Ren Y

References (51)

Title : Molecular insight into the enhanced performance of CALB toward PBDF degradation - Ren_2024_Int.J.Biol.Macromol_262_130181
Author(s) : Ren Y , Cheng L , Cheng Z , Liu Y , Li M , Yuan T , Shen Z
Ref : Int J Biol Macromol , 262 :130181 , 2024
Abstract : Poly(butylene diglycolate-co-furandicarboxylate) (PBDF) is a newly developed biodegradable copolyester. Candida antarctica lipase B (CALB) has been identified as an effective catalyst for PBDF degradation. The mechanism is elucidated using a combination of molecular dynamics simulations and quantum chemistry approaches. The findings unveil a four-step catalytic reaction pathway. Furthermore, bond analysis, charge and interaction analysis are conducted to gain a more comprehensive understanding of the PBDF degradation process. Additionally, through the introduction of single-point mutations to crucial residues in CALB's active sites, two mutants, T138I and D134I, are discovered to exhibit improved catalytic efficiency. These significant findings contribute to the advancement of our comprehension concerning the molecular mechanism of underlying copolyesters degradation, while also presenting a novel approach for expediting the degradation rate by the CALB enzyme modification.
ESTHER : Ren_2024_Int.J.Biol.Macromol_262_130181
PubMedSearch : Ren_2024_Int.J.Biol.Macromol_262_130181
PubMedID: 38360240

Title : JH degradation pathway participates in hormonal regulation of larval development of Bombyx mori following lambda-cyhalothrin exposure - Su_2023_Chemosphere_349_140871
Author(s) : Su Y , Wang W , Dai Y , Qi R , Gu H , Guo X , Liu X , Ren Y , Li F , Li B , Sun H
Ref : Chemosphere , 349 :140871 , 2023
Abstract : lambda-Cyhalothrin (lambda-cyh), a widely utilized pyrethroid insecticide, poses serious threats to non-target organisms due to its persistence nature in the environment. Exposure to low concentrations of lambda-cyh has been observed to result in prolonged larval development in Bombyx mori, leading to substantial financial losses in sericulture. The present study was undertaken to elucidate the underlying mechanisms for prolonged development caused by lambda-cyh (LC(10)) exposure. The results showed that the JH titer was significantly increased at 24 h of lambda-cyh exposure, and the JH interacting genes Methoprene-tolerant 2, Steroid Receptor Co-activator, Krppel-homolog 1, and JH binding proteins were also up-regulated. Although the target of rapamycin (Tor) genes were induced by lambda-cyh, the biosynthesis of JH in the corpora allata was not promoted. Notably, 13 JH degradation genes were found to be significantly down-regulated in the midgut of B. mori. The mRNA levels and enzyme activity assays indicated that lambda-cyh had inhibitory effects on JH esterase, JH epoxide hydrolase, and JH diol kinase (JHDK). Furthermore, the suppression of JHDK (KWMTBOMO01580) was further confirmed by both western blot and immunohistochemistry. This study has offered a comprehensive perspective on the mechanisms underlying the prolonged development caused by insecticides, and our results also hold significant implications for the safe production of sericulture.
ESTHER : Su_2023_Chemosphere_349_140871
PubMedSearch : Su_2023_Chemosphere_349_140871
PubMedID: 38056714

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 : NDRG4 Alleviates Myocardial Infarction-Induced Apoptosis through the JAK2\/STAT3 Pathway - Zhao_2022_Comput.Math.Methods.Med_2022_4869470
Author(s) : Zhao C , Ren Y , Zhang Y
Ref : Comput Math Methods Med , 2022 :4869470 , 2022
Abstract : OBJECTIVE: At present, studies have confirmed that NDRG4 is specifically expressed in the heart, while its effect on the heart is still unclear. This study is to explore the effect of NDRG4 on cardiomyocyte apoptosis caused by acute myocardial infarction (AMI). METHODS: Twenty SD rats were randomly divided into Sham (left anterior descent of heart without ligation) and AMI groups. In this study, coronary artery ligation was used to establish an AMI model, and the AMI model was verified by auxiliary examination and pathological examination. Besides, quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting (WB) was used to detect the expression level of Bax and Bcl-2 in heart tissues, and NDRG mRNA levels in tissues were also detected. qRT-PCR technology was used to verify the transfection efficiency of NDRG4 in H9C2 cells, and the change of apoptosis level of H9C2 cells was detected by Cell Counting Kit-8 (CCK-8) assay and TUNEL staining; besides, the expression level of apoptosis-related factors was detected by WB and qRT-PCR technology. Simultaneously with the modeling of rats, we injected adenovirus (Ad) into the heart tissue and examined the structural and functional changes of the rat heart. Then, WB technology was used to detect the expression level of the JAK2/STAT3 signaling pathway. RESULTS: The heart function and heart structure of rats in the MI group were dramatically worse, and the expression level of NDRG4 was also dramatically reduced. The overexpression of NDRG4 in H9C2 cells can effectively inhibit the ischemia/hypoxia- (I/H-) induced decrease in cell viability and increase in apoptosis rate and inhibit the increase in Bax/Bcl-2 ratio. Moreover, overexpression of NDRG4 in heart tissue can effectively improve the cardiac function and structural destruction caused by MI. In addition, NDRG4 can inhibit JAK2/STAT3 pathway activation. CONCLUSION: The expression of NDRG4 in the MI tissue of rats was suppressed, while overexpression of NDRG4 by injection of Ad can obviously protect the rat heart. Furthermore, overexpression of NDRG4 in H9C2 cells can effectively inhibit the I/H-induced decrease in cell viability and increase in apoptosis rate, and this may be related to the inhibition of the JAK2/STAT3 signaling pathway.
ESTHER : Zhao_2022_Comput.Math.Methods.Med_2022_4869470
PubMedSearch : Zhao_2022_Comput.Math.Methods.Med_2022_4869470
PubMedID: 35126626
Gene_locus related to this paper: human-NDRG4

Title : Rapid Mining of Novel alpha-Glucosidase and Lipase Inhibitors from Streptomyces sp. HO1518 Using UPLC-QTOF-MS\/MS - Xu_2022_Mar.Drugs_20_
Author(s) : Xu J , Liu Z , Feng Z , Ren Y , Liu H , Wang Y
Ref : Mar Drugs , 20 : , 2022
Abstract : A rapid and sensitive method using ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) was applied for the analysis of the metabolic profile of acarviostatin-containing aminooligosaccharides derived from Streptomyces sp. HO1518. A total of ninety-eight aminooligosaccharides, including eighty potential new compounds, were detected mainly based on the characteristic fragment ions originating from quinovosidic bond cleavages in their molecules. Following an LC-MS-guided separation technique, seven new aminooligosaccharides (10-16) along with four known related compounds (17-20) were obtained directly from the crude extract of strain HO1518. Compounds 10-13 represent the first examples of aminooligosaccharides with a rare acarviostatin II02-type structure. In addition, all isolates displayed considerable inhibitory effects on three digestive enzymes, which revealed that the number of the pseudo-trisaccharide core(s), the feasible length of the oligosaccharides, and acyl side chain exerted a crucial influence on their bioactivities. These results demonstrated that the UPLC-QTOF-MS/MS-based metabolomics approach could be applied for the rapid identification of aminooligosaccharides and other similar structures in complex samples. Furthermore, this study highlights the potential of acylated aminooligosaccharides with conspicuous alpha-glucosidase and lipase inhibition for the future development of multi-target anti-diabetic drugs.
ESTHER : Xu_2022_Mar.Drugs_20_
PubMedSearch : Xu_2022_Mar.Drugs_20_
PubMedID: 35323488

Title : Genes, Structural, and Biochemical Characterization of Four Chlorophyllases from Solanum lycopersicum - Liu_2022_Int.J.Mol.Sci_23_11716
Author(s) : Liu G , Meng X , Ren Y , Zhang M , Chen Z , Zhang Z , Pang X , Zhang X
Ref : Int J Mol Sci , 23 :11716 , 2022
Abstract : Recent studies have confirmed that chlorophyllase (CLH), a long-found chlorophyll (Chl) dephytylation enzyme for initiating Chl catabolism, has no function in leaf senescence-related Chl breakdown. Yet, CLH is considered to be involved in fruit degreening and responds to external and hormonal stimuli. The purpose of this work was to elucidate in detail the biochemical, structural properties, and gene expression of four CLHs from the Solanum lycopersicum genome so as to understand the roles of Solanum lycopersicum chlorophyllases (SlCLHs). SlCLH1/4 were the predominantly expressed CLH genes during leaf and fruit development/ripening stages, and SlCLH1 in mature green fruit was modulated by light. SlCLH1/2/3/4 contained a highly conserved GHSXG lipase motif and a Ser-Asp-His catalytic triad. We identified Ser159, Asp226, and His258 as the essential catalytic triad by site-directed mutagenesis in recombinant SlCLH1. Kinetic analysis of the recombinant enzymes revealed that SlCLH1 had high hydrolysis activities against Chl a, Chl b, and pheophytin a (Phein a), but preferred Chl a and Chl b over Phein a; SlCLH2/3 only showed very low activity to Chl a and Chl b, while SlCLH4 showed no Chl dephytylation activity. The recombinant SlCLH1/2/3 had different pH stability and temperature optimum. Removal of the predicted N-terminal processing peptide caused a partial loss of activity in recombinant SlCLH1/2 but did not compromise SlCLH3 activity. These different characteristics among SlCLHs imply that they may have different physiological functions in tomato.
ESTHER : Liu_2022_Int.J.Mol.Sci_23_11716
PubMedSearch : Liu_2022_Int.J.Mol.Sci_23_11716
PubMedID: 36233017

Title : Sublethal Effects of Thiamethoxam on Biological Traits and Detoxification Enzyme Activities in the Small Brown Planthopper, Laodelphax striatellus (Falln) - Cai_2022_J.Econ.Entomol__
Author(s) : Cai Y , Dou T , Gao F , Wang G , Dong Y , Song N , An S , Yin X , Liu X , Ren Y
Ref : J Econ Entomol , : , 2022
Abstract : The small brown planthopper (Laodelphax striatellus (Falln), Hemiptera: Delphacidae), is an important agricultural pest of rice, and neonicotinoid insecticides are commonly used for controlling L. striatellus. However, the sublethal effects of thiamethoxam on L. striatellus remain relatively unknown. In this study, an age-stage life table procedure was used to evaluate the sublethal effects of thiamethoxam on the biological parameters of L. striatellus. Additionally, activities of carboxylesterase, glutathione S-transferase, and cytochrome P450 monooxygenase in the third instar nymphs were analyzed. The results indicated that the survival time of F0 adults and the fecundity of female adults decreased significantly after the third instar nymphs were treated with sublethal concentrations of thiamethoxam (LC15 0.428 mg/liter and LC30 0.820 mg/liter). The developmental duration, adult preoviposition period, total preoviposition period, and mean generation time of the F1 generation increased significantly, whereas the fecundity of the female adults, intrinsic rate of increase (ri), and finite rate of increase (Lambda) decreased significantly. The oviposition period was significantly shorter for the insects treated with LC30 than for the control insects. Neither sublethal concentrations had significant effects on the adult longevity, net reproduction rate (R0), or gross reproduction rate (GRR) of the F1 generation. The activities of carboxylesterase, glutathione-S-transferase, and cytochrome P450 monooxygenase increased significantly after the thiamethoxam treatments. These results indicate that sublethal concentrations of thiamethoxam can inhibit L. striatellus population growth and enhance detoxification enzyme activities.
ESTHER : Cai_2022_J.Econ.Entomol__
PubMedSearch : Cai_2022_J.Econ.Entomol__
PubMedID: 36351784

Title : Expression, characterization, and immobilization of a novel SGNH esterase Est882 and its potential for pyrethroid degradation - Zong_2022_Front.Microbiol_13_1069754
Author(s) : Zong W , Su W , Xie Q , Gu Q , Deng X , Ren Y , Li H
Ref : Front Microbiol , 13 :1069754 , 2022
Abstract : The widely-used pyrethroid pesticides have attracted public attention because of their potentials to cause environmental pollution and toxic effects on non-target organisms. Esterase is a kind of hydrolytic enzyme that can catalyze the cleavage or formation of ester bonds. it plays a pivotal role in the decomposition of pyrethroids and esters containing industrial pollutants through the hydrolysis of ester bonds. Here, a new esterase gene est882 was successfully screened, which encodes Est882, a SGNH family esterase composed of 294 amino acids. It was heterogeneously expressed, identified and immobilized. Multiple sequence alignment showed that Est882 had a typical GDS(X) conserved motif and a catalytic triad composed of Ser79, Asp269 and His275. Phylogenetic analysis showed that Est882 shall belong to a new esterase family. Biochemical characterization demonstrated that the optimum condition was 40 degreesC and pH 9.0. Est882 immobilization was studied with mesoporous silica SBA-15 as the carrier and found to significantly improve the tolerance and stability of Est882. Its optimum pH increased to 10.0 and stabilized within pH 8.0-11.0. Free Est882 can effectively degrade various pyrethroids within 30 min, with a degradation rate above 80%. The immobilized Est882 yet degraded more than 70% of pyrethroids within 30 min. The present study indicated that Est882 has outstanding potential in bioremediation of a pyrethroid-polluted environment. These characteristics endow Est882 with potential values in various industrial applications and hydrolysis of pyrethroid residues.
ESTHER : Zong_2022_Front.Microbiol_13_1069754
PubMedSearch : Zong_2022_Front.Microbiol_13_1069754
PubMedID: 36620037

Title : Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA - Liu_2022_Plant.Cell_34_3301
Author(s) : Liu T , Zhang X , Zhang H , Cheng Z , Liu J , Zhou C , Luo S , Luo W , Li S , Xing X , Chang Y , Shi C , Ren Y , Zhu S , Lei C , Guo X , Wang J , Zhao Z , Wang H , Zhai H , Lin Q , Wan J
Ref : Plant Cell , 34 :3301 , 2022
Abstract : Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.
ESTHER : Liu_2022_Plant.Cell_34_3301
PubMedSearch : Liu_2022_Plant.Cell_34_3301
PubMedID: 35670739

Title : Berberine Ameliorates Glucose Metabolism in Diabetic Rats through the alpha7 Nicotinic Acetylcholine Receptor-Related Cholinergic Anti-Inflammatory Pathway - Wang_2021_Planta.Med__
Author(s) : Wang D , Ren Y , Sun W , Gong J , Zou X , Dong H , Xu L , Wang K , Lu F
Ref : Planta Med , : , 2021
Abstract : Berberine is an isoquinoline derivative alkaloid extracted from Chinese herbs. Recent studies have demonstrated the therapeutic effect of berberine on glucose metabolic disorders. However, its specific mechanism is still unclear. Our study aimed to research the glucose-lowering effect of berberine in diabetic rats and to reveal the possible role of the cholinergic anti-inflammatory pathway. Diabetic rats induced by administration of a high-calorie diet and streptozocin tail vein injection were assessed by the oral glucose tolerance test. Then, the diabetic rats were divided into two groups, those with or without the alpha7 nicotinic acetylcholine receptor gene downregulated, respectively, followed by treatment including berberine for 6 weeks. Results of this study show that the administration of berberine downregulated levels of fasting blood glucose and fasting insulin, and ameliorated insulin resistance in diabetic rats. Treatment with berberine inhibited acetylcholinesterase activity, and upregulated acetylcholine levels in the serum and alpha7 nicotinic acetylcholine receptor gene expression in the liver tissue. Meanwhile, berberine reversed elevated expression of cytokines interleukin-1beta and TNF-alpha in the serum and downregulated nuclear factor kappaB expression. However, berberine administration showed no glucose-lowering or anti-inflammatory effect in diabetic rats in which alpha7 nicotinic acetylcholine receptor gene expression was downregulated, and acetylcholinesterase activity was also significantly inhibited. In conclusion, berberine may ameliorate glucose metabolism by activating the alpha7 nicotinic acetylcholine receptor-mediated cholinergic anti-inflammatory pathway.
ESTHER : Wang_2021_Planta.Med__
PubMedSearch : Wang_2021_Planta.Med__
PubMedID: 33682914

Title : Discovery of Aryl Formyl Piperidine Derivatives as Potent, Reversible, and Selective Monoacylglycerol Lipase Inhibitors - Zhi_2020_J.Med.Chem__
Author(s) : Zhi Z , Zhang W , Yao J , Shang Y , Hao Q , Liu Z , Ren Y , Li J , Zhang G , Wang J
Ref : Journal of Medicinal Chemistry , : , 2020
Abstract : Most of the current MAGL inhibitors function by an irreversible mechanism of action, causing a series of side effects. Herein, starting from irreversible inhibitors, 25 compounds were synthesized and evaluated in vitro for MAGL inhibition, among which, compound 36 showed the most potent inhibitory activity (IC50 = 15 nM).Crucially, docking studies demonstrated that the m-chlorine-substituted aniline fragment occupied a hydrophobic sub-pocket enclosed by side chains of Val191, Tyr194, Val270, and Lys273, which creatively identify a new key anchoring point for the development of new MAGL inhibitors. Furthermore, in vivo evaluation innovatively revealed that this reversible inhibitor 36 significantly displayed the depressive-like behaviors induced by reserpine. To the best of our knowledge, this is the first time that reversible inhibitors of MAGL were developed to support MAGL as a potential therapeutic target for depression.
ESTHER : Zhi_2020_J.Med.Chem__
PubMedSearch : Zhi_2020_J.Med.Chem__
PubMedID: 32429662

Title : A Review of the Pharmacological Properties of Psoralen - Ren_2020_Front.Pharmacol_11_571535
Author(s) : Ren Y , Song X , Tan L , Guo C , Wang M , Liu H , Cao Z , Li Y , Peng C
Ref : Front Pharmacol , 11 :571535 , 2020
Abstract : Psoralen is the principal bioactive component in the dried fruits of Cullen corylifolium (L.) Medik (syn. Psoralea corylifolia L), termed "Buguzhi" in traditional Chinese medicine (TCM). Recent studies have demonstrated that psoralen displays multiple bioactive properties, beneficial for the treatment of osteoporosis, tumors, viruses, bacteria, and inflammation. The present review focuses on the research evidence relating to the properties of psoralen gathered over recent years. Firstly, multiple studies have demonstrated that psoralen exerts strong anti-osteoporotic effects via regulation of osteoblast/osteoclast/chondrocyte differentiation or activation due to the participation in multiple molecular mechanisms of the wnt/beta-catenin, bone morphogenetic protein (BMP), inositol-requiring enzyme 1 (IRE1)/apoptosis signaling kinase 1 (ASK1)/c-jun N-terminal kinase (JNK) and the Protein Kinase B(AKT)/activator protein-1 (AP-1) axis, and the expression of miR-488, peroxisome proliferators-activated receptor-gamma (PPARgamma), and matrix metalloproteinases (MMPs). In addition, the antitumor properties of psoralen are associated with the induction of ER stress-related cell death via enhancement of PERK: Pancreatic Endoplasmic Reticulum Kinase (PERK)/activating transcription factor (ATF), 78kD glucose-regulated protein (GRP78)/C/EBP homologous protein (CHOP), and 94kD glucose-regulated protein (GRP94)/CHOP signaling, and inhibition of P-glycoprotein (P-gp) or ATPase that overcomes multidrug resistance. Furthermore, multiple articles have shown that the antibacterial, anti-inflammatory and neuroprotective effects of psoralen are a result of its interaction with viral polymerase (Pol), destroying the formation of biofilm, and regulating the activation of tumor necrosis factor alpha (TNF-alpha), transforming growth factor beta (TGF-beta), interleukin 4/5/6/8/12/13 (IL-4/5/6/8/12/13), GATA-3, acetylcholinesterase (AChE), and the hypothalamic-pituitary-adrenal (HPA) axis. Finally, the toxic effects and mechanisms of action of psoralen have also been reviewed.
ESTHER : Ren_2020_Front.Pharmacol_11_571535
PubMedSearch : Ren_2020_Front.Pharmacol_11_571535
PubMedID: 33013413

Title : Genome-wide analyses as part of the international FTLD-TDP whole-genome sequencing consortium reveals novel disease risk factors and increases support for immune dysfunction in FTLD - Pottier_2019_Acta.Neuropathol_137_879
Author(s) : Pottier C , Ren Y , Perkerson RB, 3rd , Baker M , Jenkins GD , van Blitterswijk M , DeJesus-Hernandez M , van Rooij JGJ , Murray ME , Christopher E , McDonnell SK , Fogarty Z , Batzler A , Tian S , Vicente CT , Matchett B , Karydas AM , Hsiung GR , Seelaar H , Mol MO , Finger EC , Graff C , Oijerstedt L , Neumann M , Heutink P , Synofzik M , Wilke C , Prudlo J , Rizzu P , Simon-Sanchez J , Edbauer D , Roeber S , Diehl-Schmid J , Evers BM , King A , Mesulam MM , Weintraub S , Geula C , Bieniek KF , Petrucelli L , Ahern GL , Reiman EM , Woodruff BK , Caselli RJ , Huey ED , Farlow MR , Grafman J , Mead S , Grinberg LT , Spina S , Grossman M , Irwin DJ , Lee EB , Suh E , Snowden J , Mann D , Ertekin-Taner N , Uitti RJ , Wszolek ZK , Josephs KA , Parisi JE , Knopman DS , Petersen RC , Hodges JR , Piguet O , Geier EG , Yokoyama JS , Rissman RA , Rogaeva E , Keith J , Zinman L , Tartaglia MC , Cairns NJ , Cruchaga C , Ghetti B , Kofler J , Lopez OL , Beach TG , Arzberger T , Herms J , Honig LS , Vonsattel JP , Halliday GM , Kwok JB , White CL, 3rd , Gearing M , Glass J , Rollinson S , Pickering-Brown S , Rohrer JD , Trojanowski JQ , Van Deerlin V , Bigio EH , Troakes C , Al-Sarraj S , Asmann Y , Miller BL , Graff-Radford NR , Boeve BF , Seeley WW , Mackenzie IRA , van Swieten JC , Dickson DW , Biernacka JM , Rademakers R
Ref : Acta Neuropathologica , 137 :879 , 2019
Abstract : Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) represents the most common pathological subtype of FTLD. We established the international FTLD-TDP whole-genome sequencing consortium to thoroughly characterize the known genetic causes of FTLD-TDP and identify novel genetic risk factors. Through the study of 1131 unrelated Caucasian patients, we estimated that C9orf72 repeat expansions and GRN loss-of-function mutations account for 25.5% and 13.9% of FTLD-TDP patients, respectively. Mutations in TBK1 (1.5%) and other known FTLD genes (1.4%) were rare, and the disease in 57.7% of FTLD-TDP patients was unexplained by the known FTLD genes. To unravel the contribution of common genetic factors to the FTLD-TDP etiology in these patients, we conducted a two-stage association study comprising the analysis of whole-genome sequencing data from 517 FTLD-TDP patients and 838 controls, followed by targeted genotyping of the most associated genomic loci in 119 additional FTLD-TDP patients and 1653 controls. We identified three genome-wide significant FTLD-TDP risk loci: one new locus at chromosome 7q36 within the DPP6 gene led by rs118113626 (p value = 4.82e - 08, OR = 2.12), and two known loci: UNC13A, led by rs1297319 (p value = 1.27e - 08, OR = 1.50) and HLA-DQA2 led by rs17219281 (p value = 3.22e - 08, OR = 1.98). While HLA represents a locus previously implicated in clinical FTLD and related neurodegenerative disorders, the association signal in our study is independent from previously reported associations. Through inspection of our whole-genome sequence data for genes with an excess of rare loss-of-function variants in FTLD-TDP patients (n >/= 3) as compared to controls (n = 0), we further discovered a possible role for genes functioning within the TBK1-related immune pathway (e.g., DHX58, TRIM21, IRF7) in the genetic etiology of FTLD-TDP. Together, our study based on the largest cohort of unrelated FTLD-TDP patients assembled to date provides a comprehensive view of the genetic landscape of FTLD-TDP, nominates novel FTLD-TDP risk loci, and strongly implicates the immune pathway in FTLD-TDP pathogenesis.
ESTHER : Pottier_2019_Acta.Neuropathol_137_879
PubMedSearch : Pottier_2019_Acta.Neuropathol_137_879
PubMedID: 30739198

Title : Comprehensive Molecular Screening in Chinese Usher Syndrome Patients - Sun_2018_Invest.Ophthalmol.Vis.Sci_59_1229
Author(s) : Sun T , Xu K , Ren Y , Xie Y , Zhang X , Tian L , Li Y
Ref : Invest Ophthalmol Vis Sci , 59 :1229 , 2018
Abstract : Purpose: Usher syndrome (USH) refers to a group of autosomal recessive disorders causing deafness and blindness. The objectives of this study were to determine the mutation spectrum in a cohort of Chinese patients with USH and to describe the clinical features of the patients with mutations. Methods: A total of 119 probands who were clinically diagnosed with USH were recruited for genetic analysis. All probands underwent ophthalmic examinations. A combination of molecular screening methods, including targeted next-generation sequencing, Sanger-DNA sequencing, and multiplex ligation probe amplification assay, was used to detect mutations. Results: We found biallelic mutations in 92 probands (77.3%), monoallelic mutations in 5 patients (4.2%), and 1 hemizygous mutation in 1 patient (0.8%), resulting in an overall mutation detection rate of 78.2%. Overall, 132 distinct disease-causing mutations involving seven USH (ABHD12, CDH23, GPR98, MYO7A, PCDH15, USH1C, and USH2A) genes; 5 other retinal degeneration genes (CHM, CNGA1, EYS, PDE6B, and TULP1); and 1 nonsyndromic hearing loss gene (MYO15A) were identified, and 78 were novel. Mutations of MYOA7 were responsible for 60% of USH1 families, followed by PCDH15 (20%) and USH1C (10%). Mutations of USH2A accounted for 67.7% of USH2 families, and mutation c.8559-2A>G was the most frequent one, accounting for 19.1% of the identified USH2A alleles. Conclusions: Our results confirm that the mutation spectrum for each USH gene in Chinese patients differs from those of other populations. The formation of the mutation profile for the Chinese population will enable a precise genetic diagnosis for USH patients in the future.
ESTHER : Sun_2018_Invest.Ophthalmol.Vis.Sci_59_1229
PubMedSearch : Sun_2018_Invest.Ophthalmol.Vis.Sci_59_1229
PubMedID: 29625443
Gene_locus related to this paper: human-ABHD12

Title : Methylotrophic yeast Pichia pastoris as a chassis organism for polyketide synthesis via the full citrinin biosynthetic pathway - Xue_2017_J.Biotechnol_242_64
Author(s) : Xue Y , Kong C , Shen W , Bai C , Ren Y , Zhou X , Zhang Y , Cai M
Ref : J Biotechnol , 242 :64 , 2017
Abstract : With the rapid development of synthetic biology, exploring various chassis organisms has become necessary to improve the heterologous biosynthesis of natural products and pharmaceuticals. In this study, we tested the potential of the industrial methylotrophic yeast strain Pichia pastoris for the heterologous synthesis of polyketides. A recombinant P. pastoris GS-pksCT-npgA carrying the Monascus purpureus citrinin polyketide synthase gene pksCT and the Aspergillus nidulans phosphopantetheinyl transferase gene npgA was constructed. Subsequently, a specific compound was isolated and identified as citrinin intermediate trimethylated pentaketide aldehyde. On account of the hypothetic functions of the genes in the citrinin gene cluster, mpl1 encoding serine hydrolase, mpl2 encoding oxygenase, and mpl4 encoding dehydrogenase were gradually expressed. Proteins were also normally expressed, but a new compound was undetected. Basing on the recently reported citrinin gene cluster in Monascus ruber, we obtained two other genes (mpl6 and mpl7) participating in citrinin biosynthesis by genome walking in M. purpureus. Then, we co-transformed intron-removed mpl6 and mpl7 into the P. pastoris strain carrying pksCT, npgA, mpl1, mpl2, and mpl4. All genes were activated by the methanol-induced AOX1 promoter, and a complete biosynthetic pathway of citrinin was assembled. Finally, citrinin was successfully produced under methanol induction in P. pastoris. These results prove that P. pastoris is a promising chassis organism for polyketide production.
ESTHER : Xue_2017_J.Biotechnol_242_64
PubMedSearch : Xue_2017_J.Biotechnol_242_64
PubMedID: 27913218
Gene_locus related to this paper: monpu-cita

Title : Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes - Sun_2017_Mol.Plant_10_1293
Author(s) : Sun H , Wu S , Zhang G , Jiao C , Guo S , Ren Y , Zhang J , Zhang H , Gong G , Jia Z , Zhang F , Tian J , Lucas WJ , Doyle JJ , Li H , Fei Z , Xu Y
Ref : Mol Plant , 10 :1293 , 2017
Abstract : The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima x C. moschata interspecific F(1) hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.
ESTHER : Sun_2017_Mol.Plant_10_1293
PubMedSearch : Sun_2017_Mol.Plant_10_1293
PubMedID: 28917590
Gene_locus related to this paper: cucma-a0a6j1jlb1 , cucma-a0a6j1i8e2 , cucma-a0a6j1hwl6

Title : Preventative effects of fermented Chimonobambusa quadrangularis shoot on activated carbon-induced constipation - Li_2017_Exp.Ther.Med_13_1093
Author(s) : Li G , Zou X , Kuang G , Ren Y , Deng C , Lin Q , Zhao X , Xu S , Song JL
Ref : Exp Ther Med , 13 :1093 , 2017
Abstract : The present study aimed to determine the preventative effects of fermented Chimonobambusa quadrangularis shoot (FCQS) on activated carbon constipation in Kun Ming mice. FCQS has a more loose fiber tissue structure than unfermented fresh C. quadrangularis shoot (CQS), which is preferable for relieving constipation. In mice fed with FCQS for 9 days the time from consumption to their first black stool defecation (117 min) was shorter than the control group (192 min) and the CQS group (148 min); however, it was longer than the normal (85 min) and bisacodyl treatment (99 min) groups. The gastrointestinal transit of the FCQS group (73.8%) was increased, as compared with the control (37.9%) and CQS (61.7%) groups; however, it was decreased as compared with the normal (100%) and bisacodyl (88.3%) groups. By observing the hemotoxylin and eosin-stained section of mice intestine, it was demonstrated that FCQS reduced injury to the intestinal tract resulting from constipation and alleviated the damage caused to the intestinal villi over the effects observed in the CQS group. Furthermore, FCQS was also able to increase the serum levels of motilin, endothelin-1, vasoactive intestinal peptide and acetylcholinesterase compared with the control group. c-Kit, stem cell factor (SCF), glial cell-derived neurotrophic factor (GDNF) mRNA and protein expression levels in the small intestinal cells of FCQS-fed mice were increased, as compared with CQS-fed mice. Transient receptor potential cation channel subfamily V member 1 (TRPV1) and nitric oxide synthase (NOS) expression levels of small intestinal cells of FCQS-fed mice were reduced, as compared with CQS-fed mice. These findings demonstrated that FCQS may induce improved preventative effects on constipation, compared with CQS.
ESTHER : Li_2017_Exp.Ther.Med_13_1093
PubMedSearch : Li_2017_Exp.Ther.Med_13_1093
PubMedID: 28450948

Title : Serum vitamin D3 does not correlate with liver fibrosis in chronic hepatitis C - Ren_2015_World.J.Gastroenterol_21_11152
Author(s) : Ren Y , Liu M , Zhao J , Ren F , Chen Y , Li JF , Zhang JY , Qu F , Zhang JL , Duan ZP , Zheng SJ
Ref : World J Gastroenterol , 21 :11152 , 2015
Abstract : AIM: To investigate the relationship between serum vitamin D3 levels and liver fibrosis or inflammation in treatment-naive Chinese patients with chronic hepatitis C (CHC).
METHODS: From July 2010 to June 2011, we enrolled 122 CHC patients and 11 healthy controls from Dingxi city, Gansu Province, China. The patients were infected with Hepatitis C virus (HCV) during blood cell re-transfusion following plasma donation in 1992-1995, and had never received antiviral treatment. At present, all the patients except two underwent liver biopsy with ultrasound guidance. The Scheuer Scoring System was used to evaluate hepatic inflammation and the Metavir Scoring System was used to evaluate hepatic fibrosis. Twelve-hour overnight fasting blood samples were collected in the morning of the day of biopsy. Serum levels of alanine aminotransferase, aspartate aminotransferase, total bilirubin, direct bilirubin, cholinesterase, prothrombin activity, albumin, gamma-glutamyl transpeptidase, hemoglobin, calcium and phosphorus were determined. Serum HCV RNA levels were measured by real-time PCR. Serum levels of 25-hydroxyvitamin D3 [25(OH)D3] and 24,25-dihydroxyvitamin D3 [24,25(OH)2D3] were measured by high-performance liquid chromatography tandem mass spectrometry.
RESULTS: Serum levels of 25(OH)D3 but not 24,25(OH)2D3 were significantly lower in CHC patients than in control subjects. Serum 25(OH)D3 levels did not correlate with liver fibrosis, inflammation, patient age, or levels of alanine aminotransferase, aspartate aminotransferase, total bilirubin, direct bilirubin, prothrombin activity, cholinesterase or HCV RNA. However, serum 25(OH)D3 levels did correlate with serum 24,25(OH)2D3 levels. Serum 25(OH)D3 and 24,25(OH)2D3 levels, and the 25(OH)D3/24,25(OH)2D3 ratio, have no difference among the fibrosis stages or inflammation grades. CONCLUSION: We found that serum levels of 25(OH)D3 and its degradation metabolite 24,25(OH)2D3 did not correlate with liver fibrosis in treatment-naive Chinese patient with CHC.
ESTHER : Ren_2015_World.J.Gastroenterol_21_11152
PubMedSearch : Ren_2015_World.J.Gastroenterol_21_11152
PubMedID: 26494969

Title : Structural insights into the specific recognition of N-heterocycle biodenitrogenation-derived substrates by microbial amide hydrolases - Wu_2014_Mol.Microbiol_91_1009
Author(s) : Wu G , Chen D , Tang H , Ren Y , Chen Q , Lv Y , Zhang Z , Zhao YL , Yao Y , Xu P
Ref : Molecular Microbiology , 91 :1009 , 2014
Abstract : N-heterocyclic compounds from industrial wastes, including nicotine, are environmental pollutants or toxicants responsible for a variety of health problems. Microbial biodegradation is an attractive strategy for the removal of N-heterocyclic pollutants, during which carbon-nitrogen bonds in N-heterocycles are converted to amide bonds and subsequently severed by amide hydrolases. Previous studies have failed to clarify the molecular mechanism through which amide hydrolases selectively recognize diverse amide substrates and complete the biodenitrogenation process. In this study, structural, computational and enzymatic analyses showed how the N-formylmaleamate deformylase Nfo and the maleamate amidase Ami, two pivotal amide hydrolases in the nicotine catabolic pathway of Pseudomonas putida S16, specifically recognize their respective substrates. In addition, comparison of the alpha-beta-alpha groups of amidases, which include Ami, pinpointed several subgroup-characteristic residues differentiating the two classes of amide substrates as containing either carboxylate groups or aromatic rings. Furthermore, this study reveals the molecular mechanism through which the specially tailored active sites of deformylases and amidases selectively recognize their unique substrates. Our work thus provides a thorough elucidation of the molecular mechanism through which amide hydrolases accomplish substrate-specific recognition in the microbial N-heterocycles biodenitrogenation pathway.
ESTHER : Wu_2014_Mol.Microbiol_91_1009
PubMedSearch : Wu_2014_Mol.Microbiol_91_1009
PubMedID: 24397579
Gene_locus related to this paper: psep6-f8g0m2

Title : Direct mass spectrometry analysis of biofluid samples using slug-flow microextraction nano-electrospray ionization - Ren_2014_Angew.Chem.Int.Ed.Engl_53_14124
Author(s) : Ren Y , McLuckey MN , Liu J , Ouyang Z
Ref : Angew Chem Int Ed Engl , 53 :14124 , 2014
Abstract : Direct mass spectrometry (MS) analysis of biofluids with simple procedures represents a key step in the translation of MS techniques to clinical and point-of-care applications. The current study reports the development of a single-step method using slug-flow microextraction and nano-electrospray ionization for MS analysis of organic compounds in blood and urine. High sensitivity and quantitation precision have been achieved in the analysis of therapeutic and illicit drugs in 5 muL samples. Real-time chemical derivatization has been incorporated for analyzing anabolic steroids. The monitoring of enzymatic functions has also been demonstrated with cholinesterase in wet blood. The reported study encourages the future development of disposable cartridges, which function with simple operation to replace the traditional complex laboratory procedures for MS analysis of biological samples.
ESTHER : Ren_2014_Angew.Chem.Int.Ed.Engl_53_14124
PubMedSearch : Ren_2014_Angew.Chem.Int.Ed.Engl_53_14124
PubMedID: 25284028

Title : Isolation and characterization of carbendazim-degrading Rhodococcus erythropolis djl-11 - Zhang_2013_PLoS.One_8_e74810
Author(s) : Zhang X , Huang Y , Harvey PR , Li H , Ren Y , Li J , Wang J , Yang H
Ref : PLoS ONE , 8 :e74810 , 2013
Abstract : Carbendazim (methyl 1H-benzimidazol-2-yl carbamate) is one of the most widely used fungicides in agriculture worldwide, but has been reported to have adverse effects on animal health and ecosystem function. A highly efficient carbendazim-degrading bacterium (strain dj1-11) was isolated from carbendazim-contaminated soil samples via enrichment culture. Strain dj1-11 was identified as Rhodococcus erythropolis based on morphological, physiological and biochemical characters, including sequence analysis of the 16S rRNA gene. In vitro degradation of carbendazim (1000 mg.L(-1)) by dj1-11 in minimal salts medium (MSM) was highly efficient, and with an average degradation rate of 333.33 mg.L(-1).d(-1) at 28 degreesC. The optimal temperature range for carbendazim degradation by dj1-11 in MSM was 25-30 degreesC. Whilst strain dj1-11 was capable of metabolizing cabendazim as the sole source of carbon and nitrogen, degradation was significantly (P<0.05) increased by addition of 12.5 mM NH4NO3. Changes in MSM pH (4-9), substitution of NH4NO3 with organic substrates as N and C sources or replacing Mg(2+) with Mn(2+), Zn(2+) or Fe(2+) did not significantly affect carbendazim degradation by dj1-11. During the degradation process, liquid chromatography-mass spectrometry (LC-MS) detected the metabolites 2-aminobenzimidazole and 2-hydroxybenzimidazole. A putative carbendazim-hydrolyzing esterase gene was cloned from chromosomal DNA of djl-11 and showed 99% sequence homology to the mheI carbendazim-hydrolyzing esterase gene from Nocardioides sp. SG-4G.
ESTHER : Zhang_2013_PLoS.One_8_e74810
PubMedSearch : Zhang_2013_PLoS.One_8_e74810
PubMedID: 24098350
Gene_locus related to this paper: 9acto-c8cp46

Title : Draft Genome Sequence of a Benzothiophene-Desulfurizing Bacterium, Gordona terrae Strain C-6 - Wang_2013_Genome.Announc_1_e00381
Author(s) : Wang W , Ma T , Ren Y , Li G
Ref : Genome Announc , 1 : , 2013
Abstract : Gordona terrae strain C-6 was isolated from oil-contaminated soil and is capable of desulfurizing benzothiophene (BT). Here we report the draft genome sequence of G. terrae strain C-6, which may help to reveal the genetic basis of the BT biodesulfurization pathway.
ESTHER : Wang_2013_Genome.Announc_1_e00381
PubMedSearch : Wang_2013_Genome.Announc_1_e00381
PubMedID: 23788548
Gene_locus related to this paper: 9acto-h5ue78 , 9acto-h5ujj3 , 9acto-j9rte6 , 9acto-j9rnp4 , 9acto-h5ui26 , 9actn-r7y6f1 , 9actn-r7ybz2

Title : D14-SCFD3-dependent degradation of D53 regulates strigolactone signalling - Zhou_2013_Nature_504_406
Author(s) : Zhou F , Lin Q , Zhu L , Ren Y , Zhou K , Shabek N , Wu F , Mao H , Dong W , Gan L , Ma W , Gao H , Chen J , Yang C , Wang D , Tan J , Zhang X , Guo X , Wang J , Jiang L , Liu X , Chen W , Chu J , Yan C , Ueno K , Ito S , Asami T , Cheng Z , Lei C , Zhai H , Wu C , Wang H , Zheng N , Wan J
Ref : Nature , 504 :406 , 2013
Abstract : Strigolactones (SLs), a newly discovered class of carotenoid-derived phytohormones, are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Despite the rapid progress in elucidating the SL biosynthetic pathway, the perception and signalling mechanisms of SL remain poorly understood. Here we show that DWARF 53 (D53) acts as a repressor of SL signalling and that SLs induce its degradation. We find that the rice (Oryza sativa) d53 mutant, which produces an exaggerated number of tillers compared to wild-type plants, is caused by a gain-of-function mutation and is insensitive to exogenous SL treatment. The D53 gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with the alpha/beta hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL perception. We demonstrate that, in a D14- and D3-dependent manner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth. Our combined genetic and biochemical data reveal that D53 acts as a repressor of the SL signalling pathway, whose hormone-induced degradation represents a key molecular link between SL perception and responses.
ESTHER : Zhou_2013_Nature_504_406
PubMedSearch : Zhou_2013_Nature_504_406
PubMedID: 24336215

Title : Genomic analysis of Pseudomonas putida: genes in a genome island are crucial for nicotine degradation - Tang_2012_Sci.Rep_2_377
Author(s) : Tang H , Yao Y , Wang L , Yu H , Ren Y , Wu G , Xu P
Ref : Sci Rep , 2 :377 , 2012
Abstract : Nicotine is an important chemical compound in nature that has been regarded as an environmental toxicant causing various preventable diseases. Several bacterial species are adapted to decompose this heterocyclic compound, including Pseudomonas and Arthrobacter. Pseudomonas putida S16 is a bacterium that degrades nicotine through the pyrrolidine pathway, similar to that present in animals. The corresponding late steps of the nicotine degradation pathway in P. putida S16 was first proposed and demonstrated to be from 2,5-dihydroxy-pyridine through the intermediates N-formylmaleamic acid, maleamic acid, maleic acid, and fumaric acid. Genomics of strain S16 revealed that genes located in the largest genome island play a major role in nicotine degradation and may originate from other strains, as suggested by the constructed phylogenetic tree and the results of comparative genomic analysis. The deletion of gene hpo showed that this gene is essential for nicotine degradation. This study defines the mechanism of nicotine degradation.
ESTHER : Tang_2012_Sci.Rep_2_377
PubMedSearch : Tang_2012_Sci.Rep_2_377
PubMedID: 22530095

Title : Facile, high efficiency immobilization of lipase enzyme on magnetic iron oxide nanoparticles via a biomimetic coating - Ren_2011_BMC.Biotechnol_11_63
Author(s) : Ren Y , Rivera JG , He L , Kulkarni H , Lee DK , Messersmith PB
Ref : BMC Biotechnol , 11 :63 , 2011
Abstract : BACKGROUND: Immobilization of lipase on appropriate solid supports is one way to improve their stability and activity, and can be reused for large scale applications. A sample, cost- effective and high loading capacity method is still challenging. RESULTS: A facile method of lipase immobilization was developed in this study, by the use of polydopamine coated magnetic nanoparticles (PD-MNPs). Under optimal conditions, 73.9% of the available lipase was immobilized on PD-MNPs, yielding a lipase loading capacity as high as 429 mg/g. Enzyme assays revealed that lipase immobilized on PD-MNPs displayed enhanced pH and thermal stability compared to free lipase. Furthermore, lipase immobilized on PD-MNPs was easily isolated from the reaction medium by magnetic separation and retained more than 70% of initial activity after 21 repeated cycles of enzyme reaction followed by magnetic separation. CONCLUSIONS: Immobilization of enzyme onto magnetic iron oxide nanoparticles via poly-dopamine film is economical, facile and efficient.
ESTHER : Ren_2011_BMC.Biotechnol_11_63
PubMedSearch : Ren_2011_BMC.Biotechnol_11_63
PubMedID: 21649934

Title : Complete genome sequence of Pusillimonas sp. T7-7, a cold-tolerant diesel oil-degrading bacterium isolated from the Bohai Sea in China - Cao_2011_J.Bacteriol_193_4021
Author(s) : Cao B , Ma T , Ren Y , Li G , Li P , Guo X , Ding P , Feng L
Ref : Journal of Bacteriology , 193 :4021 , 2011
Abstract : Pusillimonas sp. T7-7 is a diesel oil-degrading cold-tolerant bacterium isolated from the benthal mud of a petroleum-contaminated site in Bohai Sea, China. We present here the complete genome sequence of T7-7. Genome analysis revealed many features of typical marine bacteria, including the absence of intact sugar metabolic pathways, the presence of glyoxylate and gluconeogenesis pathways, and the abilities for nitrate assimilation and denitrification, as well as sulfate reduction and sulfite oxidation. The presence of novel genes for the degradation of diesel oils was suggested.
ESTHER : Cao_2011_J.Bacteriol_193_4021
PubMedSearch : Cao_2011_J.Bacteriol_193_4021
PubMedID: 21622753
Gene_locus related to this paper: pusst-f4grw7

Title : Complete genome sequence of Aeromonas veronii strain B565 - Li_2011_J.Bacteriol_193_3389
Author(s) : Li Y , Liu Y , Zhou Z , Huang H , Ren Y , Zhang Y , Li G , Wang L
Ref : Journal of Bacteriology , 193 :3389 , 2011
Abstract : Aeromonas veronii strain B565 was isolated from aquaculture pond sediment in China. We present here the complete genome sequence of B565 and compare it with 2 published genome sequences of pathogenic strains in the Aeromonas genus. The result represents an independent stepwise acquisition of virulence factors of pathogenic strains in this genus.
ESTHER : Li_2011_J.Bacteriol_193_3389
PubMedSearch : Li_2011_J.Bacteriol_193_3389
PubMedID: 21551296
Gene_locus related to this paper: aervb-f4d864 , aervb-f4d9b7 , 9gamm-u1fsk6 , aervb-f4dgq1

Title : Complete genome sequence of a Yersinia enterocolitica Old World (3\/O:9) strain and comparison with the New World (1B\/O:8) strain - Wang_2011_J.Clin.Microbiol_49_1251
Author(s) : Wang X , Li Y , Jing H , Ren Y , Zhou Z , Wang S , Kan B , Xu J , Wang L
Ref : J Clin Microbiol , 49 :1251 , 2011
Abstract : Yersinia enterocolitica is a heterogeneous bacterial species with a wide range of animal reservoirs through which human intestinal illness can be facilitated. In contrast to the epidemiological pattern observed in the United States, infections in China present a pattern similar to those in European countries and Japan, wherein "Old World" strains (biotypes 2 to 5) are prevalent. To gain insights into the evolution of Y. enterocolitica and pathogenic properties toward human hosts, we sequenced the genome of a biotype 3 strain, 105.5R(r) (O:9), obtained from a Chinese patient. Comparative genome sequence analysis with strain 8081 (1B/O:8) revealed new insights into Y. enterocolitica. Both strains have more than 14% specific genes. In strain 105.5R(r), putative virulence factors were found in strain-specific genomic pathogenicity islands that comprised a novel type III secretion system and rtx-like genes. Many of the loci representing ancestral clusters, which are believed to contribute to enteric survival and pathogenesis, are present in strain 105.5R(r) but lost in strain 8081. Insertion elements in 105.5R(r) have a pattern distinct from those in strain 8081 and were exclusively located in a strain-specific region. In summary, our comparative genome analysis indicates that these two strains may have attained their pathogenicity by completely separate evolutionary events, and the 105.5R(r) strain, a representative of the Old World biogroup, lies in a branch of Y. enterocolitica that is distinct from the "New World" 8081 strain.
ESTHER : Wang_2011_J.Clin.Microbiol_49_1251
PubMedSearch : Wang_2011_J.Clin.Microbiol_49_1251
PubMedID: 21325549
Gene_locus related to this paper: yere8-menh , yere8-y3204 , yeren-YqiA , yeren-k1bwy7

Title : Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation - Yang_2011_PLoS.Pathog_7_e1002179
Author(s) : Yang J , Wang L , Ji X , Feng Y , Li X , Zou C , Xu J , Ren Y , Mi Q , Wu J , Liu S , Liu Y , Huang X , Wang H , Niu X , Li J , Liang L , Luo Y , Ji K , Zhou W , Yu Z , Li G , Li L , Qiao M , Feng L , Zhang KQ
Ref : PLoS Pathog , 7 :e1002179 , 2011
Abstract : Nematode-trapping fungi are "carnivorous" and attack their hosts using specialized trapping devices. The morphological development of these traps is the key indicator of their switch from saprophytic to predacious lifestyles. Here, the genome of the nematode-trapping fungus Arthrobotrys oligospora Fres. (ATCC24927) was reported. The genome contains 40.07 Mb assembled sequence with 11,479 predicted genes. Comparative analysis showed that A. oligospora shared many more genes with pathogenic fungi than with non-pathogenic fungi. Specifically, compared to several sequenced ascomycete fungi, the A. oligospora genome has a larger number of pathogenicity-related genes in the subtilisin, cellulase, cellobiohydrolase, and pectinesterase gene families. Searching against the pathogen-host interaction gene database identified 398 homologous genes involved in pathogenicity in other fungi. The analysis of repetitive sequences provided evidence for repeat-induced point mutations in A. oligospora. Proteomic and quantitative PCR (qPCR) analyses revealed that 90 genes were significantly up-regulated at the early stage of trap-formation by nematode extracts and most of these genes were involved in translation, amino acid metabolism, carbohydrate metabolism, cell wall and membrane biogenesis. Based on the combined genomic, proteomic and qPCR data, a model for the formation of nematode trapping device in this fungus was proposed. In this model, multiple fungal signal transduction pathways are activated by its nematode prey to further regulate downstream genes associated with diverse cellular processes such as energy metabolism, biosynthesis of the cell wall and adhesive proteins, cell division, glycerol accumulation and peroxisome biogenesis. This study will facilitate the identification of pathogenicity-related genes and provide a broad foundation for understanding the molecular and evolutionary mechanisms underlying fungi-nematodes interactions.
ESTHER : Yang_2011_PLoS.Pathog_7_e1002179
PubMedSearch : Yang_2011_PLoS.Pathog_7_e1002179
PubMedID: 21909256
Gene_locus related to this paper: artoa-g1wyr4 , artoa-g1x1a7 , artoa-g1x3f4 , artoa-g1x3h6 , artoa-g1x9s5 , artoa-g1x9z4 , artoa-g1xcb5 , artoa-g1xhl6 , artoa-g1xjb3 , artoa-g1xjy0 , artoa-g1xkw3 , artoa-g1xnf2 , artoa-g1xnf8 , artoa-g1xqd4 , artoa-g1xqt1 , artoa-g1xte8 , artoa-g1xu91 , artoa-g1xv59 , artoa-g1x382 , artoa-g1x3q3 , artoa-g1wxl5 , artoa-g1xj75 , artoa-g1xd25 , artoa-g1wzu7 , artoa-g1xt42 , artoa-g1xhm8 , artoa-g1wy43

Title : Rates of mutation and host transmission for an Escherichia coli clone over 3 years - Reeves_2011_PLoS.One_6_e26907
Author(s) : Reeves PR , Liu B , Zhou Z , Li D , Guo D , Ren Y , Clabots C , Lan R , Johnson JR , Wang L
Ref : PLoS ONE , 6 :e26907 , 2011
Abstract : Although over 50 complete Escherichia coli/Shigella genome sequences are available, it is only for closely related strains, for example the O55:H7 and O157:H7 clones of E. coli, that we can assign differences to individual evolutionary events along specific lineages. Here we sequence the genomes of 14 isolates of a uropathogenic E. coli clone that persisted for 3 years within a household, including a dog, causing a urinary tract infection (UTI) in the dog after 2 years. The 20 mutations observed fit a single tree that allows us to estimate the mutation rate to be about 1.1 per genome per year, with minimal evidence for adaptive change, including in relation to the UTI episode. The host data also imply at least 6 host transfer events over the 3 years, with 2 lineages present over much of that period. To our knowledge, these are the first direct measurements for a clone in a well-defined host community that includes rates of mutation and host transmission. There is a concentration of non-synonymous mutations associated with 2 transfers to the dog, suggesting some selection pressure from the change of host. However, there are no changes to which we can attribute the UTI event in the dog, which suggests that this occurrence after 2 years of the clone being in the household may have been due to chance, or some unknown change in the host or environment. The ability of a UTI strain to persist for 2 years and also to transfer readily within a household has implications for epidemiology, diagnosis, and clinical intervention.
ESTHER : Reeves_2011_PLoS.One_6_e26907
PubMedSearch : Reeves_2011_PLoS.One_6_e26907
PubMedID: 22046404
Gene_locus related to this paper: ecoli-ybff , ecoli-ycfp , ecoli-YFBB , ecoli-yqia

Title : Derivation of Escherichia coli O157:H7 from its O55:H7 precursor - Zhou_2010_PLoS.One_5_e8700
Author(s) : Zhou Z , Li X , Liu B , Beutin L , Xu J , Ren Y , Feng L , Lan R , Reeves PR , Wang L
Ref : PLoS ONE , 5 :e8700 , 2010
Abstract : There are 29 E. coli genome sequences available, mostly related to studies of species diversity or mode of pathogenicity, including two genomes of the well-known O157:H7 clone. However, there have been no genome studies of closely related clones aimed at exposing the details of evolutionary change. Here we sequenced the genome of an O55:H7 strain, closely related to the major pathogenic O157:H7 clone, with published genome sequences, and undertook comparative genomic and proteomic analysis. We were able to allocate most differences between the genomes to individual mutations, recombination events, or lateral gene transfer events, in specific lineages. Major differences include a type II secretion system present only in the O55:H7 chromosome, fewer type III secretion system effectors in O55:H7, and 19 phage genomes or phagelike elements in O55:H7 compared to 23 in O157:H7, with only three common to both. Many other changes were found in both O55:H7 and O157:H7 lineages, but in general there has been more change in the O157:H7 lineages. For example, we found 50% more synonymous mutational substitutions in O157:H7 compared to O55:H7. The two strains also diverged at the proteomic level. Mutational synonymous SNPs were used to estimate a divergence time of 400 years using a new clock rate, in contrast to 14,000 to 70,000 years using the traditional clock rates. The same approaches were applied to three closely related extraintestinal pathogenic E. coli genomes, and similar levels of mutation and recombination were found. This study revealed for the first time the full range of events involved in the evolution of the O157:H7 clone from its O55:H7 ancestor, and suggested that O157:H7 arose quite recently. Our findings also suggest that E. coli has a much lower frequency of recombination relative to mutation than was observed in a comparable study of a Vibrio cholerae lineage.
ESTHER : Zhou_2010_PLoS.One_5_e8700
PubMedSearch : Zhou_2010_PLoS.One_5_e8700
PubMedID: 20090843
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-Z0347 , ecoli-Z1930 , ecoli-Z2445 , ecoli-YfhR

Title : Complete genome sequence of probiotic Bifidobacterium animalis subsp. lactis strain V9 - Sun_2010_J.Bacteriol_192_4080
Author(s) : Sun Z , Chen X , Wang J , Gao P , Zhou Z , Ren Y , Sun T , Wang L , Meng H , Chen W , Zhang H
Ref : Journal of Bacteriology , 192 :4080 , 2010
Abstract : Bifidobacterium animalis subsp. lactis strain V9 is a Chinese commercial bifidobacteria with several probiotic functions. It was isolated from a healthy Mongolian child in China. We present here the complete genome sequence of V9 and compare it to 3 other published genome sequences of B. animalis subsp. lactis strains. The result indicates the lack of polymorphism among strains of this subspecies from different continents.
ESTHER : Sun_2010_J.Bacteriol_192_4080
PubMedSearch : Sun_2010_J.Bacteriol_192_4080
PubMedID: 20511504
Gene_locus related to this paper: bifan-b2ea73 , bifan-b2eam2 , bifan-b2eck9 , biflb-c6a5u1 , bifa0-b8dw94 , bifan-b2e8c8

Title : Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047 - Ren_2010_J.Bacteriol_192_2463
Author(s) : Ren Y , Zhou Z , Guo X , Li Y , Feng L , Wang L
Ref : Journal of Bacteriology , 192 :2463 , 2010
Abstract : Enterobacter cloacae is an important nosocomial pathogen. Here, we report the completion of the genome sequence of E. cloacae ATCC 13047, the type strain of E. cloacae subsp. cloacae. Multiple sets of virulence determinant and heavy-metal resistance genes have been found in the genome. To the best of our knowledge, this is the first complete genome sequence of the E. cloacae species.
ESTHER : Ren_2010_J.Bacteriol_192_2463
PubMedSearch : Ren_2010_J.Bacteriol_192_2463
PubMedID: 20207761
Gene_locus related to this paper: ent38-y765 , entcc-d5c8z5 , entcc-d5c650 , entcl-g8lek8 , entcc-a0a0h3cfu5 , entcc-a0a0h3cpr3 , entcc-rutd

Title : The sequence and de novo assembly of the giant panda genome - Li_2010_Nature_463_311
Author(s) : Li R , Fan W , Tian G , Zhu H , He L , Cai J , Huang Q , Cai Q , Li B , Bai Y , Zhang Z , Zhang Y , Wang W , Li J , Wei F , Li H , Jian M , Nielsen R , Li D , Gu W , Yang Z , Xuan Z , Ryder OA , Leung FC , Zhou Y , Cao J , Sun X , Fu Y , Fang X , Guo X , Wang B , Hou R , Shen F , Mu B , Ni P , Lin R , Qian W , Wang G , Yu C , Nie W , Wang J , Wu Z , Liang H , Min J , Wu Q , Cheng S , Ruan J , Wang M , Shi Z , Wen M , Liu B , Ren X , Zheng H , Dong D , Cook K , Shan G , Zhang H , Kosiol C , Xie X , Lu Z , Li Y , Steiner CC , Lam TT , Lin S , Zhang Q , Li G , Tian J , Gong T , Liu H , Zhang D , Fang L , Ye C , Zhang J , Hu W , Xu A , Ren Y , Zhang G , Bruford MW , Li Q , Ma L , Guo Y , An N , Hu Y , Zheng Y , Shi Y , Li Z , Liu Q , Chen Y , Zhao J , Qu N , Zhao S , Tian F , Wang X , Wang H , Xu L , Liu X , Vinar T , Wang Y , Lam TW , Yiu SM , Liu S , Huang Y , Yang G , Jiang Z , Qin N , Li L , Bolund L , Kristiansen K , Wong GK , Olson M , Zhang X , Li S , Yang H
Ref : Nature , 463 :311 , 2010
Abstract : Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.
ESTHER : Li_2010_Nature_463_311
PubMedSearch : Li_2010_Nature_463_311
PubMedID: 20010809
Gene_locus related to this paper: ailme-ABH15 , ailme-ACHE , ailme-BCHE , ailme-d2gtv3 , ailme-d2gty9 , ailme-d2gu87 , ailme-d2gu97 , ailme-d2gve7 , ailme-d2gwu1 , ailme-d2gx08 , ailme-d2gyt0 , ailme-d2gz36 , ailme-d2gz37 , ailme-d2gz38 , ailme-d2gz39 , ailme-d2gz40 , ailme-d2h5r9 , ailme-d2h7b7 , ailme-d2h9c9 , ailme-d2h794 , ailme-d2hau7 , ailme-d2hau8 , ailme-d2hcd9 , ailme-d2hdi6 , ailme-d2heu6 , ailme-d2hga4 , ailme-d2hqw5 , ailme-d2hs98 , ailme-d2hsx4 , ailme-d2hti6 , ailme-d2htv3 , ailme-d2htz6 , ailme-d2huc7 , ailme-d2hwj8 , ailme-d2hwy7 , ailme-d2hxm1 , ailme-d2hyc8 , ailme-d2hyv2 , ailme-d2hz11 , ailme-d2hza3 , ailme-d2hzr4 , ailme-d2i1l4 , ailme-d2i2g8 , ailme-g1l7m3 , ailme-g1lu36 , ailme-g1m769 , ailme-g1mc29 , ailme-g1mdj8 , ailme-g1mdr5 , ailme-g1mfp4 , ailme-g1mfx5 , ailme-g1lj41 , ailme-g1lm28 , ailme-g1l3u1 , ailme-g1l7l1 , ailme-g1m5i3 , ailme-g1l2f6 , ailme-g1lji5 , ailme-g1lqk3 , ailme-g1l8s9 , ailme-d2h717 , ailme-d2h718 , ailme-d2h719 , ailme-d2h720 , ailme-g1m5v0 , ailme-g1m5y7 , ailme-g1lkt7 , ailme-g1l2a1 , ailme-g1lsc8 , ailme-g1lrp4 , ailme-d2gv02 , ailme-g1mik5 , ailme-g1ljr1 , ailme-g1lxw7 , ailme-d2h8b5 , ailme-d2h2r2 , ailme-d2h9w7 , ailme-g1meh3 , ailme-g1m719

Title : Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12 - Ferenci_2009_J.Bacteriol_191_4025
Author(s) : Ferenci T , Zhou Z , Betteridge T , Ren Y , Liu Y , Feng L , Reeves PR , Wang L
Ref : Journal of Bacteriology , 191 :4025 , 2009
Abstract : The genome of an Escherichia coli MC4100 strain with a lambda placMu50 fusion revealed numerous regulatory differences from MG1655, including one that arose during laboratory storage. The 194 mutational differences between MC4100(MuLac) and other K-12 sequences were mostly allocated to specific lineages, indicating the considerable mutational divergence between K-12 strains.
ESTHER : Ferenci_2009_J.Bacteriol_191_4025
PubMedSearch : Ferenci_2009_J.Bacteriol_191_4025
PubMedID: 19376874
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-YfhR

Title : The genome of the cucumber, Cucumis sativus L - Huang_2009_Nat.Genet_41_1275
Author(s) : Huang S , Li R , Zhang Z , Li L , Gu X , Fan W , Lucas WJ , Wang X , Xie B , Ni P , Ren Y , Zhu H , Li J , Lin K , Jin W , Fei Z , Li G , Staub J , Kilian A , van der Vossen EA , Wu Y , Guo J , He J , Jia Z , Tian G , Lu Y , Ruan J , Qian W , Wang M , Huang Q , Li B , Xuan Z , Cao J , Asan , Wu Z , Zhang J , Cai Q , Bai Y , Zhao B , Han Y , Li Y , Li X , Wang S , Shi Q , Liu S , Cho WK , Kim JY , Xu Y , Heller-Uszynska K , Miao H , Cheng Z , Zhang S , Wu J , Yang Y , Kang H , Li M , Liang H , Ren X , Shi Z , Wen M , Jian M , Yang H , Zhang G , Yang Z , Chen R , Ma L , Liu H , Zhou Y , Zhao J , Fang X , Fang L , Liu D , Zheng H , Zhang Y , Qin N , Li Z , Yang G , Yang S , Bolund L , Kristiansen K , Li S , Zhang X , Wang J , Sun R , Zhang B , Jiang S , Du Y
Ref : Nat Genet , 41 :1275 , 2009
Abstract : Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.
ESTHER : Huang_2009_Nat.Genet_41_1275
PubMedSearch : Huang_2009_Nat.Genet_41_1275
PubMedID: 19881527
Gene_locus related to this paper: cucsa-a0a0a0ktw5 , cucsa-a0a0a0lnt6 , cucsa-a0a0a0kpn7 , cucsa-a0a0a0lvt9 , cucsa-a0a0a0kdx8 , cucsa-a0a0a0m228 , cucsa-a0a0a0kz31 , cucsa-a0a0a0k5t5 , cucsa-a0a0a0kfs7 , cucsa-a0a0a0kjj7 , cucsa-a0a0a0kzs7 , cucsa-a0a0a0l0a6 , cucsa-a0a0a0l4w4 , cucsa-a0a0a0lpz0 , cucsa-a0a0a0ls66

Title : An integrated genetic and cytogenetic map of the cucumber genome - Ren_2009_PLoS.One_4_e5795
Author(s) : Ren Y , Zhang Z , Liu J , Staub JE , Han Y , Cheng Z , Li X , Lu J , Miao H , Kang H , Xie B , Gu X , Wang X , Du Y , Jin W , Huang S
Ref : PLoS ONE , 4 :e5795 , 2009
Abstract : The Cucurbitaceae includes important crops such as cucumber, melon, watermelon, squash and pumpkin. However, few genetic and genomic resources are available for plant improvement. Some cucurbit species such as cucumber have a narrow genetic base, which impedes construction of saturated molecular linkage maps. We report herein the development of highly polymorphic simple sequence repeat (SSR) markers originated from whole genome shotgun sequencing and the subsequent construction of a high-density genetic linkage map. This map includes 995 SSRs in seven linkage groups which spans in total 573 cM, and defines approximately 680 recombination breakpoints with an average of 0.58 cM between two markers. These linkage groups were then assigned to seven corresponding chromosomes using fluorescent in situ hybridization (FISH). FISH assays also revealed a chromosomal inversion between Cucumis subspecies [C. sativus var. sativus L. and var. hardwickii (R.) Alef], which resulted in marker clustering on the genetic map. A quarter of the mapped markers showed relatively high polymorphism levels among 11 inbred lines of cucumber. Among the 995 markers, 49%, 26% and 22% were conserved in melon, watermelon and pumpkin, respectively. This map will facilitate whole genome sequencing, positional cloning, and molecular breeding in cucumber, and enable the integration of knowledge of gene and trait in cucurbits.
ESTHER : Ren_2009_PLoS.One_4_e5795
PubMedSearch : Ren_2009_PLoS.One_4_e5795
PubMedID: 19495411
Gene_locus related to this paper: cucsa-a0a0a0ktw5 , cucsa-a0a0a0lnt6 , cucsa-a0a0a0kpn7 , cucsa-a0a0a0lvt9 , cucsa-a0a0a0kdx8 , cucsa-a0a0a0m228 , cucsa-a0a0a0kz31 , cucsa-a0a0a0k5t5 , cucsa-a0a0a0kfs7 , cucsa-a0a0a0kjj7 , cucsa-a0a0a0kzs7 , cucsa-a0a0a0l0a6 , cucsa-a0a0a0l4w4 , cucsa-a0a0a0lpz0

Title : The genome sequence of taurine cattle: a window to ruminant biology and evolution - Elsik_2009_Science_324_522
Author(s) : Elsik CG , Tellam RL , Worley KC , Gibbs RA , Muzny DM , Weinstock GM , Adelson DL , Eichler EE , Elnitski L , Guigo R , Hamernik DL , Kappes SM , Lewin HA , Lynn DJ , Nicholas FW , Reymond A , Rijnkels M , Skow LC , Zdobnov EM , Schook L , Womack J , Alioto T , Antonarakis SE , Astashyn A , Chapple CE , Chen HC , Chrast J , Camara F , Ermolaeva O , Henrichsen CN , Hlavina W , Kapustin Y , Kiryutin B , Kitts P , Kokocinski F , Landrum M , Maglott D , Pruitt K , Sapojnikov V , Searle SM , Solovyev V , Souvorov A , Ucla C , Wyss C , Anzola JM , Gerlach D , Elhaik E , Graur D , Reese JT , Edgar RC , McEwan JC , Payne GM , Raison JM , Junier T , Kriventseva EV , Eyras E , Plass M , Donthu R , Larkin DM , Reecy J , Yang MQ , Chen L , Cheng Z , Chitko-McKown CG , Liu GE , Matukumalli LK , Song J , Zhu B , Bradley DG , Brinkman FS , Lau LP , Whiteside MD , Walker A , Wheeler TT , Casey T , German JB , Lemay DG , Maqbool NJ , Molenaar AJ , Seo S , Stothard P , Baldwin CL , Baxter R , Brinkmeyer-Langford CL , Brown WC , Childers CP , Connelley T , Ellis SA , Fritz K , Glass EJ , Herzig CT , Iivanainen A , Lahmers KK , Bennett AK , Dickens CM , Gilbert JG , Hagen DE , Salih H , Aerts J , Caetano AR , Dalrymple B , Garcia JF , Gill CA , Hiendleder SG , Memili E , Spurlock D , Williams JL , Alexander L , Brownstein MJ , Guan L , Holt RA , Jones SJ , Marra MA , Moore R , Moore SS , Roberts A , Taniguchi M , Waterman RC , Chacko J , Chandrabose MM , Cree A , Dao MD , Dinh HH , Gabisi RA , Hines S , Hume J , Jhangiani SN , Joshi V , Kovar CL , Lewis LR , Liu YS , Lopez J , Morgan MB , Nguyen NB , Okwuonu GO , Ruiz SJ , Santibanez J , Wright RA , Buhay C , Ding Y , Dugan-Rocha S , Herdandez J , Holder M , Sabo A , Egan A , Goodell J , Wilczek-Boney K , Fowler GR , Hitchens ME , Lozado RJ , Moen C , Steffen D , Warren JT , Zhang J , Chiu R , Schein JE , Durbin KJ , Havlak P , Jiang H , Liu Y , Qin X , Ren Y , Shen Y , Song H , Bell SN , Davis C , Johnson AJ , Lee S , Nazareth LV , Patel BM , Pu LL , Vattathil S , Williams RL, Jr. , Curry S , Hamilton C , Sodergren E , Wheeler DA , Barris W , Bennett GL , Eggen A , Green RD , Harhay GP , Hobbs M , Jann O , Keele JW , Kent MP , Lien S , McKay SD , McWilliam S , Ratnakumar A , Schnabel RD , Smith T , Snelling WM , Sonstegard TS , Stone RT , Sugimoto Y , Takasuga A , Taylor JF , Van Tassell CP , Macneil MD , Abatepaulo AR , Abbey CA , Ahola V , Almeida IG , Amadio AF , Anatriello E , Bahadue SM , Biase FH , Boldt CR , Carroll JA , Carvalho WA , Cervelatti EP , Chacko E , Chapin JE , Cheng Y , Choi J , Colley AJ , de Campos TA , De Donato M , Santos IK , de Oliveira CJ , Deobald H , Devinoy E , Donohue KE , Dovc P , Eberlein A , Fitzsimmons CJ , Franzin AM , Garcia GR , Genini S , Gladney CJ , Grant JR , Greaser ML , Green JA , Hadsell DL , Hakimov HA , Halgren R , Harrow JL , Hart EA , Hastings N , Hernandez M , Hu ZL , Ingham A , Iso-Touru T , Jamis C , Jensen K , Kapetis D , Kerr T , Khalil SS , Khatib H , Kolbehdari D , Kumar CG , Kumar D , Leach R , Lee JC , Li C , Logan KM , Malinverni R , Marques E , Martin WF , Martins NF , Maruyama SR , Mazza R , McLean KL , Medrano JF , Moreno BT , More DD , Muntean CT , Nandakumar HP , Nogueira MF , Olsaker I , Pant SD , Panzitta F , Pastor RC , Poli MA , Poslusny N , Rachagani S , Ranganathan S , Razpet A , Riggs PK , Rincon G , Rodriguez-Osorio N , Rodriguez-Zas SL , Romero NE , Rosenwald A , Sando L , Schmutz SM , Shen L , Sherman L , Southey BR , Lutzow YS , Sweedler JV , Tammen I , Telugu BP , Urbanski JM , Utsunomiya YT , Verschoor CP , Waardenberg AJ , Wang Z , Ward R , Weikard R , Welsh TH, Jr. , White SN , Wilming LG , Wunderlich KR , Yang J , Zhao FQ
Ref : Science , 324 :522 , 2009
Abstract : To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
ESTHER : Elsik_2009_Science_324_522
PubMedSearch : Elsik_2009_Science_324_522
PubMedID: 19390049
Gene_locus related to this paper: bovin-2neur , bovin-a0jnh8 , bovin-a5d7b7 , bovin-ACHE , bovin-balip , bovin-dpp4 , bovin-dpp6 , bovin-e1bi31 , bovin-e1bn79 , bovin-est8 , bovin-f1mbd6 , bovin-f1mi11 , bovin-f1mr65 , bovin-f1n1l4 , bovin-g3mxp5 , bovin-q0vcc8 , bovin-q2kj30 , bovin-q3t0r6 , bovin-thyro

Title : Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia - Hou_2008_Biol.Direct_3_26
Author(s) : Hou S , Makarova KS , Saw JH , Senin P , Ly BV , Zhou Z , Ren Y , Wang J , Galperin MY , Omelchenko MV , Wolf YI , Yutin N , Koonin EV , Stott MB , Mountain BW , Crowe MA , Smirnova AV , Dunfield PF , Feng L , Wang L , Alam M
Ref : Biol Direct , 3 :26 , 2008
Abstract : BACKGROUND: The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. RESULTS: We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins. CONCLUSION: The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria. REVIEWERS: This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.
ESTHER : Hou_2008_Biol.Direct_3_26
PubMedSearch : Hou_2008_Biol.Direct_3_26
PubMedID: 18593465
Gene_locus related to this paper: meti4-b3dw86 , meti4-b3dx04

Title : Comparison of acetylcholinesterase from three field populations of Liposcelis paeta Pearman (Psocoptera: Liposcelididae): Implications of insecticide resistance - Ren_2008_Pestic.Biochem.Physiol_90_196
Author(s) : Ren Y , Wei X-Q , Wu S , Dou W , Wang J-J
Ref : Pesticide Biochemistry and Physiology , 90 :196 , 2008
Abstract : The toxicological and biochemical characteristics of acetylcholinesterases (AChE) in Liposcelis paeta Pearman were investigated in three field populations collected from Nanyang city of Henan Province (NY), Wuzhou (WZ) and Hezhou (HZ) Cities of Guangxi Province, China. The result of bioassay showed that the LC50s of the NY (281.4802 mg/m2) and the WZ (285.0655 mg/m2) to dichlorvos were 1.156-fold and 1.171-fold higher than that of the HZ (243.5197 mg/m2), respectively. Compared to NY population, the activity per insect and the specific activity of AChE in WZ and HZ populations were significantly higher, and significant kinetic differences among the three populations were also observed. The apparent Michaelis-Menten constant (Km) for acetylthiocholine iodide (ATChI) was obviously lower in NY than that in WZ and HZ populations, indicating a higher affinity to the substrate ATChI in the NY population. The affinity to the substrate ATChI between WZ and HZ population was also significantly different. As for Vmax, the values of WZ and HZ populations were significantly greater when compared to that for NY population, suggesting a possible over expression of AChE in the former two populations. The inhibition studies of AChE indicated that paraoxon-ethyl, demeton-S-methyl, carbaryl, and eserine all possessed some inhibitory effects on AChE in L. paeta. The results of I50S suggested that when compared to the other two populations, while AChE from HZ population was less sensitive to paraoxon-ethyl and demeton-S-methyl. The contradiction with the result of the bioassay might be due to the different insecticides used in the bioassay. Although both carbaryl and eserine had excellent inhibitory effects, there was no significant difference among the three populations. The statistical analysis of the bimolecular rate constants (ki) was consistent with the above situation that carbamates expressed remarkable inhibitory effects. It was noticeable that NY population was most sensitive to carbaryl while least to eserine. The differences in AChE among three populations may attribute to the difference in control practices for psocids between Henan and Guangxi Provinces.
ESTHER : Ren_2008_Pestic.Biochem.Physiol_90_196
PubMedSearch : Ren_2008_Pestic.Biochem.Physiol_90_196
PubMedID:
Gene_locus related to this paper: 9neop-D2KI31

Title : A recalibrated molecular clock and independent origins for the cholera pandemic clones - Feng_2008_PLoS.One_3_e4053
Author(s) : Feng L , Reeves PR , Lan R , Ren Y , Gao C , Zhou Z , Cheng J , Wang W , Wang J , Qian W , Li D , Wang L
Ref : PLoS ONE , 3 :e4053 , 2008
Abstract : Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6(th) (1899-1923) and 7(th) (1961-present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7(th) pandemic clone, while the 6(th) pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6(th) pandemic isolate, and compared them with the published 7(th) pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7(th) pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed. We then used this to estimate the divergence date of the 6(th) and 7(th) pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000-50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.
ESTHER : Feng_2008_PLoS.One_3_e4053
PubMedSearch : Feng_2008_PLoS.One_3_e4053
PubMedID: 19115014
Gene_locus related to this paper: vibch-VC1974 , vibch-VC2610 , vibch-VC2718 , vibch-y1892 , vibch-y2276

Title : Novel mutations of the lipoprotein lipase gene associated with hypertriglyceridemia in members of type 2 diabetic pedigrees - Hu_2007_J.Lipid.Res_48_1681
Author(s) : Hu Y , Ren Y , Luo RZ , Mao X , Li X , Cao X , Guan L , Chen X , Li J , Long Y , Zhang X , Tian H
Ref : J Lipid Res , 48 :1681 , 2007
Abstract : Increased plasma triglyceride and free fatty acid levels are frequently associated with type 2 diabetes mellitus (T2DM). To test the hypothesis that LPL gene mutations contribute to the hypertriglyceridemia observed in members of T2DM pedigrees, we screened the LPL gene in 53 hypertriglyceridemic members of 26 families. Four known and three novel mutations were identified. All three novel mutations, Lys312insC, Thr361insA, and double mutation Lys312insC + Asn291Ser, are clinically associated with hypertriglyceridemia. In vitro mutagenesis and expression studies confirm that these variants are associated with a significant reduction in LPL activity. The modeled structures displaying the Lys312insC and Thr361insA mutations showed loss of the activity-related C-terminal domain in the LPL protein. Another novel double mutation, Lys312insC + Asn291Ser, resulted in the loss of the catalytic ability of LPL attributable to the complete loss of the C-terminal domain and alteration in the heparin association site. Thus, these novel mutations of the LPL gene contribute to the hypertriglyceridemia observed in members of type 2 diabetic pedigrees.
ESTHER : Hu_2007_J.Lipid.Res_48_1681
PubMedSearch : Hu_2007_J.Lipid.Res_48_1681
PubMedID: 17476032

Title : Evolutionary and biomedical insights from the rhesus macaque genome - Gibbs_2007_Science_316_222
Author(s) : Gibbs RA , Rogers J , Katze MG , Bumgarner R , Weinstock GM , Mardis ER , Remington KA , Strausberg RL , Venter JC , Wilson RK , Batzer MA , Bustamante CD , Eichler EE , Hahn MW , Hardison RC , Makova KD , Miller W , Milosavljevic A , Palermo RE , Siepel A , Sikela JM , Attaway T , Bell S , Bernard KE , Buhay CJ , Chandrabose MN , Dao M , Davis C , Delehaunty KD , Ding Y , Dinh HH , Dugan-Rocha S , Fulton LA , Gabisi RA , Garner TT , Godfrey J , Hawes AC , Hernandez J , Hines S , Holder M , Hume J , Jhangiani SN , Joshi V , Khan ZM , Kirkness EF , Cree A , Fowler RG , Lee S , Lewis LR , Li Z , Liu YS , Moore SM , Muzny D , Nazareth LV , Ngo DN , Okwuonu GO , Pai G , Parker D , Paul HA , Pfannkoch C , Pohl CS , Rogers YH , Ruiz SJ , Sabo A , Santibanez J , Schneider BW , Smith SM , Sodergren E , Svatek AF , Utterback TR , Vattathil S , Warren W , White CS , Chinwalla AT , Feng Y , Halpern AL , Hillier LW , Huang X , Minx P , Nelson JO , Pepin KH , Qin X , Sutton GG , Venter E , Walenz BP , Wallis JW , Worley KC , Yang SP , Jones SM , Marra MA , Rocchi M , Schein JE , Baertsch R , Clarke L , Csuros M , Glasscock J , Harris RA , Havlak P , Jackson AR , Jiang H , Liu Y , Messina DN , Shen Y , Song HX , Wylie T , Zhang L , Birney E , Han K , Konkel MK , Lee J , Smit AF , Ullmer B , Wang H , Xing J , Burhans R , Cheng Z , Karro JE , Ma J , Raney B , She X , Cox MJ , Demuth JP , Dumas LJ , Han SG , Hopkins J , Karimpour-Fard A , Kim YH , Pollack JR , Vinar T , Addo-Quaye C , Degenhardt J , Denby A , Hubisz MJ , Indap A , Kosiol C , Lahn BT , Lawson HA , Marklein A , Nielsen R , Vallender EJ , Clark AG , Ferguson B , Hernandez RD , Hirani K , Kehrer-Sawatzki H , Kolb J , Patil S , Pu LL , Ren Y , Smith DG , Wheeler DA , Schenck I , Ball EV , Chen R , Cooper DN , Giardine B , Hsu F , Kent WJ , Lesk A , Nelson DL , O'Brien W E , Prufer K , Stenson PD , Wallace JC , Ke H , Liu XM , Wang P , Xiang AP , Yang F , Barber GP , Haussler D , Karolchik D , Kern AD , Kuhn RM , Smith KE , Zwieg AS
Ref : Science , 316 :222 , 2007
Abstract : The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
ESTHER : Gibbs_2007_Science_316_222
PubMedSearch : Gibbs_2007_Science_316_222
PubMedID: 17431167
Gene_locus related to this paper: macmu-3neur , macmu-ACHE , macmu-BCHE , macmu-f6rul6 , macmu-f6sz31 , macmu-f6the6 , macmu-f6unj2 , macmu-f6wtx1 , macmu-f6zkq5 , macmu-f7aa58 , macmu-f7ai42 , macmu-f7aim4 , macmu-f7buk8 , macmu-f7cfi8 , macmu-f7cnr2 , macmu-f7cu68 , macmu-f7flv1 , macmu-f7ggk1 , macmu-f7hir7 , macmu-g7n054 , macmu-KANSL3 , macmu-TEX30 , macmu-Y4neur , macmu-g7n4x3 , macmu-i2cy02 , macmu-f7ba84 , macmu-CES2 , macmu-h9er02 , macmu-a0a1d5rbr3 , macmu-a0a1d5q4k5 , macmu-g7mxj6 , macmu-f7dn71 , macmu-f7hkw9 , macmu-f7hm08 , macmu-g7mke4 , macmu-a0a1d5rh04 , macmu-h9fud6 , macmu-f6qwx1 , macmu-f7h4t2 , macmu-h9zaw9 , macmu-f7h550 , macmu-a0a1d5q9w1 , macmu-f7gkb9 , macmu-f7hp78 , macmu-a0a1d5qvu5

Title : Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir - Feng_2007_Proc.Natl.Acad.Sci.U.S.A_104_5602
Author(s) : Feng L , Wang W , Cheng J , Ren Y , Zhao G , Gao C , Tang Y , Liu X , Han W , Peng X , Liu R , Wang L
Ref : Proc Natl Acad Sci U S A , 104 :5602 , 2007
Abstract : The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic bacillus isolated from a deep oil reservoir in Northern China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The genome reveals that NG80-2 is well equipped for adaptation into a wide variety of environmental niches, including oil reservoirs, by possessing genes for utilization of a broad range of energy sources, genes encoding various transporters for efficient nutrient uptake and detoxification, and genes for a flexible respiration system including an aerobic branch comprising five terminal oxidases and an anaerobic branch comprising a complete denitrification pathway for quick response to dissolved oxygen fluctuation. The identification of a nitrous oxide reductase gene has not been previously described in Gram-positive bacteria. The proteome further reveals the presence of a long-chain alkane degradation pathway; and the function of the key enzyme in the pathway, the long-chain alkane monooxygenase LadA, is confirmed by in vivo and in vitro experiments. The thermophilic soluble monomeric LadA is an ideal candidate for treatment of environmental oil pollutions and biosynthesis of complex molecules.
ESTHER : Feng_2007_Proc.Natl.Acad.Sci.U.S.A_104_5602
PubMedSearch : Feng_2007_Proc.Natl.Acad.Sci.U.S.A_104_5602
PubMedID: 17372208
Gene_locus related to this paper: geotd-g3jwz2 , geoka-q5l1n0 , geotn-a4ijt0 , geotn-a4ilq0 , geotn-a4is13 , geotn-a4isp0 , geotn-a4isp3

Title : Acetylcholinesterase inhibitors from plants and fungi - Houghton_2006_Nat.Prod.Rep_23_181
Author(s) : Houghton PJ , Ren Y , Howes MJ
Ref : Nat Prod Rep , 23 :181 , 2006
Abstract : This review describes 183 compounds obtained from plants and fungi which have been shown to inhibit acetylcholinesterase. The mechanism of action of cholinesterase, together with the binding sites, and, where this is known, the mode of action of inhibitors is described. The relative activities of the different compounds are recorded. The strongest inhibitors are generally alkaloids although some meroterpenoids from fungi have also been found to be active and display better selectivity.
ESTHER : Houghton_2006_Nat.Prod.Rep_23_181
PubMedSearch : Houghton_2006_Nat.Prod.Rep_23_181
PubMedID: 16572227

Title : Relevant activities of extracts and constituents of animals used in traditional Chinese medicine for central nervous system effects associated with Alzheimer's disease - Ren_2006_J.Pharm.Pharmacol_58_989
Author(s) : Ren Y , Houghton P , Hider RC
Ref : J Pharm Pharmacol , 58 :989 , 2006
Abstract : The centipede Scolopendra subspinipes mutilans L. Koch ('Wugong'), the beetle Mylabris phalerata Pallas ('Ban mao') and the earthworm Pheretima aspergillum Chen ('DiLong') have a reputation in traditional Chinese medicine for reducing symptoms of central nervous system decline, including memory loss. A series of extracts of all three organisms was tested for acetylcholinesterase (AChE) inhibition and copper ion binding effects, the latter likely to reduce oxidative damage caused by excess copper. The beetle and centipede chloroform extracts showed the strongest AChE inhibitory effects (30.6% inhibition at 105 microg mL(-1) and 32.3% inhibition at 167 microg mL(-1), respectively) and, in the case of the centipede, this was traced to the unsaturated fatty acids present using bioassay-guided fractionation. Cantharidin from the beetle was shown to have AChE activity (31% inhibition at 1 muM, 0.196 microg mL(-1)), making it a major contributor to the activity of the beetle extract. The earthworm showed no AChE inhibitory activity. Since unsaturated fatty acids have not been previously reported to have AChE inhibitory activity, a series of related compounds was tested to determine structure-activity relationships. It was found that activity existed where there was a chain length of more than 16 C atoms with at least one unsaturated bond in the chain. The carboxylic acid group was also necessary for activity. The fatty acids present in the centipede also showed the ability to bind copper ions when tested using a novel thin layer chromatography method designed to detect copper-binding compounds. The activities reported give some support to the use of the beetle and centipede in traditional Chinese medicine for improving cognitive function.
ESTHER : Ren_2006_J.Pharm.Pharmacol_58_989
PubMedSearch : Ren_2006_J.Pharm.Pharmacol_58_989
PubMedID: 16805960

Title : Robust axonal sprouting and synaptogenesis in organotypic slice cultures of rat cerebellum exposed to increased potassium chloride - Chen_2005_Brain.Res_1057_88
Author(s) : Chen S , Hirata K , Ren Y , Sugimori M , Llinas R , Hillman DE
Ref : Brain Research , 1057 :88 , 2005
Abstract : Organotypic slices of the rat cerebellum, cultured in physiological levels [K+]o (5 mM) for 14 days, loose the majority of granule cells in the anterior lobe resulting in few axons and atypical Purkinje cell dendrites with vacant spines. When the culture medium was switched from 5 mM to 20, 30 or 40 mM [K+]o during the last 7 days of cultures, slices developed axons with numerous vesicle-filled boutons that made synaptic contact with Purkinje cell spines. Most boutons had one or two spine profile contacts, while some were unusually large. Enlarged boutons abutted Purkinje cell somata or their dendrites, causing intervening spines to invaginate terminals to form rosette synaptic complexes. Calbindin immuno-labeling excluded Purkinje cell axonal collaterals as the source of rosette boutons and suggested a granule cell origin. Quantification of vacant spines as compared to those on boutons revealed a threshold for potassium, between 10 and 20 mM, where the number of synaptic spines increased and vacant spines decreased drastically. These findings suggest that elevated [K+]o triggers an activity-dependent plasticity in rat cerebellar slice cultures by promoting axonal sprouting with formation of vesicle-filled boutons and synaptogenesis on open receptor sites of Purkinje cell spines.
ESTHER : Chen_2005_Brain.Res_1057_88
PubMedSearch : Chen_2005_Brain.Res_1057_88
PubMedID: 16125152

Title : Secretion, purification, and characterization of a recombinant Aspergillus oryzae tannase in Pichia pastoris - Zhong_2004_Protein.Expr.Purif_36_165
Author(s) : Zhong X , Peng L , Zheng S , Sun Z , Ren Y , Dong M , Xu A
Ref : Protein Expr Purif , 36 :165 , 2004
Abstract : Tannase (tannin acyl hydrolase) is an industrially important enzyme produced by a large number of fungi, which hydrolyzes the ester and depside bonds of gallotannins and gallic acid esters. In the present work, a tannase from Aspergillus oryzae has been cloned and expressed in Pichia pastoris. The catalytic activity of the recombinant enzyme was assayed. A secretory form of enzyme was made with the aid of Saccharomyces cerevisiae alpha-factor, and a simple procedure purification protocol yielded tannase in pure form. The productivity of secreted tannase achieved 7000 IU/L by fed-batch culture. Recombinant tannase had a molecular mass of 90 kDa, which consisted of two kinds of subunits linked by a disulfide bond(s). Our study is the first report on the heterologous expression of tannase suggesting that the P. pastoris system represents an attractive means of generating large quantities of tannase for both research and industrial purpose.
ESTHER : Zhong_2004_Protein.Expr.Purif_36_165
PubMedSearch : Zhong_2004_Protein.Expr.Purif_36_165
PubMedID: 15249037
Gene_locus related to this paper: aspor-tan

Title : Novel diterpenoid acetylcholinesterase inhibitors from Salvia miltiorhiza - Ren_2004_Planta.Med_70_201
Author(s) : Ren Y , Houghton PJ , Hider RC , Howes MJ
Ref : Planta Med , 70 :201 , 2004
Abstract : Acetylcholinesterase (AChE, EC 3.1.1.7) inhibitors are the only registered drugs used to treat Alzheimer's disease (AD). New AChE inhibitors may contribute to the design of new pharmaceuticals and supply information which will facilitate the understanding of the interaction between inhibitors and the enzyme. The dried root of Salvia miltiorhiza is called 'Danshen' in China, and has been used for the treatment of cerebrovascular disease and CNS deterioration in old age for over one thousand years. In this work, a modified Ellman method was used to guide the fractionation of the active AChE inhibitory compounds from an acetone extract. Four inhibitory compounds, dihydrotanshinone, cryptotanshinone, tanshinone I and tanshinone IIA were isolated, and the structures were identified by comparison of their spectral characteristics with previous reports. The inhibitory activities of dihydrotanshinone and cryptotanshinone were dose-dependent, their IC (50) values being 1.0 microM and 7.0 microM, respectively. These two compounds were the major inhibitory compounds in the extract as judged by HPLC analysis, forming 0.054 % w/w and 0.23 % w/w in the dried root, respectively, and in mixture they appear to be less active than as isolated compounds. The clogP values of dihydrotanshinone, cryptotanshinone, tanshinone I and tanshinone IIA were calculated as 2.4, 3.4, 4.8 and 5.8, respectively, which indicate that these compounds have potential to penetrate the blood-brain barrier. This is the first example of diterpenoids as inhibitors of AChE.
ESTHER : Ren_2004_Planta.Med_70_201
PubMedSearch : Ren_2004_Planta.Med_70_201
PubMedID: 15114495

Title : Genome sequence of the Brown Norway rat yields insights into mammalian evolution - Gibbs_2004_Nature_428_493
Author(s) : Gibbs RA , Weinstock GM , Metzker ML , Muzny DM , Sodergren EJ , Scherer S , Scott G , Steffen D , Worley KC , Burch PE , Okwuonu G , Hines S , Lewis L , DeRamo C , Delgado O , Dugan-Rocha S , Miner G , Morgan M , Hawes A , Gill R , Celera , Holt RA , Adams MD , Amanatides PG , Baden-Tillson H , Barnstead M , Chin S , Evans CA , Ferriera S , Fosler C , Glodek A , Gu Z , Jennings D , Kraft CL , Nguyen T , Pfannkoch CM , Sitter C , Sutton GG , Venter JC , Woodage T , Smith D , Lee HM , Gustafson E , Cahill P , Kana A , Doucette-Stamm L , Weinstock K , Fechtel K , Weiss RB , Dunn DM , Green ED , Blakesley RW , Bouffard GG , de Jong PJ , Osoegawa K , Zhu B , Marra M , Schein J , Bosdet I , Fjell C , Jones S , Krzywinski M , Mathewson C , Siddiqui A , Wye N , McPherson J , Zhao S , Fraser CM , Shetty J , Shatsman S , Geer K , Chen Y , Abramzon S , Nierman WC , Havlak PH , Chen R , Durbin KJ , Egan A , Ren Y , Song XZ , Li B , Liu Y , Qin X , Cawley S , Cooney AJ , D'Souza LM , Martin K , Wu JQ , Gonzalez-Garay ML , Jackson AR , Kalafus KJ , McLeod MP , Milosavljevic A , Virk D , Volkov A , Wheeler DA , Zhang Z , Bailey JA , Eichler EE , Tuzun E , Birney E , Mongin E , Ureta-Vidal A , Woodwark C , Zdobnov E , Bork P , Suyama M , Torrents D , Alexandersson M , Trask BJ , Young JM , Huang H , Wang H , Xing H , Daniels S , Gietzen D , Schmidt J , Stevens K , Vitt U , Wingrove J , Camara F , Mar Alba M , Abril JF , Guigo R , Smit A , Dubchak I , Rubin EM , Couronne O , Poliakov A , Hubner N , Ganten D , Goesele C , Hummel O , Kreitler T , Lee YA , Monti J , Schulz H , Zimdahl H , Himmelbauer H , Lehrach H , Jacob HJ , Bromberg S , Gullings-Handley J , Jensen-Seaman MI , Kwitek AE , Lazar J , Pasko D , Tonellato PJ , Twigger S , Ponting CP , Duarte JM , Rice S , Goodstadt L , Beatson SA , Emes RD , Winter EE , Webber C , Brandt P , Nyakatura G , Adetobi M , Chiaromonte F , Elnitski L , Eswara P , Hardison RC , Hou M , Kolbe D , Makova K , Miller W , Nekrutenko A , Riemer C , Schwartz S , Taylor J , Yang S , Zhang Y , Lindpaintner K , Andrews TD , Caccamo M , Clamp M , Clarke L , Curwen V , Durbin R , Eyras E , Searle SM , Cooper GM , Batzoglou S , Brudno M , Sidow A , Stone EA , Payseur BA , Bourque G , Lopez-Otin C , Puente XS , Chakrabarti K , Chatterji S , Dewey C , Pachter L , Bray N , Yap VB , Caspi A , Tesler G , Pevzner PA , Haussler D , Roskin KM , Baertsch R , Clawson H , Furey TS , Hinrichs AS , Karolchik D , Kent WJ , Rosenbloom KR , Trumbower H , Weirauch M , Cooper DN , Stenson PD , Ma B , Brent M , Arumugam M , Shteynberg D , Copley RR , Taylor MS , Riethman H , Mudunuri U , Peterson J , Guyer M , Felsenfeld A , Old S , Mockrin S , Collins F
Ref : Nature , 428 :493 , 2004
Abstract : The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
ESTHER : Gibbs_2004_Nature_428_493
PubMedSearch : Gibbs_2004_Nature_428_493
PubMedID: 15057822
Gene_locus related to this paper: rat-abhea , rat-abheb , rat-cd029 , rat-d3zaw4 , rat-dpp9 , rat-d3zhq1 , rat-d3zkp8 , rat-d3zuq1 , rat-d3zxw8 , rat-d4a4w4 , rat-d4a7w1 , rat-d4a9l7 , rat-d4a071 , rat-d4aa31 , rat-d4aa33 , rat-d4aa61 , rat-dglb , rat-f1lz91 , rat-Kansl3 , rat-nceh1 , rat-Tex30 , ratno-1hlip , ratno-1neur , ratno-1plip , ratno-2neur , ratno-3neur , ratno-3plip , ratno-ABH15 , ratno-ACHE , ratno-balip , ratno-BCHE , ratno-cauxin , ratno-Ces1d , ratno-Ces1e , ratno-Ces2f , ratno-d3ze31 , ratno-d3zp14 , ratno-d3zxi3 , ratno-d3zxq0 , ratno-d3zxq1 , ratno-d4a3d4 , ratno-d4aa05 , ratno-dpp4 , ratno-dpp6 , ratno-est8 , ratno-FAP , ratno-hyep , ratno-hyes , ratno-kmcxe , ratno-lmcxe , ratno-LOC246252 , ratno-MGLL , ratno-pbcxe , ratno-phebest , ratno-Ppgb , ratno-q4qr68 , ratno-q6ayr2 , ratno-q6q629 , ratno-SPG21 , ratno-thyro , rat-m0rc77 , rat-a0a0g2k9y7 , rat-a0a0g2kb83 , rat-d3zba8 , rat-d3zbj1 , rat-d3zcr8 , rat-d3zxw5 , rat-d4a340 , rat-f1lvg7 , rat-m0r509 , rat-m0r5d4 , rat-b5den3 , rat-d3zxk4 , rat-d4a1b6 , rat-d3zmg4 , rat-ab17c

Title : Thermostable esterase from Thermoanaerobacter tengcongensis: high-level expression, purification and characterization - Zhang_2003_Biotechnol.Lett_25_1463
Author(s) : Zhang J , Liu J , Zhou J , Ren Y , Dai X , Xiang H
Ref : Biotechnol Lett , 25 :1463 , 2003
Abstract : The lipA gene encoding a thermostable esterase was cloned from Thermoanaerobacter tengcongensis and over-expressed in Escherichia coli. The recombinant esterase, with a molecular mass of approx. 43 kDa determined by SDS-PAGE, was purified to homogeneity through Sephadex G-100 gel filtration. The purified enzyme actively hydrolyzed tributyrin but not olive oil. Maximum activity was observed on p-nitrophenyl (NP)-propionate (C3) and p-NP-butyrate (C4), with little activity towards p-NP-palmitate (C16). The esterase was optimally active at 70 degrees C (over 15 min) and at pH 9. It is highly thermostable, with a residual activity greater than 80% after incubation at 50 degrees C for more than 10 h. The activity was not inhibited by 5 mM EDTA and PMSF, indicating the esterase is not a metalloenzyme and may contain a specific structure around the catalytic serine residue. In addition, it was stable for 1 h at 37 degrees C in 1% CHAPS and Triton X-100 but not stable in 1% Tween 20 or SDS.
ESTHER : Zhang_2003_Biotechnol.Lett_25_1463
PubMedSearch : Zhang_2003_Biotechnol.Lett_25_1463
PubMedID: 14514051
Gene_locus related to this paper: thete-LIPA