleic Acids Research , 33 :1690 , 2005
Abstract : Salmonella enterica serovar Choleraesuis (S. Choleraesuis), a highly invasive serovar among non-typhoidal Salmonella, usually causes sepsis or extra-intestinal focal infections in humans. S. Choleraesuis infections have now become particularly difficult to treat because of the emergence of resistance to multiple antimicrobial agents. The 4.7 Mb genome sequence of a multidrug-resistant S. Choleraesuis strain SC-B67 was determined. Genome wide comparison of three sequenced Salmonella genomes revealed that more deletion events occurred in S. Choleraesuis SC-B67 and S.Typhi CT18 relative to S. Typhimurium LT2. S. Choleraesuis has 151 pseudogenes, which, among the three Salmonella genomes, include the highest percentage of pseudogenes arising from the genes involved in bacterial chemotaxis signal-transduction pathways. Mutations in these genes may increase smooth swimming of the bacteria, potentially allowing more effective interactions with and invasion of host cells to occur. A key regulatory gene of TetR/AcrR family, acrR, was inactivated through the introduction of an internal stop codon resulting in overexpression of AcrAB that appears to be associated with ciprofloxacin resistance. While lateral gene transfer providing basic functions to allow niche expansion in the host and environment is maintained during the evolution of different serovars of Salmonella, genes providing little overall selective benefit may be lost rapidly. Our findings suggest that the formation of pseudogenes may provide a simple evolutionary pathway that complements gene acquisition to enhance virulence and antimicrobial resistance in S. Choleraesuis.
ESTHER : Chiu_2005_Nucleic.Acids.Res_33_1690
PubMedSearch : Chiu_2005_Nucleic.Acids.Res_33_1690
PubMedID: 15781495
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-a1yjl0 , salty-AES , salty-BIOH , salty-DLHH , salty-ENTF , salty-FES , salty-IROD , salty-P74847 , salty-PLDB , salty-STM0332 , salty-STM2547 , salty-STM4506 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YHET , salty-YQIA

Title : Clustered pathway genes in aflatoxin biosynthesis -
Author(s) : Yu J , Chang PK , Ehrlich KC , Cary JW , Bhatnagar D , Cleveland TE , Payne GA , Linz JE , Woloshuk CP , Bennett JW
Ref : Applied Environmental Microbiology , 70 :1253 , 2004
PubMedID: 15006741
Gene_locus related to this paper: aspor-PKSL1 , asppa-q6ueg5

Title : Completed sequence of aflatoxin pathway gene cluster in Aspergillus parasiticus - Yu_2004_FEBS.Lett_564_126
Author(s) : Yu J , Bhatnagar D , Cleveland TE
Ref : FEBS Letters , 564 :126 , 2004
Abstract : An 82-kb Aspergillus parasiticus genomic DNA region representing the completed sequence of the well-organized aflatoxin pathway gene cluster has been sequenced and annotated. In addition to the 19 reported and characterized aflatoxin pathway genes and the four sugar utilization genes in this cluster, we report here the identification of six newly identified genes which are putatively involved in aflatoxin formation. The function of these genes, the cluster organization and its significance in gene expression are discussed.
ESTHER : Yu_2004_FEBS.Lett_564_126
PubMedSearch : Yu_2004_FEBS.Lett_564_126
PubMedID: 15094053
Gene_locus related to this paper: aspor-PKSL1 , asppa-q6ueg5

Title : Pharmacogenomic assessment of carboxylesterases 1 and 2 - Marsh_2004_Genomics_84_661
Author(s) : Marsh S , Xiao M , Yu J , Ahluwalia R , Minton M , Freimuth RR , Kwok PY , McLeod HL
Ref : Genomics , 84 :661 , 2004
Abstract : Human carboxylesterases 1 and 2 (CES1 and CES2) catalyze the hydrolysis of many exogenous compounds. Alterations in carboxylesterase sequences could lead to variability in both the inactivation of drugs and the activation of prodrugs. We resequenced CES1 and CES2 in multiple populations (n = 120) to identify single-nucleotide polymorphisms and confirmed the novel SNPs in healthy European and African individuals (n = 190). Sixteen SNPs were found in CES1 (1 per 300 bp) and 11 in CES2 (1 per 630 bp) in at least one population. Allele frequencies and estimated haplotype frequencies varied significantly between African and European populations. No association between SNPs in CES1 or CES2 was found with respect to RNA expression in normal colonic mucosa; however, an intronic SNP (IVS10-88) in CES2 was associated with reduced CES2 mRNA expression in colorectal tumors. Functional analysis of the novel polymorphisms described in this study is now warranted to identify putative roles in drug metabolism.
ESTHER : Marsh_2004_Genomics_84_661
PubMedSearch : Marsh_2004_Genomics_84_661
PubMedID: 15475243
Gene_locus related to this paper: human-CES1 , human-CES2

Title : The Aspergillus parasiticus estA-encoded esterase converts versiconal hemiacetal acetate to versiconal and versiconol acetate to versiconol in aflatoxin biosynthesis - Chang_2004_Appl.Environ.Microbiol_70_3593
Author(s) : Chang PK , Yabe K , Yu J
Ref : Applied Environmental Microbiology , 70 :3593 , 2004
Abstract : In aflatoxin biosynthesis, the pathway for the conversion of 1-hydroxyversicolorone to versiconal hemiacetal acetate (VHA) to versiconal (VHOH) is part of a metabolic grid. In the grid, the steps from VHA to VHOH and from versiconol acetate (VOAc) to versiconol (VOH) may be catalyzed by the same esterase. Several esterase activities are associated with the conversion of VHA to VHOH, but only one esterase gene (estA) is present in the complete aflatoxin gene cluster of Aspergillus parasiticus. We deleted the estA gene from A. parasiticus SRRC 2043, an O-methylsterigmatocystin (OMST)-accumulating strain. The estA-deleted mutants were pigmented and accumulated mainly VHA and versicolorin A (VA). A small amount of VOAc and other downstream aflatoxin intermediates, including VHOH, versicolorin B, and OMST, also were accumulated. In contrast, a VA-accumulating mutant, NIAH-9, accumulated VA exclusively and neither VHA nor VOAc were produced. Addition of the esterase inhibitor dichlorvos (dimethyl 2,2-dichlorovinylphosphate) to the transformation recipient strain RHN1, an estA-deleted mutant, or NIAH-9 resulted in the accumulation of only VHA and VOAc. In in vitro enzyme assays, the levels of the esterase activities catalyzing the conversion of VHA to VHOH in the cell extracts of two estA-deleted mutants were decreased to approximately 10% of that seen with RHN1. Similar decreases in the esterase activities catalyzing the conversion of VOAc to VOH were also obtained. Thus, the estA-encoded esterase catalyzes the conversion of both VHA to VHOH and VOAc to VOH during aflatoxin biosynthesis.
ESTHER : Chang_2004_Appl.Environ.Microbiol_70_3593
PubMedSearch : Chang_2004_Appl.Environ.Microbiol_70_3593
PubMedID: 15184162
Gene_locus related to this paper: asppa-q6ueg5

Title : Development of cholinergic projections to cortex. -
Author(s) : Robertson RT , Yu J
Ref : Cholinergic Mechanisms, CRC Press :381 , 2004

Title : Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution - Hillier_2004_Nature_432_695
Author(s) : Hillier LW , Miller W , Birney E , Warren W , Hardison RC , Ponting CP , Bork P , Burt DW , Groenen MA , Delany ME , Dodgson JB , Chinwalla AT , Cliften PF , Clifton SW , Delehaunty KD , Fronick C , Fulton RS , Graves TA , Kremitzki C , Layman D , Magrini V , McPherson JD , Miner TL , Minx P , Nash WE , Nhan MN , Nelson JO , Oddy LG , Pohl CS , Randall-Maher J , Smith SM , Wallis JW , Yang SP , Romanov MN , Rondelli CM , Paton B , Smith J , Morrice D , Daniels L , Tempest HG , Robertson L , Masabanda JS , Griffin DK , Vignal A , Fillon V , Jacobbson L , Kerje S , Andersson L , Crooijmans RP , Aerts J , van der Poel JJ , Ellegren H , Caldwell RB , Hubbard SJ , Grafham DV , Kierzek AM , McLaren SR , Overton IM , Arakawa H , Beattie KJ , Bezzubov Y , Boardman PE , Bonfield JK , Croning MD , Davies RM , Francis MD , Humphray SJ , Scott CE , Taylor RG , Tickle C , Brown WR , Rogers J , Buerstedde JM , Wilson SA , Stubbs L , Ovcharenko I , Gordon L , Lucas S , Miller MM , Inoko H , Shiina T , Kaufman J , Salomonsen J , Skjoedt K , Ka-Shu Wong G , Wang J , Liu B , Yu J , Yang H , Nefedov M , Koriabine M , deJong PJ , Goodstadt L , Webber C , Dickens NJ , Letunic I , Suyama M , Torrents D , von Mering C , Zdobnov EM , Makova K , Nekrutenko A , Elnitski L , Eswara P , King DC , Yang S , Tyekucheva S , Radakrishnan A , Harris RS , Chiaromonte F , Taylor J , He J , Rijnkels M , Griffiths-Jones S , Ureta-Vidal A , Hoffman MM , Severin J , Searle SM , Law AS , Speed D , Waddington D , Cheng Z , Tuzun E , Eichler E , Bao Z , Flicek P , Shteynberg DD , Brent MR , Bye JM , Huckle EJ , Chatterji S , Dewey C , Pachter L , Kouranov A , Mourelatos Z , Hatzigeorgiou AG , Paterson AH , Ivarie R , Brandstrom M , Axelsson E , Backstrom N , Berlin S , Webster MT , Pourquie O , Reymond A , Ucla C , Antonarakis SE , Long M , Emerson JJ , Betran E , Dupanloup I , Kaessmann H , Hinrichs AS , Bejerano G , Furey TS , Harte RA , Raney B , Siepel A , Kent WJ , Haussler D , Eyras E , Castelo R , Abril JF , Castellano S , Camara F , Parra G , Guigo R , Bourque G , Tesler G , Pevzner PA , Smit A , Fulton LA , Mardis ER , Wilson RK
Ref : Nature , 432 :695 , 2004
Abstract : We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
ESTHER : Hillier_2004_Nature_432_695
PubMedSearch : Hillier_2004_Nature_432_695
PubMedID: 15592404
Gene_locus related to this paper: chick-a0a1d5pmd9 , chick-b3tzb3 , chick-BCHE , chick-cb043 , chick-d3wgl5 , chick-e1bsm0 , chick-e1bvq6 , chick-e1bwz0 , chick-e1bwz1 , chick-e1byn1 , chick-e1bz81 , chick-e1c0z8 , chick-e1c7p7 , chick-f1nby4 , chick-f1ncz8 , chick-f1ndp3 , chick-f1nep4 , chick-f1nj68 , chick-f1njg6 , chick-f1njk4 , chick-f1njs4 , chick-f1njs5 , chick-f1nk87 , chick-f1nmx9 , chick-f1ntp8 , chick-f1nvg7 , chick-f1nwf2 , chick-f1p1l1 , chick-f1p3j5 , chick-f1p4c6 , chick-f1p508 , chick-fas , chick-h9l0k6 , chick-nlgn1 , chick-NLGN3 , chick-q5f3h8 , chick-q5zhm0 , chick-q5zi81 , chick-q5zij5 , chick-q5zin0 , chick-thyro , chick-f1nrq2 , chick-e1byd4 , chick-e1c2h6 , chick-a0a1d5pk92 , chick-a0a1d5pzg7 , chick-f1nbc2 , chick-f1nf25 , chick-f1nly5 , chick-f1p4h5 , chick-f1nzi7 , chick-f1p5k3 , chick-f1nm35 , chick-a0a1d5pl11 , chick-a0a1d5pj73 , chick-f1nxu6 , chick-a0a1d5nwc0 , chick-e1bxs8 , chick-f1p2g7 , chick-f1nd96

Title : Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans - Song_2004_DNA.Res_11_179
Author(s) : Song Y , Tong Z , Wang J , Wang L , Guo Z , Han Y , Zhang J , Pei D , Zhou D , Qin H , Pang X , Zhai J , Li M , Cui B , Qi Z , Jin L , Dai R , Chen F , Li S , Ye C , Du Z , Lin W , Yu J , Yang H , Huang P , Yang R
Ref : DNA Research , 11 :179 , 2004
Abstract : Genomics provides an unprecedented opportunity to probe in minute detail into the genomes of the world's most deadly pathogenic bacteria- Yersinia pestis. Here we report the complete genome sequence of Y. pestis strain 91001, a human-avirulent strain isolated from the rodent Brandt's vole-Microtus brandti. The genome of strain 91001 consists of one chromosome and four plasmids (pPCP1, pCD1, pMT1 and pCRY). The 9609-bp pPCP1 plasmid of strain 91001 is almost identical to the counterparts from reference strains (CO92 and KIM). There are 98 genes in the 70,159-bp range of plasmid pCD1. The 106,642-bp plasmid pMT1 has slightly different architecture compared with the reference ones. pCRY is a novel plasmid discovered in this work. It is 21,742 bp long and harbors a cryptic type IV secretory system. The chromosome of 91001 is 4,595,065 bp in length. Among the 4037 predicted genes, 141 are possible pseudo-genes. Due to the rearrangements mediated by insertion elements, the structure of the 91001 chromosome shows dramatic differences compared with CO92 and KIM. Based on the analysis of plasmids and chromosome architectures, pseudogene distribution, nitrate reduction negative mechanism and gene comparison, we conclude that strain 91001 and other strains isolated from M. brandti might have evolved from ancestral Y. pestis in a different lineage. The large genome fragment deletions in the 91001 chromosome and some pseudogenes may contribute to its unique nonpathogenicity to humans and host-specificity.
ESTHER : Song_2004_DNA.Res_11_179
PubMedSearch : Song_2004_DNA.Res_11_179
PubMedID: 15368893
Gene_locus related to this paper: yerpe-BIOH , yerpe-IRP1 , yerpe-PIP , yerpe-PLDB , yerpe-PTRB , yerpe-q8zey9 , yerpe-Y0644 , yerpe-y1616 , yerpe-y3224 , yerpe-YPLA , yerpe-YPO0180 , yerpe-YPO0667 , yerpe-YPO0773 , yerpe-YPO0776 , yerpe-YPO0986 , yerpe-YPO1501 , yerpe-YPO1997 , yerpe-YPO2002 , yerpe-YPO2336 , yerpe-YPO2526 , yerpe-YPO2638 , yerpe-YPO2814

Title : Large-scale cDNA transfection screening for genes related to cancer development and progression - Wan_2004_Proc.Natl.Acad.Sci.U.S.A_101_15724
Author(s) : Wan D , Gong Y , Qin W , Zhang P , Li J , Wei L , Zhou X , Li H , Qiu X , Zhong F , He L , Yu J , Yao G , Jiang H , Qian L , Yu Y , Shu H , Chen X , Xu H , Guo M , Pan Z , Chen Y , Ge C , Yang S , Gu J
Ref : Proc Natl Acad Sci U S A , 101 :15724 , 2004
Abstract : A large-scale assay was performed by transfecting 29,910 individual cDNA clones derived from human placenta, fetus, and normal liver tissues into human hepatoma cells and 22,926 cDNA clones into mouse NIH 3T3 cells. Based on the results of colony formation in hepatoma cells and foci formation in NIH 3T3 cells, 3,806 cDNA species (8,237 clones) were found to possess the ability of either stimulating or inhibiting cell growth. Among them, 2,836 (6,958 clones) were known genes, 372 (384 clones) were previously unrecognized genes, and 598 (895 clones) were unigenes of uncharacterized structure and function. A comprehensive analysis of the genes and the potential mechanisms for their involvement in the regulation of cell growth is provided. The genes were classified into four categories: I, genes related to the basic cellular mechanism for growth and survival; II, genes related to the cellular microenvironment; III, genes related to host-cell systemic regulation; and IV, genes of miscellaneous function. The extensive growth-regulatory activity of genes with such highly diversified functions suggests that cancer may be related to multiple levels of cellular and systemic controls. The present assay provides a direct genomewide functional screening method. It offers a better understanding of the basic machinery of oncogenesis, including previously undescribed systemic regulatory mechanisms, and also provides a tool for gene discovery with potential clinical applications.
ESTHER : Wan_2004_Proc.Natl.Acad.Sci.U.S.A_101_15724
PubMedSearch : Wan_2004_Proc.Natl.Acad.Sci.U.S.A_101_15724
PubMedID: 15498874

Title : Poster (98) Development of acetylcholinesterase-positive cholinergic projections to hippocampus and cingulate cortex: role of neurotrophins -
Author(s) : Robertson RT , Yu J
Ref : In: Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects , (Inestrosa NC, Campos EO) P. Universidad Catolica de Chile-FONDAP Biomedicina :372 , 2004

Title : Aflatoxin biosynthesis cluster gene cypA is required for G aflatoxin formation - Ehrlich_2004_Appl.Environ.Microbiol_70_6518
Author(s) : Ehrlich KC , Chang PK , Yu J , Cotty PJ
Ref : Applied Environmental Microbiology , 70 :6518 , 2004
Abstract : Aspergillus flavus isolates produce only aflatoxins B1 and B2, while Aspergillus parasiticus and Aspergillus nomius produce aflatoxins B1, B2, G1, and G2. Sequence comparison of the aflatoxin biosynthesis pathway gene cluster upstream from the polyketide synthase gene, pksA, revealed that A. flavus isolates are missing portions of genes (cypA and norB) predicted to encode, respectively, a cytochrome P450 monooxygenase and an aryl alcohol dehydrogenase. Insertional disruption of cypA in A. parasiticus yielded transformants that lack the ability to produce G aflatoxins but not B aflatoxins. The enzyme encoded by cypA has highest amino acid identity to Gibberella zeae Tri4 (38%), a P450 monooxygenase previously shown to be involved in trichodiene epoxidation. The substrate for CypA may be an intermediate formed by oxidative cleavage of the A ring of O-methylsterigmatocystin by OrdA, the P450 monooxygenase required for formation of aflatoxins B1 and B2.
ESTHER : Ehrlich_2004_Appl.Environ.Microbiol_70_6518
PubMedSearch : Ehrlich_2004_Appl.Environ.Microbiol_70_6518
PubMedID: 15528514
Gene_locus related to this paper: aspfl-q5vdc0 , aspno-q5vd72 , aspno-q5vd79 , aspor-PKSL1 , aspor-q2ufz8

Title : Substrate-induced lipase gene expression and aflatoxin production in Aspergillus parasiticus and Aspergillus flavus - Yu_2003_J.Appl.Microbiol_95_1334
Author(s) : Yu J , Mohawed SM , Bhatnagar D , Cleveland TE
Ref : J Appl Microbiol , 95 :1334 , 2003
Abstract : AIMS: To establish a relationship between lipase gene expression and aflatoxin production by cloning the lipA gene and studying its expression pattern in several aflatoxigenic and nontoxigenic isolates of Aspergillus flavus and A. parasiticus. METHODS AND
RESULTS: We have cloned a gene, lipA, that encodes a lipase involved in the breakdown of lipids from aflatoxin-producing A. flavus, A. parasiticus and two nonaflatoxigenic A. flavus isolates, wool-1 and wool-2. The lipA gene was transcribed under diverse media conditions, however, no mature mRNA was detected unless the growth medium was supplemented with 0.5% soya bean or peanut oil or the fungus was grown in lipid-rich medium such as coconut medium. The expression of the lipase gene (mature mRNA) under substrate-induced conditions correlated well with aflatoxin production in aflatoxigenic species A. flavus (SRRC 1007) and A. parasiticus (SRRC 143).
CONCLUSIONS: Substrate-induced lipase gene expression might be indirectly related to aflatoxin formation by providing the basic building block 'acetate' for aflatoxin synthesis. No direct relationship between lipid metabolism and aflatoxin production can be ascertained, however, lipase gene expression correlates well with aflatoxin formation. SIGNIFICANCE AND IMPACT OF THE STUDY: Lipid substrate induces and promotes aflatoxin formation. It gives insight into genetic and biochemical aspects of aflatoxin formation.
ESTHER : Yu_2003_J.Appl.Microbiol_95_1334
PubMedSearch : Yu_2003_J.Appl.Microbiol_95_1334
PubMedID: 14633008
Gene_locus related to this paper: aspor-MDLB

Title : Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157 - Jin_2002_Nucleic.Acids.Res_30_4432
Author(s) : Jin Q , Yuan Z , Xu J , Wang Y , Shen Y , Lu W , Wang J , Liu H , Yang J , Yang F , Zhang X , Zhang J , Yang G , Wu H , Qu D , Dong J , Sun L , Xue Y , Zhao A , Gao Y , Zhu J , Kan B , Ding K , Chen S , Cheng H , Yao Z , He B , Chen R , Ma D , Qiang B , Wen Y , Hou Y , Yu J
Ref : Nucleic Acids Research , 30 :4432 , 2002
Abstract : We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a 4 607 203 bp chromosome and a 221 618 bp virulence plasmid, designated pCP301. While the plasmid shows minor divergence from that sequenced in serotype 5a, striking characteristics of the chromosome have been revealed. The S.flexneri chromosome has, astonishingly, 314 IS elements, more than 7-fold over those possessed by its close relatives, the non-pathogenic K12 strain and enterohemorrhagic O157:H7 strain of Escherichia coli. There are 13 translocations and inversions compared with the E.coli sequences, all involve a segment larger than 5 kb, and most are associated with deletions or acquired DNA sequences, of which several are likely to be bacteriophage-transmitted pathogenicity islands. Furthermore, S.flexneri, resembling another human-restricted enteric pathogen, Salmonella typhi, also has hundreds of pseudogenes compared with the E.coli strains. All of these could be subjected to investigations towards novel preventative and treatment strategies against shigellosis.
ESTHER : Jin_2002_Nucleic.Acids.Res_30_4432
PubMedSearch : Jin_2002_Nucleic.Acids.Res_30_4432
PubMedID: 12384590
Gene_locus related to this paper: ecoli-Aes , ecoli-yafa , ecoli-ycfp , ecoli-yqia , ecoli-YfhR , shifl-AES , shifl-BIOH , shifl-entf , shifl-FES , shifl-PLDB , shifl-PTRB , shifl-SF1334 , shifl-SF1808 , shifl-SF3046 , shifl-SF3908 , shifl-yafa , shifl-YBFF , shifl-YCDJ , shifl-YCJY , shifl-YFBB , shifl-YHET , shifl-YIEL , shifl-YJFP , shifl-YPFH

Title : Characterization of a partial duplication of the aflatoxin gene cluster in Aspergillus parasiticus ATCC 56775 - Chang_2002_Appl.Microbiol.Biotechnol_58_632
Author(s) : Chang PK , Yu J
Ref : Applied Microbiology & Biotechnology , 58 :632 , 2002
Abstract : A partial duplication of the complete aflatoxin gene cluster containing homologues of aflR-aflJ-adhA-estA-norA-ver1and omtB was identified from Aspergillus parasiticus ATCC 56775. The genes, verA-avnA-verB-avfA, between ver1 and omtB in the complete gene cluster, however, were not found. One-hybrid assays showed that the duplicated aflRgene ( aflR2) encoded a protein that could activate transcription just as that encoded by aflR1,the aflR gene in the complete gene cluster. Two-hybrid assays showed that AFLR2 also interacted with a putative coactivator, AFLJ1, at comparable levels to AFLR1. Deletion of aflR1 resulted in the loss of production of aflatoxin precursors, which suggested that aflR2could not completely replace the function of aflR1. Point mutations found in adhA2, pre-termination in ver1B and norA2,and a large deletion in omtB2 probably render these duplicated genes to become nonfunctional. A close examination of the history of isolates reported to have a partial duplication suggested that duplication of the aflatoxin cluster is not a prevalent event.
ESTHER : Chang_2002_Appl.Microbiol.Biotechnol_58_632
PubMedSearch : Chang_2002_Appl.Microbiol.Biotechnol_58_632
PubMedID: 11956746
Gene_locus related to this paper: asppa-ESTA1.2

Title : Cloning and functional expression of an esterase gene in Aspergillus parasitcus - Yu_2002_Mycopathologia_156_227
Author(s) : Yu J , Chang PK , Bhatnagar D , Cleveland TE
Ref : Mycopathologia , 156 :227 , 2002
Abstract : Within the 80 kb aflatoxin pathway gene cluster characterized earlier, and between adhA and norA genes, we have identified an estA gene encoding an esterase from wild type strain Aspergillus parasiticus SRRC 143. The 1,500 bp genomic DNA and 945 bp cDNA sequences were determined for estA. Outside of the aflatoxin pathway gene cluster, an additional copy of the estA gene (named estA2) was also cloned from the same A. parasiticus strain. Comparison of the estA and estA2 sequences showed 9 substitutions within the 314 amino acid residues of their gene products, and no apparent defect was identified in the estA2. The estA gene is a homolog of the stcI gene identified in A. nidulans involved in the biosynthesis of sterigmatocystin and dihydro-sterigmatocystin for the conversion of versiconal hemiacetal acetate to versiconal. Reverse-transcriptase polymerase chain reaction (RT-PCR) experiments demonstrated that the estA is constitutively expressed. And only this estA gene, which is located within the aflatoxin pathway gene cluster, is expressed; no expression of the estA2 gene was detected under both aflatoxin conducive and non-conducive conditions. Possible reasons for the preferential expression of the estA over the estA2 gene have been discussed.
ESTHER : Yu_2002_Mycopathologia_156_227
PubMedSearch : Yu_2002_Mycopathologia_156_227
PubMedID: 12749588
Gene_locus related to this paper: asppa-q6ueg5

Title : Basal forebrain cholinergic cell attachment and neurite outgrowth on organotypic slice cultures of hippocampal formation - Tsai_2002_Neurosci_115_815
Author(s) : Tsai ES , Haraldson SJ , Baratta J , Lander AD , Yu J , Robertson RT
Ref : Neuroscience , 115 :815 , 2002
Abstract : Distributions of somata and neurites of cholinergic neurons were studied after seeding dissociated cells onto organotypic slice cultures. Slice cultures were made from hippocampal formation and adjacent cortical regions from rats or mice. Dissociated cell suspensions of basal forebrain tissue from rat or mouse fetuses were seeded onto the slice cultures. Combined cultures were maintained for 1-21 days in vitro. Cultures processed for acetylcholinesterase (AChE) histochemistry demonstrated non-random patterns of cholinergic cells and their neurites. Labeled cells appeared most frequently in the molecular layer of the dentate gyrus, and in the deeper layers of cortical regions adjacent to the hippocampus. Neurites extending from these labeled cells appeared to target the dentate molecular layer and the cortical subplate layer. By 4 days in vitro, AChE-positive basal forebrain cells display several short and thick neurites that appear to be dendrites, and one long process that appears to be an axon. By 5 days in vitro, dendrites are well developed; by 7 days the presumed axon has extended widely over the cortical target zone. These neurites are maintained through 3 weeks in culture. Distributions of cells varied with the age of the slice. AChE-labeled cells were not seen overlying hippocampal tissue when dissociated cells were seeded on slice cultures made from day 0 rats, but a few labeled cells were seen when seeded on slices from day 2 rats. Clear non-random patterns of labeled cells and neurite outgrowth were seen on slice cultures from day 5 or older pups. The non-random distribution seen with AChE-positive neurons was not seen using other techniques that labeled all cells (non-selective fluorescent labels) or all neurons; these techniques resulted in labeled cells scattered apparently homogenously across the slice culture.These studies demonstrate a non-random pattern of attachment or differentiation of basal forebrain cholinergic neurons when these cells are seeded onto cultured cortical slices; this pattern mimics the normal patterns of basal forebrain cholinergic projections to these cortical regions. These data suggest that the factors that normally guide basal forebrain-derived cholinergic axons to their target cells in vivo are present and detectable in this model system.
ESTHER : Tsai_2002_Neurosci_115_815
PubMedSearch : Tsai_2002_Neurosci_115_815
PubMedID: 12435420

Title : A complete sequence of the T. tengcongensis genome - Bao_2002_Genome.Res_12_689
Author(s) : Bao Q , Tian Y , Li W , Xu Z , Xuan Z , Hu S , Dong W , Yang J , Chen Y , Xue Y , Xu Y , Lai X , Huang L , Dong X , Ma Y , Ling L , Tan H , Chen R , Wang J , Yu J , Yang H
Ref : Genome Res , 12 :689 , 2002
Abstract : Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we sequenced its 2,689,445-bp genome from an isolate, MB4(T) (Genbank accession no. AE008691). The genome encodes 2588 predicted coding sequences (CDS). Among them, 1764 (68.2%) are classified according to homology to other documented proteins, and the rest, 824 CDS (31.8%), are functionally unknown. One of the interesting features of the T. tengcongensis genome is that 86.7% of its genes are encoded on the leading strand of DNA replication. Based on protein sequence similarity, the T. tengcongensis genome is most similar to that of Bacillus halodurans, a mesophilic eubacterium, among all fully sequenced prokaryotic genomes up to date. Computational analysis on genes involved in basic metabolic pathways supports the experimental discovery that T. tengcongensis metabolizes sugars as principal energy and carbon source and utilizes thiosulfate and element sulfur, but not sulfate, as electron acceptors. T. tengcongensis, as a gram-negative rod by empirical definitions (such as staining), shares many genes that are characteristics of gram-positive bacteria whereas it is missing molecular components unique to gram-negative bacteria. A strong correlation between the G + C content of tDNA and rDNA genes and the optimal growth temperature is found among the sequenced thermophiles. It is concluded that thermophiles are a biologically and phylogenetically divergent group of prokaryotes that have converged to sustain extreme environmental conditions over evolutionary timescale.
ESTHER : Bao_2002_Genome.Res_12_689
PubMedSearch : Bao_2002_Genome.Res_12_689
PubMedID: 11997336
Gene_locus related to this paper: thete-DAP2 , thete-LIPA , thete-LIPA3 , thete-MHPC , thete-MHPC2 , thete-MHPC3 , thete-MHPC4 , thete-PLDB , thete-TTE1809 , thetn-DAP2.2

Title : Arrival of afferents and the differentiation of target neurons: studies of developing cholinergic projections to the dentate gyrus - Makuch_2001_Neurosci_104_81
Author(s) : Makuch R , Baratta J , Karaelias LD , Lauterborn JC , Gall CM , Yu J , Robertson RT
Ref : Neuroscience , 104 :81 , 2001
Abstract : This study examined the relationship between the development of cholinergic axons originating from the septum and a group of their target cells, the granule cells of the dentate gyrus of the rat. Acetylcholinesterase histochemistry was used to identify septal cholinergic afferents to the dentate gyrus; parallel studies used anterograde movement of a carbocyanine dye to label the septal projections. Septal cholinergic axons are present in the molecular layer of the internal blade of the dentate gyrus shortly after birth, but these axons do not reach the external blade until several days later. Results demonstrate that acetylcholinesterase positive septal axons grow into the external blade of the dentate gyrus only after the recently generated granule cells have coalesced to form a clearly defined layer. Results from studies using in situ hybridization techniques demonstrate that dentate gyrus granule cells express messenger RNAs for brain derived neurotrophic factor and for neurotrophic factor 3 shortly after formation of the granule cell layer. Ingrowth of septal cholinergic axons follows two days after the formation of the external blade of the dentate gyrus and the expression of neurotrophin messenger RNAs by the dentate granule cells. These data support the hypothesis that target cell development is a prerequisite for attracting the ingrowth of septal afferent axons.
ESTHER : Makuch_2001_Neurosci_104_81
PubMedSearch : Makuch_2001_Neurosci_104_81
PubMedID: 11311533

Title : Cloning and characterization of avfA and omtB genes involved in aflatoxin biosynthesis in three Aspergillus species - Yu_2000_Gene_248_157
Author(s) : Yu J , Woloshuk CP , Bhatnagar D , Cleveland TE
Ref : Gene , 248 :157 , 2000
Abstract : The biosynthesis of aflatoxins (B(1), G(1), B(2), and G(2)) is a multi-enzyme process controlled genetically by over 20 genes. In this study, we report the identification and characterization of the avfA gene, which was found to be involved in the conversion of averufin (AVF) to versiconal hemiacetal acetate (VHA), in Aspergillus parasiticus and A. flavus; a copy of avfA gene was also cloned from a non-aflatoxin producing strain A. sojae. Complementation of an averufin-accumulating, non-aflatoxigenic mutant strain of A. parasiticus, SRRC 165, with the avfA gene cloned from A. flavus, restored the ability of the mutant to convert AVF to VHA and to produce aflatoxins B(1), G(1), B(2), and G(2). Sequence analysis revealed that a single amino acid replacement from aspartic acid to asparagine disabled the function of the enzyme in the mutant strain SRRC 165. The A. parasiticus avfA was identified to be a homolog of previously sequenced, but functionally unassigned transcript, stcO, in A. nidulans based on sequence homology at both nucleotide (57%) and amino acid (55%) levels. In addition to avfA, another aflatoxin pathway gene, omtB, encoding for an O-methyltransferase involved in the conversion of demethylsterigmatocystin (DMST) to sterigmatocystin (ST) and dihydrodemethylsterigmatocystin (DHDMST) to dihydrosterigmatocystin (DHST), was cloned from A. parasiticus, A. flavus, and A. sojae. The omtB gene was found to be highly homologous to stcP from A. nidulans, which has been reported earlier to be involved in a similar enzymatic step for the sterigmatocystin formation in that species. RT-PCR data demonstrated that both the avfA and avfA1 as well as omtB genes in A. parasiticus were expressed only in the aflatoxin-conducive medium. An analysis of the degrees of homology for the two reported genes between the Aspergillus species A. parasiticus, A. flavus, A. nidulans and A. sojae was conducted.
ESTHER : Yu_2000_Gene_248_157
PubMedSearch : Yu_2000_Gene_248_157
PubMedID: 10806361
Gene_locus related to this paper: aspnc-a5abe5 , aspnc-a5abe8 , aspnc-a5abh9 , aspnc-a5abk1

Title : Repeated immunolesions display diminished stress response signal - Gu_2000_Int.J.Dev.Neurosci_18_177
Author(s) : Gu Z , Yu J , Werrbach-Perez K , Perez-Polo JR
Ref : Int J Developmental Neuroscience , 18 :177 , 2000
Abstract : Cholinergic basal forebrain neurons (CBFNs) retrogradely transport neurotrophins released in the hippocampus and cortex as part of a general response to injury in a process that is impaired in the aged rodent and can be spared by the exogenous addition of pharmacological doses of nerve growth factor (NGF). This observation suggests that components of stress response signal transduction pathways in the aged CNS can be exogenously activated. The extent and mechanism of the endogenous stimulation of NGF in response to injury can be mimicked via treatment with 192 IgG-saporin of rat CNS, an immunolesion model. Here we report on the use of a conditioning lesion paradigm to determine if repeated partial immunolesions have a conditioning effect on the immunolesion-induced increases in NGF protein or decreases in choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) activity. We report that chronic repeated immunolesions, as used here, were not as effective as a one time equivalent immunolesion in terms of induced NGF protein increases or decreasing ChAT and AChE activity in the hippocampus and cortex. Thus, chronic lesions resulting in cholinergic impairment typical of the aged CNS may differ from acute toxic models as a result of desensitization due to a conditioning effect of chronic subthreshold lesioning events in the CNS.
ESTHER : Gu_2000_Int.J.Dev.Neurosci_18_177
PubMedSearch : Gu_2000_Int.J.Dev.Neurosci_18_177
PubMedID: 10715572

Title : Do subplate neurons comprise a transient population of cells in developing neocortex of rats? - Robertson_2000_J.Comp.Neurol_426_632
Author(s) : Robertson RT , Annis CM , Baratta J , Haraldson S , Ingeman J , Kageyama GH , Kimm E , Yu J
Ref : Journal of Comparative Neurology , 426 :632 , 2000
Abstract : Studies were undertaken to determine whether neurons of the subplate layer represent a transient or stable population of cells in developing neocortex of rat. The first set of studies sought to determine the fraction of subplate neurons that is lost during early postnatal development. The optical dissector method was used to analyze fluorescently stained material in animals the age of postnatal day 0 (P0) to P40. These results demonstrate a reduction of slightly less than half of the total number of subplate neurons from P0 to P40. Counts of labeled cells in littermates at varied ages after [(3)H]thymidine or BRDU treatment on gestational day 14 (G14 - birthdate of occipital subplate neurons) or G18 (birthdate of layers III-IV neurons) demonstrate loss of approximately 50% of neurons in the subplate layer between P0 and P40, somewhat greater than the loss of neurons from cortical layers III-IV. The second set of studies investigated whether subplate neurons display cellular atrophy during postnatal development. Analysis of subplate neurons injected intracellularly with Lucifer yellow in fixed slice preparations indicates no reduction in soma size, number of dendrites, or extent of dendritic fields of subplate neurons taken from animals age P0 to P60. The third set of studies investigated whether functional markers of subplate neurons are reduced during postnatal development. Analysis of tissue stained histochemically for cytochrome oxidase or acetylcholinesterase, or stained immunocytochemically for GABA, somatostatin, or neuropeptide Y, demonstrate a remarkable loss of expression of staining patterns from late gestational ages to P20. These data demonstrate that, although subplate neurons seem not to be a transient population of cells in the usual sense of being eliminated by cell death or structural atrophy, the loss of histochemical and immunocytochemical markers indicates that they may be a functionally transient population of cells.
ESTHER : Robertson_2000_J.Comp.Neurol_426_632
PubMedSearch : Robertson_2000_J.Comp.Neurol_426_632
PubMedID: 11027404

Title : Possible Adhesive Function of Transiently Expressed Acetylcholinesterase in Developing Cerebral Cortex -
Author(s) : Robertson RT , Claytor KJ , Yu J
Ref : In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases , (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp. :563 , 1998

Title : Long term changes in brain cholinergic markers and nerve growth factor levels after partial immunolesion - Gu_1998_Brain.Res_801_190
Author(s) : Gu Z , Yu J , Perez-Polo JR
Ref : Brain Research , 801 :190 , 1998
Abstract : There are deficits in cholinergic basal forebrain neurons (CBFNs) in the aged brain and patients suffering Alzheimer's disease associated with a partial loss of the CBFNs. To mimic this partial loss and assess its long term effects on residual cholinergic activity and resultant target-derived nerve growth factor (NGF) levels, we produced a partial immunolesion to CBFNs with 192 IgG-saporin, an immunotoxin selectively taken up by p75NTR-bearing neurons. We measured two cholinergic markers, choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) activity, and NGF protein levels at 10 days, 1, 6 and 12 months postlesion. There were no significant changes in the cholinergic markers and the NGF protein levels in the sham-treated animal controls during the one year experiment. Ten days after 192 IgG-saporin treatment, ChAT activity decreased to 35-50% of controls in the olfactory bulb, hippocampus, and cortex. There was a minor but significant recovery of ChAT activity one year after the immunolesion in the hippocampus. Changes in AChE activity mirrored the ChAT changes but were less robust. There were transient increases in NGF protein levels in the hippocampus and cortex that returned to basal levels at 6 months and 12 months postlesion, respectively. In summary, partial immunolesions resulted in partial region-specific and time-dependent recoveries of cholinergic activity in the target areas of the basal forebrain after a partial elimination of CBFNs and a return to basal levels of NGF protein consistent with the hypothesis that the remaining CBFNs compensated for losses of ChAT and NGF due to changes in cholinergic innervation of basal forebrain target areas.
ESTHER : Gu_1998_Brain.Res_801_190
PubMedSearch : Gu_1998_Brain.Res_801_190
PubMedID: 9729378

Title : Neonatal treatment with 192 IgG-saporin produces long-term forebrain cholinergic deficits and reduces dendritic branching and spine density of neocortical pyramidal neurons - Robertson_1998_Cereb.Cortex_8_142
Author(s) : Robertson RT , Gallardo KA , Claytor KJ , Ha DH , Ku KH , Yu BP , Lauterborn JC , Wiley RG , Yu J , Gall CM , Leslie FM
Ref : Cerebral Cortex , 8 :142 , 1998
Abstract : The role of basal forebrain-derived cholinergic afferents in the development of neocortex was studied in postnatal rats. Newborn rat pups received intraventricular injections of 192 IgG-saporin. Following survival periods ranging from 2 days to 6 months, the brains were processed to document the cholinergic lesion and to examine morphological consequences. Immunocytochemistry for choline acetyltransferase (ChAT) and in situ hybridization for ChAT mRNA demonstrate a loss of approximately 75% of the cholinergic neurons in the medial septum and nucleus of the diagonal band of Broca in the basal forebrain. In situ hybridization for glutamic acid decarboxylase mRNA reveals no loss of basal forebrain GABAergic neurons. Acetylcholinesterase histochemistry demonstrates a marked reduction of the cholinergic axons in neocortex. Cholinergic axons are reduced throughout the cortical layers; this reduction is more marked in medial than in lateral cortical areas. The thickness of neocortex is reduced by approximately 10%. Retrograde labeling of layer V cortico-collicular pyramidal cells reveals a reduction in cell body size and also a reduction in numbers of branches of apical dendrites. Spine densities on apical dendrites are reduced by approximately 20-25% in 192 IgG-saporin-treated cases; no change was detected in number of spines on basal dendrites. These results indicate a developmental or maintenance role for cholinergic afferents to cerebral cortical neurons.
ESTHER : Robertson_1998_Cereb.Cortex_8_142
PubMedSearch : Robertson_1998_Cereb.Cortex_8_142
PubMedID: 9542893

Title : Specificity of attachment and neurite outgrowth of dissociated basal forebrain cholinergic neurons seeded on to organotypic slice cultures of forebrain - Robertson_1997_Neurosci_80_741
Author(s) : Robertson RT , Baratta J , Kageyama GH , Ha DH , Yu J
Ref : Neuroscience , 80 :741 , 1997
Abstract : Development and differentiation of basal forebrain-derived cholinergic neurons were studied using a new technique that combines dissociated cell cultures with organotypic slice cultures. Slices of cerebral cortex or entire forebrain hemispheres were taken from early postnatal rat pups and maintained as organotypic cultures on membranes. Dissociated cell suspensions of basal forebrain tissue, taken from rat or mouse fetuses at gestational day 15-17, were seeded on to the slice cultures. Combined cultures were maintained for two to 14 days in vitro. Cultures processed for acetylcholinesterase histochemical staining demonstrated that stained neurons display regional variation in attachment to the slice, with most attachment occurring on cortex and with no detectable attachment on the caudate-putamen. Regional differences in attachment occur between cortical areas, with medial (cingulate) cortex showing much denser cell attachment than lateral (parietal) cortex, and across cortical layers, with layer I and deep layers showing more attachment than middle cortical layers. Similar patterns were observed on slices from rat brain irrespective of whether rat or mouse dissociated cells were used. Tyrosine hydroxylase-stained dissociated cells from ventral midbrain displayed a different pattern of attachment, with prominent attachment to the caudate putamen and less apparent specificity of regional and cortical laminar attachment. Little evidence of neurite outgrowth occurred during the first two days in vitro, but by four days, acetylcholinesterase-positive basal forebrain cells displayed several short and thick neurites that appeared to be dendrites, and one long process that appeared to be an axon. By seven days in vitro, dendrites are well developed and the presumed axon has extended branches over wide areas of cortex. These studies revealed several different types of cell-tissue interaction. The degree of cell growth and differentiation ranged from robust growth when dissociated cells were seeded on to slice cultures of normal target tissue, to apparently no attachment or growth when cells were seeded on to non-target tissue. This combined technique appears to be a useful method for studies of specificity of cell attachment and patterns of neurite outgrowth.
ESTHER : Robertson_1997_Neurosci_80_741
PubMedSearch : Robertson_1997_Neurosci_80_741
PubMedID: 9276490

Title : Cholinergic innervation of cerebral cortex in organotypic slice cultures: sustained basal forebrain and transient striatal cholinergic projections - Baratta_1996_Neurosci_72_1117
Author(s) : Baratta J , Marienhagen JW , Ha D , Yu J , Robertson RT
Ref : Neuroscience , 72 :1117 , 1996
Abstract : Slices of entire forebrain hemispheres were taken from early postnatal rat pups and maintained as organotypic slice cultures. Basal forebrain cholinergic neurons, identified by histochemical staining for acetylcholinesterase, develop axons that grow rapidly into cerebral cortex. Ingrowth occurs by two routes: some axons course laterally from the basal forebrain region to reach lateral neocortex; others course dorsally from the septum to reach medial cortex. By one to two weeks in vitro, acetylcholinesterase-positive axons have extended throughout most of the cortical territory. In addition to basal forebrain cholinergic axons, the normally local circuit cholinergic neurons of the striatum also send axons into cerebral cortex. These striatum-derived axons can be distinguished from basal forebrain axons by their distinct morphological characteristics and by their different response to excision of the striatum or basal forebrain. Further, acetylcholinesterase-positive axons in cortex that originate from striatum appear to retract or degenerate after about one week in culture, while those from basal forebrain remain present and apparently healthy beyond two weeks. These data document the basal forebrain cholinergic ingrowth into cerebral cortex using this whole hemisphere slice culture system and also demonstrate different degrees of maintenance of cortical afferents that are derived from different subcortical sources.
ESTHER : Baratta_1996_Neurosci_72_1117
PubMedSearch : Baratta_1996_Neurosci_72_1117
PubMedID: 8735234

Title : The Aspergillus parasiticus polyketide synthase gene pksA, a homolog of Aspergillus nidulans wA, is required for aflatoxin B1 biosynthesis - Chang_1995_Mol.Gen.Genet_248_270
Author(s) : Chang PK , Cary JW , Yu J , Bhatnagar D , Cleveland TE
Ref : Molecular & General Genetics , 248 :270 , 1995
Abstract : Aflatoxins comprise a group of polyketide-derived carcinogenic mycotoxins produced by Aspergillus parasiticus and Aspergillus flavus. By transformation with a disruption construct, pXX, we disrupted the aflatoxin pathway in A. parasiticus SRRC 2043, resulting in the inability of this strain to produce aflatoxin intermediates as well as a major yellow pigment in the transformants. The disruption was attributed to a single-crossover, homologous integration event between pXX and the recipient A. parasiticus genome at a specific locus, designated pksA. Sequence analysis suggest that pksA is a homolog of the Aspergillus nidulans wA gene, a polyketide synthase gene involved in conidial wall pigment biosynthesis. The conserved beta-ketoacyl synthase, acyltransferase and acyl carrier-protein domains were present in the deduced amino acid sequence of the pksA product. No beta-ketoacyl reductase and enoyl reductase domains were found, suggesting that pksA does not encode catalytic activities for processing beta-carbon similar to those required for long chain fatty acid synthesis. The pksA gene is located in the aflatoxin pathway gene cluster and is linked to the nor-1 gene, an aflatoxin pathway gene required for converting norsolorinic acid to averantin. These two genes are divergently transcribed from a 1.5 kb intergenic region. We propose that pksA is a polyketide synthase gene required for the early steps of aflatoxin biosynthesis.
ESTHER : Chang_1995_Mol.Gen.Genet_248_270
PubMedSearch : Chang_1995_Mol.Gen.Genet_248_270
PubMedID: 7565588
Gene_locus related to this paper: aspor-PKSL1

Title : Reduction of transiently expressed acetylcholinesterase activity in developing thalamocortical projections does not affect the mature pattern of basal forebrain projections to visual cortex - Kimm_1995_Brain.Res.Dev.Brain.Research_85_283
Author(s) : Kimm EJ , Perez CE , Yu CC , Yu J , Robertson RT
Ref : Brain Research Developmental Brain Research , 85 :283 , 1995
Abstract : Experiments tested the hypothesis that acetylcholinesterase (AChE) activity, expressed transiently in developing thalamocortical projections, serves to limit the growth of basal forebrain cholinergic projections into thalamocortical recipient zones. Newborn rats were subjected to enucleation, a procedure that eliminates transient AChE activity in developing visual cortex. After 3-8 weeks survival, AChE histochemical techniques revealed no alteration in the pattern of AChE positive basal forebrain axons in visual cortex. These data indicate that transient AChE activity in developing sensory cortex does not limit ingrowth of basal forebrain cholinergic axons.
ESTHER : Kimm_1995_Brain.Res.Dev.Brain.Research_85_283
PubMedSearch : Kimm_1995_Brain.Res.Dev.Brain.Research_85_283
PubMedID: 7600676

Title : Sustained inhibition of acetylcholinesterase activity does not disrupt early geniculocortical ingrowth to developing rat visual cortex - Ling_1995_Brain.Res.Dev.Brain.Research_86_354
Author(s) : Ling JJ , Yu J , Robertson RT
Ref : Brain Research Developmental Brain Research , 86 :354 , 1995
Abstract : Esterase activity of endogenous transiently expressed acetylcholinesterase was locally suppressed in visual cortex of infant rats for 2-5 days by the irreversible inhibitor phospholine iodide, delivered from Elvax implants. Tissue processed for anterograde movement of the carbocyanine dye DiI or anterograde transneuronal transport of wheat germ agglutinin-horseradish peroxidase revealed normal geniculocortical growth into layer IV of visual cortex. These results suggest that the catalytic activity of transiently expressed acetylcholinesterase may play little, if any, role in early development of thalamocortical systems.
ESTHER : Ling_1995_Brain.Res.Dev.Brain.Research_86_354
PubMedSearch : Ling_1995_Brain.Res.Dev.Brain.Research_86_354
PubMedID: 7544702

Title : [Predictors of hepatic functional reserve in cirrhotic patients]. [Chinese] - Zhang_1995_Zhonghua.Wai.Ke.Za.Zhi_33_38
Author(s) : Zhang X , He E , Yu J
Ref : Chinese Journal of Surgery , 33 :38 , 1995
Abstract : We have determined the interstitial ratio, hepatocyte numerical density on area (NA) by the method of Luzex-F Image Analyser, and the level of serum prealbumin (PA), choline esterase activity (ChE) by agarose immunodiffusion and ratemetry in control group (14 cases) and 25 cirrhotic patients undergoing pericardial devascularization. The results were compared with traditional hepatic function grade (Child's Grade). We found that NA, PA, and ChE are independently useful in evaluating the hepatic functional reserve in cirrhotic patients.
ESTHER : Zhang_1995_Zhonghua.Wai.Ke.Za.Zhi_33_38
PubMedSearch : Zhang_1995_Zhonghua.Wai.Ke.Za.Zhi_33_38
PubMedID: 7774444

Title : Possible Cholinergic and Non-Cholinergic Actions of Transiently Expressed Acetylcholinesterase in Thalamocortical Development Projections -
Author(s) : Robertson RT , Broide RS , Yu J , Leslie FL
Ref : In Enzyme of the Cholinesterase Family - Proceedings of Fifth International Meeting on Cholinesterases , (Quinn, D.M., Balasubramanian, A.S., Doctor, B.P., Taylor, P., Eds) Plenum Publishing Corp. :435 , 1995

Title : Transition from developing to mature patterns of acetylcholinesterase activity in rat visual cortex: implications for the time-course of geniculocortical development - Hanes_1992_Brain.Res.Dev.Brain.Research_66_97
Author(s) : Hanes MA , Robertson RT , Yu J
Ref : Brain Research Developmental Brain Research , 66 :97 , 1992
Abstract : Patterns of acetylcholinesterase (AChE) histochemical staining in cortical area 17 differ in infant and mature rats. In infants, intense AChE activity is seen as a band corresponding to layer IV and deep layer III of the visual cortex, and this staining is associated with terminal fields of geniculocortical neurons. In adult animals, AChE activity is densest in deep layer IV and layer V and is associated with projections originating in the basal forebrain. The present study investigated the transition from developing to mature patterns of AChE staining in visual cortex. Unilateral lesions were placed in either the lateral geniculate body or the basal forebrain of rats postnatal days 8 (P8) to adulthood; the effects of these lesions on patterns of AChE activity in visual cortex were studied with histochemical techniques and optical densitometry. Lesions involving the lateral geniculate body markedly reduce AChE activity in visual cortex of P12 rats, had moderate effects in P20 rats, and had no apparent effect on AChE activity of visual cortex of rats aged P40 and older. Lesions of basal forebrain had little effect on AChE activity in visual cortex of P12 animals, increasing effect in P15-35 rats, and eliminated much of AChE staining in visual cortex of adults. The period of transition from developing to mature patterns of AChE activity in visual cortex of animals bilaterally enucleated at birth was not different from the period of transition in normally sighted animals. These data indicate that mature patterns of AChE activity in visual cortex are not achieved until well into the second month of life. If transient AChE expression is characteristic of geniculocortical neurons during the period of time in which axons are proliferating within visual cortex, then these data indicate that geniculocortical connections may be forming well into the second month of life in the rat.
ESTHER : Hanes_1992_Brain.Res.Dev.Brain.Research_66_97
PubMedSearch : Hanes_1992_Brain.Res.Dev.Brain.Research_66_97
PubMedID: 1600634

Title : Basal forebrain and anterior thalamic contributions to acetylcholinesterase activity in granular retrosplenial cortex of rats - Tengelsen_1992_Brain.Res_594_10
Author(s) : Tengelsen LA , Robertson RT , Yu J
Ref : Brain Research , 594 :10 , 1992
Abstract : Histochemical studies demonstrate that granular retrosplenial cortex (cortical areas 29b and c) of the adult rat displays a characteristic laminar pattern of acetylcholinesterase (AChE) activity. While some AChE-positive axons are found in all cortical layers, most intense staining occurs in two bands that correspond to layers I and III. The present studies were directed toward identifying the neural systems underlying this AChE activity. Unilateral electrolytic or excitatory amino acid induced lesions of the basal forebrain, including the nucleus of the diagonal band, result in reductions of AChE staining throughout ipsilateral granular retrosplenial cortex; particularly noteworthy are the reductions in layer I and the deeper cortical layers. AChE staining remains in superficial layer I and in layer III. Placement of lesions in the anterior thalamus, including all of the anterior dorsal nucleus, results in reduction of AChE histochemical staining in the outer part of layer I and especially in layer III. Staining remains in much of layer I and in the deepest band of layer III. Placement of electrolytic lesions in the hypothalamus or the midbrain tegmentum produce no detectable change in the pattern of AChE in retrosplenial cortex. These results indicate that AChE activity in granular retrosplenial cortex is found primarily within afferent axons from the basal forebrain system and from anterior dorsal thalamus, and these two systems of afferents display distinct laminar patterns of termination.
ESTHER : Tengelsen_1992_Brain.Res_594_10
PubMedSearch : Tengelsen_1992_Brain.Res_594_10
PubMedID: 1467929

Title : Primary auditory cortex in the rat: transient expression of acetylcholinesterase activity in developing geniculocortical projections - Robertson_1991_Brain.Res.Dev.Brain.Research_58_81
Author(s) : Robertson RT , Mostamand F , Kageyama GH , Gallardo KA , Yu J
Ref : Brain Research Developmental Brain Research , 58 :81 , 1991
Abstract : A characteristic pattern of acetylcholinesterase (AChE) activity is expressed transiently in primary auditory cortex (cortical area 41) of developing laboratory rats during early postnatal life. This AChE activity occurs as a dense plexus in cortical layer IV and the deep part of layer III. This transient band of AChE activity is first detected by histochemical techniques on postnatal day (P) 3, reaches peak intensity at approximately P8-10, and declines to form the adult pattern by P23. The ventral nucleus of the medial geniculate body of the thalamus also displays prominent, and transient, staining for AChE. This intense staining for AChE, found within neuronal somata and neuropil, is detected at the time of birth, reaches peak intensity around P8, and declines to adult levels by P16. The areal and laminar patterns of the transient band of AChE activity in temporal cortex correspond to the patterns of anterograde transneuronal labeling of geniculocortical terminals following injection of wheat germ agglutinin conjugated to horseradish peroxidase (WGA-HRP) into the inferior colliculus. Placement of lesions that include the medial geniculate nucleus or the geniculocortical axons results in a marked decrease in AChE staining in thalamorecipient layers of auditory cortex. Placement of lesions that include the medial globus pallidus reduce AChE staining of some axons in temporal cortex of developing rats, but the dense band of AChE in layers III and IV remains. Placement of lesions in the inferior colliculus in newborn animals results in marked decrease in AChE staining in cells of the ipsilateral ventral medial geniculate nucleus and in ipsilateral auditory cortex of developing pups. These data indicate that transiently expressed AChE activity is characteristic of geniculocortical neurons, including their somata in the medial geniculate body and their terminal axons in primary auditory cortex. This AChE activity is expressed early in postnatal development, probably during the time when thalamocortical axons are proliferating in cortical layer IV and forming synaptic contacts with cortical neurons.
ESTHER : Robertson_1991_Brain.Res.Dev.Brain.Research_58_81
PubMedSearch : Robertson_1991_Brain.Res.Dev.Brain.Research_58_81
PubMedID: 2015657

Title : Neural systems contributing to acetylcholinesterase histochemical staining in primary visual cortex of the adult rat - Robertson_1990_Brain.Res_509_181
Author(s) : Robertson RT , Fehrenbach CJ , Yu J
Ref : Brain Research , 509 :181 , 1990
Abstract : Histochemical studies demonstrate that cortical area 17 (primary visual cortex) of the adult rat displays a characteristic laminar pattern of acetylcholinesterase (AChE) activity. While AChE-positive axons are found throughout the cortical layers, most intense staining occurs in a band that corresponds to layer V and the deep portion of layer IV. The present studies were directed toward determining the neural systems containing this AChE activity. Unilateral electrolytic or excitatory amino acid induced lesions of the basal forebrain result in reductions of AChE staining in ipsilateral visual cortex, particularly in layers IV and V. Electrolytic or scalpel lesions, placed in white matter underlying dorsal and lateral neocortex to interrupt basal forebrain projections to visual cortex, also reduce AChE staining in visual cortex. Lesions in the cingulate bundle and supracallosal stria reduced AChE staining retrosplenial cortex but did not affect staining visual cortex. Placement of electrolytic lesions in the hypothalamus produced no detectable change in the pattern of AChE in visual cortex. Electrolytic lesions in the midbrain tegmentum, placed to interrupt ascending axons from brainstem monoamine neurons, produced no detectable change in the pattern of AChE in visual cortex. Placement of lesions in the dorsal thalamus that include all of the dorsal lateral geniculate nucleus did not alter AChE staining in visual cortex. The results indicate that AChE activity in adult visual cortex is found primarily within afferent axons from the basal forebrain system. These data demonstrate further that the AChE staining characteristic of adult visual cortex is associated with neural systems that are distinctly different from those associated with AChE staining in visual cortex of the infant rat.
ESTHER : Robertson_1990_Brain.Res_509_181
PubMedSearch : Robertson_1990_Brain.Res_509_181
PubMedID: 2322817

Title : Patterns of transiently expressed acetylcholinesterase activity in cerebral cortex and dorsal thalamus of developing rats with cytotoxin-induced microencephaly - Robertson_1990_Int.J.Dev.Neurosci_8_223
Author(s) : Robertson RT , Gragnola TG , Yu J
Ref : Int J Developmental Neuroscience , 8 :223 , 1990
Abstract : Previous studies have demonstrated that acetylcholinesterase (AChE) activity is expressed transiently by thalamocortical neurons of primary sensory systems in developing rat pups. In the present study, prenatal treatment with methylazoxymethanol acetate (MAM) on embryonic day 15, 16, or 17 resulted in rat pups with cerebral cortices markedly reduced in thickness and areal extent. Histochemical studies demonstrated that AChE staining occurs in fiber-like plexuses in primary visual, auditory, and somatosensory regions of developing cerebral cortex of MAM-treated animals, just as in normal developing rats, but that the transient patterns of AChE are found more superficially than normal and they occur in an abnormal patchy distribution. Neuronal somata in thalamic lateral geniculate, medial geniculate and ventral basal nuclei of MAM-treated animals show transient AChE staining indistinguishable from that seen in normal animals. These data indicate: (1) AChE is expressed transiently by thalamocortical neurons in MAM-treated animals, (2) intensity of the transiently expressed AChE is not affected by MAM-induced loss of cortical neurons, and (3) the abnormal AChE patterns in cortex likely reflect the abnormal distributions of thalamocortical terminal fields that are characteristic of MAM-treated animals.
ESTHER : Robertson_1990_Int.J.Dev.Neurosci_8_223
PubMedSearch : Robertson_1990_Int.J.Dev.Neurosci_8_223
PubMedID: 2327291

Title : Intraocular injections of tetrodotoxin reduce transiently expressed acetylcholinesterase activity in developing rat visual cortex - Robertson_1989_Brain.Res.Dev.Brain.Research_46_69
Author(s) : Robertson RT , Ambe RK , Yu J
Ref : Brain Research Developmental Brain Research , 46 :69 , 1989
Abstract : Geniculo-recipient layers of primary visual cortex in the rat display a transient pattern of acetylcholinesterase (AChE) activity during the second postnatal week of life. Previous work has demonstrated that neonatal enucleations markedly reduce the transient AChE activity in visual cortex. The present studies were undertaken to determine the effects of reduced afferent neural activity on expression of the transient pattern of AChE activity. Rat pups received intraocular injections of tetrodotoxin (TTX) on postnatal days (PND) 3, 5, 7, 9 and 11 and were sacrificed on PND 12. Some animals were enucleated on PND 3. Brain sections were processed for AChE histochemistry and analyzed by optical densitometry. These experiments show that uniocular injections result in a markedly decreased level of AChE activity in layer IV of the medial part of cortical area 17 contralateral to the injected eye. The degree of reduction of AChE activity from repeated TTX injections was similar to the degree of reduction following enucleation on PND 3. Binocular injections of TTX result in a reduction of AChE activity in layer IV throughout cortical area 17, similar to the effects of binocular enucleation on PND 3. Experiments combining injection of horseradish peroxidase along with TTX on PND 11 demonstrate that retinal ganglion cells of TTX injected eyes are still capable of anterograde axonal transport. These data demonstrate that normal innervation and afferent activity are necessary for the transient expression of AChE activity by geniculocortical neurons.
ESTHER : Robertson_1989_Brain.Res.Dev.Brain.Research_46_69
PubMedSearch : Robertson_1989_Brain.Res.Dev.Brain.Research_46_69
PubMedID: 2706772

Title : Neonatal enucleations reduce number, size, and acetylcholinesterase histochemical staining of neurons in the dorsal lateral geniculate nucleus of developing rats - Robertson_1989_Brain.Res.Dev.Brain.Research_47_209
Author(s) : Robertson RT , Poon HK , Duran MR , Yu J
Ref : Brain Research Developmental Brain Research , 47 :209 , 1989
Abstract : Previous studies have demonstrated that transient patterns of acetylcholinesterase (AChE) activity are characteristic of geniculo-recipient regions of rat cortical area 17 during the second and third postnatal weeks of life. Neonatal enucleation results in a marked reduction of this transiently expressed cortical AChE. Parallel studies have demonstrated that the dorsal lateral geniculate nucleus (dLGN) also expresses AChE transiently during development. The present study examines neuronal number and size as well as AChE histochemical staining in the dLGN of normal and neonatally enucleated rat pups to determine whether changes in dLGN neurons could account for the decreased visual cortical AChE staining that results from neonatal enucleation. Changes in 4 parameters in dLGN were noted after neonatal enucleation. First, a 26-37% shrinkage in the volume of dLGN occurred contralateral to enucleation. Second, enucleation resulted in a loss of 16-30% of AChE-stained neuronal somata. Third, remaining AChE-positive neuronal somata appeared shrunken by approximately 40%. Fourth, intensity of AChE histochemical staining of individual dLGN neurons was reduced by approximately 24% following neonatal enucleation. These data suggest that loss of transient AChE activity in cortical area 17 consequent to neonatal enucleation is secondary to enucleation-induced alterations in the dLGN; these alterations include loss of neurons, shrinkage of neurons, and an apparent decrease in the ability of neurons to synthesize AChE. These data support the hypothesis that geniculocortical projection neurons express AChE transiently during development of geniculocortical connectivity and indicate that normal afferent connections and/or activity are important for the transient expression of AChE by these neurons.
ESTHER : Robertson_1989_Brain.Res.Dev.Brain.Research_47_209
PubMedSearch : Robertson_1989_Brain.Res.Dev.Brain.Research_47_209
PubMedID: 2743558

Title : Transient patterns of acetylcholinesterase activity in developing thalamus: a comparative study in rodents - Robertson_1989_Brain.Res.Dev.Brain.Research_48_309
Author(s) : Robertson RT , Poon HK , Mirrafati SJ , Yu J
Ref : Brain Research Developmental Brain Research , 48 :309 , 1989
Abstract : This paper describes acetylcholinesterase (AChE) activity in the dorsal thalamus of several rodents, including rat, mouse, gerbil, hamster and guinea pig. Tissue from fetal, neonatal, and adult animals was studied using histochemical techniques. Developing animals of all species display prominent AChE staining in the ventral medial geniculate nucleus and the ventral posterior nucleus, while adult animals show very light staining in these thalamic regions. Similarly, the dorsal lateral geniculate nucleus of all species shows stronger staining in developing animals than in adults. These data indicate that transient expression of AChE activity in primary sensory thalamic nuclei is a characteristic common to a variety of rodents.
ESTHER : Robertson_1989_Brain.Res.Dev.Brain.Research_48_309
PubMedSearch : Robertson_1989_Brain.Res.Dev.Brain.Research_48_309
PubMedID: 2776300

Title : Investigations of the origins of transient acetylcholinesterase activity in developing rat visual cortex - Robertson_1988_Brain.Res_469_1
Author(s) : Robertson RT , Hanes MA , Yu J
Ref : Brain Research , 469 :1 , 1988
Abstract : Transient acetylcholinesterase (AChE) activity is characteristic of cortical area 17 of the developing laboratory rat during the second and third postnatal weeks of life. This AChE activity is most intense in a band that corresponds to cortical layer IV and the deep part of layer III, but also is found in the outer half of cortical layer I and in layer VI. The morphology of the pattern of the histochemical reaction product indicates that the transient AChE is characteristic of an axonal terminal field. The present report describes results of 3 sets of experiments aimed at determining the source of transient AChE in cortical area 17. First, placement of lesions in portions of the basal forebrain or in the cingulate bundle results in a decrease in the general pattern of AChE throughout occipital cortex and especially in layer I, but the transient bands of AChE in layers III-IV of cortical area 17 are not eliminated. Second, kainic acid or cobalt chloride injections in cortical area 17 result in the loss of many AChE-positive neuronal somata but do not eliminate the transient pattern of AChE in thalamo-recipient layers of cortical area 17. Similarly, treatment of fetuses with mitotic inhibitors that eliminate many of the neurons destined for granular and supragranular layers does not eliminate transient patterns of AChE. Third, lesions that include the lateral geniculate nucleus of the thalamus or geniculocortical projections result in a marked loss of the pattern of AChE in thalamo-recipient layers of cortical area 17, without significant loss in other layers of area 17 or in other regions of occipital cortex. These data support the hypothesis that the transient AChE found in thalamo-recipient layers of cortical area 17 is contained within geniculocortical axon terminals.
ESTHER : Robertson_1988_Brain.Res_469_1
PubMedSearch : Robertson_1988_Brain.Res_469_1
PubMedID: 3401792

Title : Effects of neonatal monocular and binocular enucleation on transient acetylcholinesterase activity in developing rat visual cortex - Robertson_1987_Brain.Res_430_185
Author(s) : Robertson RT , Fogolin RP , Tijerina AA , Yu J
Ref : Brain Research , 430 :185 , 1987
Abstract : Geniculo-recipient layers of visual cortical area 17 in the laboratory rat display a transient pattern of acetylcholinesterase (AChE) activity during the second and third postnatal weeks of life. The appearance of the AChE histochemical reaction product and its distribution in thalamic recipient layers of cortical area 17 suggest that this transient AChE serves as a marker for the region of geniculocortical axon terminals. In the present study, infant rats were enucleated monocularly or binocularly on the day of birth. Animals were sacrificed at postnatal days 5-21. Frozen sections cut in either the transverse plane or parallel to the pial surface were processed for AChE histochemistry. Neonatal monocular enucleation resulted in a marked reduction of transient AChE activity in thalamic recipient layers of the medial part of area 17 contralateral to the enucleated orbit, i.e., the monocular segment of area 17. No loss of AChE was observed in area 17 ipsilateral to the enucleation. Pigmented and albino strains of rats did not differ significantly in the extent to which monocular enucleation reduced the transient AChE in contralateral visual cortex. Neonatal binocular enucleation resulted in an almost complete loss of AChE histochemical staining in thalamic recipient layers throughout cortical area 17, without loss of AChE in other cortical regions. These data support the hypothesis that transient AChE serves as a marker for the region of geniculocortical axon terminals, and also demonstrate that the transient expression of AChE in visual cortex depends upon normal innervation or activity of the geniculocortical neurons.
ESTHER : Robertson_1987_Brain.Res_430_185
PubMedSearch : Robertson_1987_Brain.Res_430_185
PubMedID: 3607512