Author Report for: Du YNo contact information in database for Du Y
Du Y, Li C, Hao YF, Zhao C, Yan Q, Yao D, Li L, Zhang W Ref: Journal of Neurology, :, 2022 : PubMed ESTHER: Du_2022_J.Neurol__ PubMedSearch: Du 2022 J.Neurol PubMedID: 35243555 Abstract BACKGROUND: Generalized AChR-MG is an archetype of B cell-mediated autoimmune disorders, and use of biologic agent rituximab (RTX) for B cell depletion is generally limited to immunosuppressive therapy-refractory cases. However, benefit of RTX monotherapy and individualized regimen with optimal dosage in early stage of new-onset generalized AChR-MG still remains to be elucidated. In this retrospective study, we explore the efficacy and safety of personalized regimen of 100 mg low-dose rituximab monotherapy in treating new-onset generalized AChR-MG. METHODS: Thirteen new-onset generalized AChR-MG patients were enrolled for the study, initiating RTX treatment from November 2017 to August 2020. The individualized low-dose RTX monotherapy protocol consisted of 100 mg induction treatment weekly with no more than three circles, followed by reinfusion (100 mg once) sequentially according to whether achieving primary endpoint and peripheral CD19 + B-cell repopulation <= 1% of total lymphocytes at each visit (every 3 months). Outcome measures included MGFA-PIS Minimal Manifestation (MM) or better status (primary endpoint), changes in QMG, MMT, MG-ADL and MGQOL-15 scores (secondary endpoint), as well as cholinesterase inhibitors dosage. RESULTS: All 13 patients achieved the primary endpoint in parallel with significant improvement of QMG, MMT, MG-ADL MGQOL-15 scores, and reduction of cholinesterase inhibitors dose. A total of 52 visits were performed during follow-up, and only 10 assessments presenting peripheral CD19 + B-cell repopulation (<= 1%) without "MM or better status" were followed by RTX reinfusions (100 mg once) for clinical remission. The total dosage of RTX was only 346.15 +/- 96.74 mg (including 269.23 +/- 63.04 mg for induction and 76.92 +/- 59.91 mg for reinfusion), which seemed to be much lower than those dosages used in new-onset generalized AChR-MG as described previously. Moreover, compared with patients without thymoma, thymectomy markedly delayed initiation of RTX for patients with thymoma (log-rank test, p = 0.0002), but the delaying treatments showed no influence on the time for achieving primary outcome (log-rank test, p = 0.2517). CONCLUSION: Our study firstly showed that individualized regimen of low-dose RTX monotherapy is effective and safe for early treatment of new-onset generalized AChR-MG, and practicable for directing RTX reinfusion and withdrawal. Moreover, the monotherapy protocol was also indicated to be extensively applicable in both new-onset AChR-MG with thymoma (thymectomy) and without thymoma. Title: Biosensor Based on Covalent Organic Framework Immobilized Acetylcholinesterase for Ratiometric Detection of Carbaryl Luo Y, Wu N, Wang L, Song Y, Du Y, Ma G Ref: Biosensors (Basel), 12:, 2022 : PubMed ESTHER: Luo_2022_Biosensors.(Basel)_12_ PubMedSearch: Luo 2022 Biosensors.(Basel) 12 PubMedID: 36005021 Abstract A ratiometric electrochemical biosensor based on a covalent organic framework (COF(Thi-TFPB)) loaded with acetylcholinesterase (AChE) was developed. First, an electroactive COF(Thi-TFPB) with a two-dimensional sheet structure, positive charge and a pair of inert redox peaks was synthesized via a dehydration condensation reaction between positively charged thionine (Thi) and 1,3,5-triformylphenylbenzene (TFPB). The immobilization of AChE on the positively charged electrode surface was beneficial for maintaining its bioactivity and achieving the best catalytic effect; therefore, the positively charged COF(Thi-TFPB) was an appropriate support material for AChE. Furthermore, the COF(Thi-TFPB) provided a stable internal reference signal for the constructed AChE inhibition-based electrochemical biosensor to eliminate various effects which were unrelated to the detection of carbaryl. The sensor had a linear range of 2.2-60 microM with a detection limit of 0.22 microM, and exhibited satisfactory reproducibility, stability and anti-interference ability for the detection of carbaryl. This work offers a possibility for the application of COF-based materials in the detection of low-level pesticide residues. Title: Lipase-catalyzed hydrazine insertion for the synthesis of N'-alkyl benzohydrazides Yu Y, Li F, Li J, Zheng X, Tian H, Mahmut Z, Du Y, Dai Y, Wang L Ref: Biotechnol Appl Biochem, :, 2022 : PubMed ESTHER: Yu_2022_Biotechnol.Appl.Biochem__ PubMedSearch: Yu 2022 Biotechnol.Appl.Biochem PubMedID: 35285069 Abstract N'-alkyl benzohydrazides are classic organic compounds that have been widely utilized in organic chemistry. In this study, an efficient method was developed for the synthesis of N'-alkyl benzohydrazides by hydrazine insertion catalyzed by lipase. Under the optimal conditions (Morita-Baylis-Hillman ketone [1 mmol], phenylhydrazine [1.3 mmol], N,N-dimethylformamide [2 mL], lipase [20 mg], room temperature, 12 h), satisfactory yields (71%-97%) and substrate tolerance were obtained when porcine pancreatic lipase was used as biocatalyst. These findings imply the great potential for the lipase-catalyzed synthesis of N'-alkyl benzohydrazides and extend the utilization of lipase in organic chemistry. This article is protected by copyright. All rights reserved. Title: First-in-human neuroimaging of soluble epoxide hydrolase using [(18)F]FNDP PET Coughlin JM, Slania S, Du Y, Shinehouse LK, Brosnan MK, Azad BB, Holt DP, Fan H, Lesniak WG and Pomper MG <4 more author(s)> Coughlin JM, Slania S, Du Y, Shinehouse LK, Brosnan MK, Azad BB, Holt DP, Fan H, Lesniak WG, Minn I, Rowe SP, Dannals RF, Horti AG, Pomper MG (- 4) Ref: Eur J Nucl Med Mol Imaging, :, 2021 : PubMed ESTHER: Coughlin_2021_Eur.J.Nucl.Med.Mol.Imaging__ PubMedSearch: Coughlin 2021 Eur.J.Nucl.Med.Mol.Imaging PubMedID: 33585963 Abstract PURPOSE: Soluble epoxide hydrolase (sEH) is an enzyme with putative effect on neuroinflammation through its influence on the homeostasis of polyunsaturated fatty acids and related byproducts. sEH is an enzyme that metabolizes anti-inflammatory epoxy fatty acids to the corresponding, relatively inert 1,2-diols. A high availability or activity of sEH promotes vasoconstriction and inflammation in local tissues that may be linked to neuropsychiatric diseases. We developed [(18)F]FNDP to study sEH in vivo with positron emission tomography (PET). METHODS: Brain PET using bolus injection of [(18)F]FNDP followed by emission imaging lasting 90 or 180 min was completed in healthy adults (5 males, 2 females, ages 40-53 years). The kinetic behavior of [(18)F]FNDP was evaluated using a radiometabolite-corrected arterial plasma input function with compartmental or graphical modeling approaches. RESULTS: [(18)F]FNDP PET was without adverse effects. Akaike information criterion favored the two-tissue compartment model (2TCM) in all ten regions of interest. Regional total distribution volume (V(T)) values from each compartmental model and Logan analysis were generally well identified except for corpus callosum V(T) using the 2TCM. Logan analysis was assessed as the choice model due to stability of regional V(T) values from 90-min data and due to high correlation of Logan-derived regional V(T) values with those from the 2TCM. [(18)F]FNDP binding was higher in human cerebellar cortex and thalamus relative to supratentorial cortical regions, which aligns with reported expression patterns of the epoxide hydrolase 2 gene in human brain. CONCLUSION: These data support further use of [(18)F]FNDP PET to study sEH in human brain. Title: Insecticidal and Enzyme Inhibitory Activities of Isothiocyanates against Red Imported Fire Ants, Solenopsis invicta Du Y, Grodowitz MJ, Chen J Ref: Biomolecules, 10:, 2020 : PubMed ESTHER: Du_2020_Biomolecules_10_ PubMedSearch: Du 2020 Biomolecules 10 PubMedID: 32380698 Abstract Contact and fumigation toxicity of four isothiocyanates (ITCs), including allyl isothiocyanate (AITC), 3-butenyl isothiocyanate (3BITC), 3-(methylthio) propyl isothiocyanate (3MPITC) and 2-phenylethyl isothiocyanate (2PEITC), were evaluated against the red imported fire ant worker, Solenopsis invicta Buren. 2PEITC and 3MPITC exhibited strong contact toxicity. The median lethal dose (LD50)value of AITC, 2PEITC and 3MPITC were 7.99, 2.36 and 2.09 microg/ant respectively. In addition, AITC and 3MPITC also showed strong fumigation toxicity but not 2PEITC. The median lethal concentration (LC50) values of AITC and 3MPITC were 32.49 and 57.6 microg/L, respectively. In contrast, 3BITC did not exhibit any contact and fumigation toxicity even at 100 mug/muL. Esterase (EST), glutathione S-transferase (GST) and acetylcholinesterase (AChE)-inhibiting activities were assessed for three ITCs in S. invicta workers. All three ITCs inhibited both EST and GST activities but not AChE. The in vitro half maximal inhibitory concentration (IC50)values of AITC, 2PEITC and 3MPITC for GST were 3.32, 0.61 and 0.66 microg/microL, respectively. These results suggested that naturally occurring ITCs might be potentially useful for developing fire ants control products. Title: PET imaging of soluble epoxide hydrolase in non-human primate brain with [(18)F]FNDP Du Y, Minn I, Foss C, Lesniak WG, Hu F, Dannals RF, Pomper MG, Horti AG Ref: EJNMMI Res, 10:67, 2020 : PubMed ESTHER: Du_2020_EJNMMI.Res_10_67 PubMedSearch: Du 2020 EJNMMI.Res 10 67 PubMedID: 32572592 Abstract PURPOSE: Soluble epoxide hydrolase (sEH) is a promising candidate positron emission tomography (PET) imaging biomarker altered in various disorders, including vascular cognitive impairment (VCI), Alzheimer's disease (AD), Parkinson's disease (PD), stroke, and depression, known to regulate levels of epoxyeicosatrienoic acids (EETs) and play an important role in neurovascular coupling. [(18)F]FNDP, a PET radiotracer for imaging sEH, was evaluated through quantitative PET imaging in the baboon brain, radiometabolite analysis, and radiation dosimetry estimate. METHODS: Baboon [(18)F]FNDP dynamic PET studies were performed at baseline and with blocking doses of the selective sEH inhibitor AR-9281 to evaluate sEH binding specificity. Radiometabolites of [(18)F]FNDP in mice and baboons were measured by high-performance liquid chromatography. Regional brain distribution volume (VT) of [(18)F]FNDP was computed from PET using radiometabolite-corrected arterial input functions. Full body distribution of [(18)F]FNDP was studied in CD-1 mice, and the human effective dose was estimated using OLINDA/EXM software. RESULTS: [(18)F]FNDP exhibited high and rapid brain uptake in baboons. AR-9281 blocked [(18)F]FNDP uptake dose-dependently with a baseline VT of 10.9 +/- 2.4 mL/mL and a high-dose blocking VT of 1.0 +/- 0.09 mL/mL, indicating substantial binding specificity (91.70 +/- 1.74%). The VND was estimated as 0.865 +/- 0.066 mL/mL. The estimated occupancy values of AR-9281 were 99.2 +/- 1.1% for 1 mg/kg, 88.6 +/- 1.3% for 0.1 mg/kg, and 33.8 +/- 3.8% for 0.02 mg/kg. Murine biodistribution of [(18)F]FNDP enabled an effective dose estimate for humans (0.032 mSv/MBq). [(18)F]FNDP forms hydrophilic radiometabolites in murine and non-human primate plasma. However, only minute amounts of the radiometabolites entered the animal brain (< 2% in mice). CONCLUSIONS: [(18)F]FNDP is a highly sEH-specific radiotracer that is suitable for quantitative PET imaging in the baboon brain. [(18)F]FNDP holds promise for translation to human subjects. Title: Role of oxylipins generated from dietary PUFAs in the modulation of endothelial cell function Du Y, Taylor CG, Aukema HM, Zahradka P Ref: Prostaglandins Leukot Essent Fatty Acids, 160:102160, 2020 : PubMed ESTHER: Du_2020_Prostaglandins.Leukot.Essent.Fatty.Acids_160_102160 PubMedSearch: Du 2020 Prostaglandins.Leukot.Essent.Fatty.Acids 160 102160 PubMedID: 32717531 Abstract Oxylipins, which are circulating bioactive lipids generated from polyunsaturated fatty acids (PUFAs) by cyclooxygenase, lipooxygenase and cytochrome P450 enzymes, have diverse effects on endothelial cells. Although studies of the effects of oxylipins on endothelial cell function are accumulating, a review that provides a comprehensive compilation of current knowledge and recent advances in the context of vascular homeostasis is lacking. This is the first compilation of the various in vitro, ex vivo and in vivo reports to examine the effects and potential mechanisms of action of oxylipins on endothelial cells. The aggregate data indicate docosahexaenoic acid-derived oxylipins consistently show beneficial effects related to key endothelial cell functions, whereas oxylipins derived from other PUFAs exhibit both positive and negative effects. Furthermore, information is lacking for certain oxylipin classes, such as those derived from alpha-linolenic acid, which suggests additional studies are required to achieve a full understanding of how oxylipins affect endothelial cells. Title: Clinical analysis of Chinese anti-low-density-lipoprotein-receptor-associated protein 4 antibodies in patients with myasthenia gravis Li M, Han J, Zhang Y, Lv J, Zhang J, Zhao X, Ren L, Fang H, Yang J and Gao F <4 more author(s)> Li M, Han J, Zhang Y, Lv J, Zhang J, Zhao X, Ren L, Fang H, Yang J, Cui X, Zhang Q, Li Q, Du Y, Gao F (- 4) Ref: Eur Journal of Neurology, 26:1296, 2019 : PubMed ESTHER: Li_2019_Eur.J.Neurol_26_1296 PubMedSearch: Li 2019 Eur.J.Neurol 26 1296 PubMedID: 31050101 Abstract BACKGROUND AND PURPOSE: Low-density-lipoprotein-receptor-associated protein 4 (LRP4) autoantibodies have recently been detected in myasthenia gravis (MG), but little is known about the clinical characteristics associated with this serological type. In this study, the clinical features of Chinese patients with anti-LRP4 antibody-positive MG were characterized. METHODS: A total of 2172 MG serum samples were collected from patients in various parts of China. An enzyme-linked immunosorbent assay was used to detect acetylcholine receptor (AChR) antibody and titin antibody, and cell-based assays were used to detect muscle-specific kinase antibody and LRP4 antibody. Clinical data for patients with MG were collected from different provinces in China. RESULTS: In total, 16 (0.8%) patients with LRP4-MG were found amongst 2172 total patients, including three patients with AChR/LRP4-MG. Additionally, 13 (2.9%) patients with LRP4-MG were found amongst 455 patients with double seronegative MG. The ratio of males to females for these 13 patients was 1:1.6, and 53.8% patients were children. A total of 91.7% of cases exhibited initial ocular involvement, and 58.3% of cases exhibited simple eye muscle involvement. Responses to acetylcholinesterase inhibitors and prednisone were observed. CONCLUSION: The expanded sample confirmed that the positive rate of LRP4 antibodies in China is lower than that in western countries. Our results highlighted the differences between LRP4-MG and other antibody groups. Children and female patients with LRP4-MG have a higher prevalence, often involving the ocular muscles and limb muscles. The clinical symptoms are mild, and satisfactory responses to treatment are often achieved. Title: Exosomes from activated hepatic stellate cells contain GLUT1 and PKM2: a role for exosomes in metabolic switch of liver nonparenchymal cells Wan L, Xia T, Du Y, Liu J, Xie Y, Zhang Y, Guan F, Wu J, Wang X, Shi C Ref: FASEB Journal, :fj201802675R, 2019 : PubMed ESTHER: Wan_2019_FASEB.J__fj201802675R PubMedSearch: Wan 2019 FASEB.J fj201802675R PubMedID: 30970216 Abstract The mechanism of exosomes derived from activated hepatic stellate cells (HSCs) involved in liver fibrosis is poorly understood. We previously reported that hypoxia-inducible factor 1 (Hif-1) regulated HSC activation, and, therefore, we investigated in current work whether Hif-1 regulates exosome secretion and the metabolic switch of HSCs, thus affecting the metabolism of liver nonparenchymal cells. In this study, the characteristics of exosomes from HSCs were assessed via electron microscopy, Western blot analysis, and acetylcholinesterase activity. Confocal microscopy was used to measure the uptake of exosomes by quiescent HSCs, Kupffer cells (KCs), and liver sinusoidal endothelial cells (LSECs). Hif-1alpha was inhibited via 2-ME or specific small interfering RNAs to investigate its role in exosomes derived from HSCs. It was determined that glucose transporter 1 and pyruvate kinase M2 were increasingly expressed in fibrotic liver samples, cell lysates, and exosomes derived from activated HSCs. Exosomes released from HSCs were associated with activation and glucose uptake of HSCs. Delivery of exosomes from activated HSCs induced glycolysis of quiescent HSCs, KCs, and LSECs. Disruption of Hif-1 expression suppressed the glycolysis effect delivered by exosomes. Conclusively, our results demonstrated that exosomes secreted by activated HSCs affect the metabolic switch of liver nonparenchymal cells via delivery of glycolysis-related proteins. These findings represent a novel mechanism that contributes to liver fibrosis and has significant implications for new diagnosis and treatment of liver diseases.-Wan, L., Xia, T., Du, Y., Liu, J., Xie, Y., Zhang, Y., Guan, F., Wu, J., Wang, X., Shi, C. Exosomes from activated hepatic stellate cells contain GLUT1 and PKM2: a role for exomes in metabolic switch of liver nonparenchymal cells. Title: In Vitro and in Vivo Evaluation of (11)C-Labeled Azetidinecarboxylates for Imaging Monoacylglycerol Lipase by PET Imaging Studies Cheng R, Mori W, Ma L, Alhouayek M, Hatori A, Zhang Y, Ogasawara D, Yuan G, Chen Z and Liang SH <16 more author(s)> Cheng R, Mori W, Ma L, Alhouayek M, Hatori A, Zhang Y, Ogasawara D, Yuan G, Chen Z, Zhang X, Shi H, Yamasaki T, Xie L, Kumata K, Fujinaga M, Nagai Y, Minamimoto T, Svensson M, Wang L, Du Y, Ondrechen MJ, Vasdev N, Cravatt BF, Fowler C, Zhang MR, Liang SH (- 16) Ref: Journal of Medicinal Chemistry, 61:2278, 2018 : PubMed ESTHER: Cheng_2018_J.Med.Chem_61_2278 PubMedSearch: Cheng 2018 J.Med.Chem 61 2278 PubMedID: 29481079 Abstract Monoacylglycerol lipase (MAGL) is the principle enzyme for metabolizing endogenous cannabinoid ligand 2-arachidonoyglycerol (2-AG). Blockade of MAGL increases 2-AG levels, resulting in subsequent activation of the endocannabinoid system, and has emerged as a novel therapeutic strategy to treat drug addiction, inflammation, and neurodegenerative diseases. Herein we report a new series of MAGL inhibitors, which were radiolabeled by site-specific labeling technologies, including (11)C-carbonylation and spirocyclic iodonium ylide (SCIDY) radiofluorination. The lead compound [(11)C]10 (MAGL-0519) demonstrated high specific binding and selectivity in vitro and in vivo. We also observed unexpected washout kinetics with these irreversible radiotracers, in which in vivo evidence for turnover of the covalent residue was unveiled between MAGL and azetidine carboxylates. This work may lead to new directions for drug discovery and PET tracer development based on azetidine carboxylate inhibitor scaffold. Title: Surrogating and redirection of pyrazolo[1,5-a]pyrimidin-7(4H)-one core, a novel class of potent and selective DPP-4 inhibitors Deng X, Shen J, Zhu H, Xiao J, Sun R, Xie F, Lam C, Wang J, Qiao Y and Jiang F <5 more author(s)> Deng X, Shen J, Zhu H, Xiao J, Sun R, Xie F, Lam C, Wang J, Qiao Y, Tavallaie MS, Hu Y, Du Y, Li J, Fu L, Jiang F (- 5) Ref: Bioorganic & Medicinal Chemistry, 26:903, 2018 : PubMed ESTHER: Deng_2018_Bioorg.Med.Chem_26_903 PubMedSearch: Deng 2018 Bioorg.Med.Chem 26 903 PubMedID: 29373269 Abstract The initial focus on characterizing novel pyrazolo[1,5-a]pyrimidin-7(4H)-one derivatives as DPP-4 inhibitors, led to a potent and selective inhibitor compound b2. This ligand exhibits potent in vitro DPP-4 inhibitory activity (IC(50): 80 nM), while maintaining other key cellular parameters such as high selectivity, low cytotoxicity and good cell viability. Subsequent optimization of b2 based on docking analysis and structure-based drug design knowledge resulted in d1. Compound d1 has nearly 2-fold increase of inhibitory activity (IC(50): 49 nM) and over 1000-fold selectivity against DPP-8 and DPP-9. Further in vivo IPGTT assays showed that compound b2 effectively reduce glucose excursion by 34% at the dose of 10 mg/kg in diabetic mice. Herein we report the optimization and design of a potent and highly selective series of pyrazolo[1,5-a]pyrimidin-7(4H)-one DPP-4 inhibitors. Title: Acetylcholine and necroptosis are players in follicular development in primates Du Y, Bagnjuk K, Lawson MS, Xu J, Mayerhofer A Ref: Sci Rep, 8:6166, 2018 : PubMed ESTHER: Du_2018_Sci.Rep_8_6166 PubMedSearch: Du 2018 Sci.Rep 8 6166 PubMedID: 29670172 Abstract Acetylcholine (ACh) in the ovary and its actions were linked to survival of human granulosa cells in vitro and improved fertility of rats in vivo. These effects were observed upon experimental blockage of the ACh-degrading enzyme (ACH esterase; ACHE), by Huperzine A. We now studied actions of Huperzine A in a three-dimensional culture of macaque follicles. Because a form of programmed necrotic cell death, necroptosis, was previously identified in human granulosa cells in vitro, we also studied actions of necrostatin-1 (necroptosis inhibitor). Blocking the breakdown of ACh by inhibiting ACHE, or interfering with necroptosis, did not improve the overall follicle survival, but promoted the growth of macaque follicles from the secondary to the small antral stage in vitro, which was correlated with oocyte development. The results from this translational model imply that ovarian function and fertility in primates may be improved by pharmacological interference with ACHE actions and necroptosis. Title: Omega-6 fatty acids down-regulate matrix metalloproteinase expression in a coronary heart disease-induced rat model Lu N, Du Y, Li H, Luo Y, Ouyang B, Chen Y, Yang Y, Yang L Ref: International Journal of Experimental Pathology, 99:210, 2018 : PubMed ESTHER: Lu_2018_Int.J.Exp.Pathol_99_210 PubMedSearch: Lu 2018 Int.J.Exp.Pathol 99 210 PubMedID: 30443948 Abstract The present study investigated the therapeutic potential of omega-6 fatty acids, according to their effects on antioxidant markers and matrix metalloproteinases (MMPs), in coronary heart disease-induced rats. Rats were grouped into group I (sham control), group II (control), group III (0.5 g/kg bwt of omega-6 fatty acids) and group IV (1 g/kg bwt of omega-6 fatty acids). Reactive oxygen species (ROS), malondialdehyde (MDA), superoxide dismutase (SOD), reduced glutathione (GSH), catalase, glutathione peroxidase (Gpx) and acetylcholinesterase (AChE) enzyme activities were determined. ROS and MDA were substantially reduced, whereas SOD, catalase, Gpx and AChE were significantly increased, following supplementation with omega-6 fatty acids. MMP-2 mRNA expression was drastically increased by 95% in group II. Treatment significantly reduced MMP-2 mRNA expression by 12.3% and 26.7% in groups III and IV respectively. MMP-9 mRNA expression drastically increased, by 121%, in group II. Treatment significantly reduced MMP-9 mRNA expression by 22.6% and 29.4% in groups III and IV respectively. MMP-2 protein expression was drastically increased, by 81%, in group II. Treatment significantly reduced MMP-2 protein expression by 9.4% and 26% in groups III and IV respectively. MMP-9 protein expression was drastically increased, by 100%, in group II. Treatment significantly reduced MMP-9 protein expression by 18.9% and 26.9% in groups III and IV respectively. In summary, the consumption of omega-6 fatty acids significantly decreased MDA and ROS, while SOD, catalase, GHS, Gpx and AChE were increased. Furthermore, omega-6 fatty acids significantly downregulated MMP-2 and MMP-9 expression in our coronary heart disease-induced rat model. Title: Thiolation Protein-Based Transfer of Indolyl to a Ribosomally Synthesized Polythiazolyl Peptide Intermediate during the Biosynthesis of the Side-Ring System of Nosiheptide Qiu Y, Du Y, Zhang F, Liao R, Zhou S, Peng C, Guo Y, Liu W Ref: Journal of the American Chemical Society, 139:18186, 2017 : PubMed ESTHER: Qiu_2017_J.Am.Chem.Soc_139_18186 PubMedSearch: Qiu 2017 J.Am.Chem.Soc 139 18186 PubMedID: 29200275 Gene_locus related to this paper: stras-c6fx50 Abstract Nosiheptide, a potent bicyclic member of the family of thiopeptide antibiotics, possesses a distinctive l-Trp-derived indolyl moiety. The way in which this moiety is incorporated into a ribosomally synthesized and post-translationally modified thiopeptide remains poorly understood. Here, we report that NosK, an alpha/beta-hydrolase fold protein, mediates the transfer of indolyl from NosJ, a discrete thiolation protein, to a linear pentathiazolyl peptide intermediate rather than its genetically encoded untreated precursor. This intermediate results from enzymatic processing of the peptide precursor, in which five of the six l-Cys residues are transformed into thiazoles but Cys4 selectively remains unmodified for indolyl substitution via a thioester exchange. Determining the timing of indolyl incorporation, which expands the chemical space of a thiopeptide framework, facilitates mechanistic access to the unusual logic of post-translational modifications in the biosynthesis of nosiheptide-type thiopeptide members that share a similar compact side-ring system. Title: Proteomic analysis of ubiquitinated proteins from deltamethrin-resistant and susceptible strains of the diamondback moth, Plutella Xylostella L Cheng L, Du Y, Hu J, Jiao D, Li J, Zhou Z, Xu Q, Li F Ref: Archives of Insect Biochemistry & Physiology, 90:70, 2015 : PubMed ESTHER: Cheng_2015_Arch.Insect.Biochem.Physiol_90_70 PubMedSearch: Cheng 2015 Arch.Insect.Biochem.Physiol 90 70 PubMedID: 25983007 Abstract Ubiquitin, a small protein consisting of 76 amino acids, acts in protein degradation, DNA repair, signal transduction, transcriptional regulation, and receptor control through endocytosis. Using proteomics, we compared the differentially ubiquitinated proteins between a deltamethrin-resistant (DR) strain and a deltamethrin-sensitive (DS) strain in third-instar larvae of the diamondback moth. We used polyubiquitin affinity beads to enrich ubiquitinated proteins and then performed one-dimensional SDS-PAGE separation and mass spectrometric identification. In the DR strain, We found 17 proteins that were upregulated (relative to the DS strain), including carbonic anhydrase family members, ADP ribosylation factor 102F CG11027-PA, protein kinase 61C, phospholipase A2 , dihydrolipoamide dehydrogenase, tyrosine hydroxylase, and heat shock proteins, and five proteins that were downregulated in the DS strain, including carboxylesterase and DNA cytosine-5 methyltransferase. These results were also verified by qPCR. The differentially ubiquitinated proteins/enzymes were mainly responsible for protein binding, catalytic activity, and molecular transducer activity. These results improve our understanding of the relationship between protein ubiquitination and the deltamethrin stress response. Title: Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov Lai Q, Li G, Liu X, Du Y, Sun F, Shao Z Ref: Antonie Van Leeuwenhoek, 107:1065, 2015 : PubMed ESTHER: Lai_2015_Antonie.Van.Leeuwenhoek_107_1065 PubMedSearch: Lai 2015 Antonie.Van.Leeuwenhoek 107 1065 PubMedID: 25663028 Gene_locus related to this paper: 9rhob-a0a0a0eep0 Abstract A taxonomic study was carried out on strain 22II-S11g(T), which was isolated from the surface seawater of the Atlantic Ocean. The bacterium was found to be Gram-negative, rod shaped without flagellum, oxidase positive and weakly catalase positive. Growth was observed at NaCl concentrations of 0.5-9 % and at temperatures of 10-41 degrees C. The isolate was incapable of gelatin hydrolysis and unable to reduce nitrate to nitrite, degrade aesculin and Tween 80. On the basis of 16S rRNA gene sequence similarity, strain 22II-S11g(T) was found to be most closely related to Oceanicola batsensis HTCC2597(T) (97.26 %), followed by Oceanicola nitratireducens JLT1210(T) (96.39 %), whilst other species of genus Oceanicola shared 94.00-96.34 % sequence similarity. However, it showed low similarity to Oceanicola granulosus HTCC2516(T) (94.79 %), the type species of the genus Oceanicola. Phylogenetic analysis showed that strain 22II-S11g(T) formed a clade with six species currently classified in the genus Oceanicola, but strain O. granulosus HTCC2516(T) and strain O. litoreus M-M22(T) clustered with two other genera respectively. The ANI values between strain 22II-S11g(T) and two type strains (O. batsensis HTCC2597(T) and O. granulosus HTCC2516(T)) are 91.86 and 91.81 % respectively. The digital DNA-DNA hybridization estimate values between strain 22II-S11g(T) and two type strains (O. batsensis HTCC2597(T) and O. granulosus HTCC2516(T)) are 23.4 +/- 2.4 and 20.0 +/- 2.3 %, respectively. The principal fatty acids were identified as summed feature 8 (C18:1 omega7c/omega6c), C16:0, C18:1 omega7c11-methyl and C12:0 3OH. The G+C content determined from the draft genome sequence is 64.1 mol%. The respiratory quinone was determined to be Q-10 (100 %). Phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, phosphatidylcholine, a phospholipid and three lipids were identified in the polar lipids. The combined genotypic and phenotypic data also show that strain 22II-S11g(T) should not be assigned to the genus Oceanicola; consequently strain 22II-S11g(T) is concluded to represent a novel species of a novel genus in the family Rhodobacteraceae, for which the name Pseudooceanicola atlanticus gen. nov., sp. nov. is proposed (type strain 22II-S11g(T) = KCTC 42004(T) = LMG 27424(T) = MCCC 1A09160(T)). Six misclassified species should be transferred to the novel genus Pseudooceanicola as follows: O. batsensis should be transferred to the genus Pseudooceanicola as Pseudooceanicola batsensis comb. nov. (type strain HTCC2597(T) = ATCC BAA-863(T) = DSM 15984(T) = KCTC 12145(T)); Oceanicola marinus should be transferred to the genus Pseudooceanicola as Pseudooceanicola marinus comb. nov. (type strain AZO-C(T) = LMG 23705(T) = BCRC 17591(T)); O. nitratireducens should be transferred to the genus Pseudooceanicola as Pseudooceanicola nitratireducens comb. nov. (type strain JLT1210(T) = LMG 24663(T) = CGMCC 1.7292(T)); Oceanicola nanhaiensis should be transferred to the genus Pseudooceanicola as Pseudooceanicola nanhaiensis comb. nov. (type strain SS011B1-20(T) = LMG 23508(T) = CGMCC 1.6293(T)); Oceanicola antarcticus should be transferred to the genus Pseudooceanicola as Pseudooceanicola antarcticus comb. nov. (type strain Ar-45(T) = CGMCC 1.12662(T) = LMG 27868(T)); and Oceanicola flagellatus should be transferred to the genus Pseudooceanicola as Pseudooceanicola flagellatus comb. nov. (type strain DY470(T) = CGMCC 1.12664(T) = LMG 27871(T)). Title: Aestuariivita atlantica sp. nov., isolated from deep-sea sediment Li G, Lai Q, Du Y, Liu X, Sun F, Shao Z Ref: Int J Syst Evol Microbiol, 65:3281, 2015 : PubMed ESTHER: Li_2015_Int.J.Syst.Evol.Microbiol_65_3281 PubMedSearch: Li 2015 Int.J.Syst.Evol.Microbiol 65 3281 PubMedID: 26297013 Gene_locus related to this paper: 9rhob-a0a0l1ju54 Abstract A novel strain, 22II-S11-z3T, was isolated from the deep-sea sediment of the Atlantic Ocean. The bacterium was aerobic, Gram-staining-negative, oxidase-positive and catalase-negative, oval- to rod-shaped, and non-motile. Growth was observed at salinities of 1-9 % NaCl and temperatures of 10-45 degrees C. The isolate could hydrolyse aesculin and Tweens 20, 40 and 80, but not gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S11-z3T belonged to the genus Aestuariivita, with highest sequence similarity to Aestuariivita boseongensis KCTC 42052T (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain 22II-S11-z3T and A. boseongensis KCTC 42052T were 71.5 % and 20.0 +/- 2.3 %, respectively. The G+C content of the chromosomal DNA was 65.5 mol%. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1omega7c/omega6c) (35.2 %), C19 : 0 cyclo omega8c (20.9 %), C16 : 0 (11.8 %), 11-methyl C18 : 1omega7c (11.4 %) and C12 : 1 3-OH (9.4 %). The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, nine unidentified phospholipids, one unidentified aminolipid and two unidentified lipids were present. The combined genotypic and phenotypic data show that strain 22II-S11-z3T represents a novel species of the genus Aestuariivita, for which the name Aestuariivita atlantica sp. nov. is proposed, with the type strain 22II-S11-z3T ( = KCTC 42276T = MCCC 1A09432T). Title: Tamlana nanhaiensis sp. nov., isolated from surface seawater collected from the South China Sea Liu X, Lai Q, Du Y, Li G, Sun F, Shao Z Ref: Antonie Van Leeuwenhoek, 107:1189, 2015 : PubMed ESTHER: Liu_2015_Antonie.Van.Leeuwenhoek_107_1189 PubMedSearch: Liu 2015 Antonie.Van.Leeuwenhoek 107 1189 PubMedID: 25735434 Gene_locus related to this paper: 9flao-a0a0d7w993 Abstract A polyphasic taxonomic study was performed on a strain, designated FHC16(T), which was isolated from surface seawater collected from the South China Sea. Cells of strain FHC16(T) are Gram stain-negative, oxidase- and catalase-positive and non-motile rods. Growth was observed at 15-37 degreesC (optimum, 25-30 degreesC), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 3%). 16S rRNA gene sequence analysis showed that strain FHC16(T) is most closely related to Tamlana sedimentorum JCM 19808(T) (98.2% sequence similarity). The ANI value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was found to be 81.82-81.81%. The DNA-DNA hybridization estimated value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was determined to be 25.8 +/- 2.41%. The principal fatty acids (>5% of the total) were found to be iso-C(15:0), iso G-C(15:1), iso-C(17:0) 3-OH, iso-C(15:0) 3-OH and summed feature 3 (comprising C(16:1)omega7c/C(16:1)omega6c). The strain was found to have MK-6 as the major respiratory menaquinone, which is consistent with the other three recognized Tamlana species, T. sedimentorum, Tamlana crocina and Tamlana agarivorans. The polar lipids were found to comprise phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids and seven unidentified lipids. The G+C content of the chromosomal DNA was determined to be 34.2 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain FHC16(T) is considered to represent a novel species of the genus Tamlana, for which the name Tamlana nanhaiensis sp. nov. is proposed. The type strain is FHC16(T) (.LMG 27420(T) = CGMCC 1.12469(T) = MCCC 1A06648(T)). Title: Butyrylcholinesterase K Variant and Alzheimer's Disease Risk: A Meta-Analysis Wang Z, Jiang Y, Wang X, Du Y, Xiao D, Deng Y, Wang J Ref: Med Sci Monit, 21:1408, 2015 : PubMed ESTHER: Wang_2015_Med.Sci.Monit_21_1408 PubMedSearch: Wang 2015 Med.Sci.Monit 21 1408 PubMedID: 25978873 Abstract Background Although many studies have estimated the association between the butyrylcholinesterase (BCHE) K variant and Alzheimer's disease (AD) risk, the results are still controversial. We thus conducted this meta-analysis. Material and Methods We searched NCBI, Medline, Web of Science, and Embase databases to find all eligible studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association. Results We found a significant association between BCHE K variant and AD risk (OR=1.20; 95% CI 1.03-1.39; P=0.02). In the stratified analysis by ethnicity, we observed a significant association between BCHE K variant and AD risk in Asians (OR=1.32; 95% CI 1.02-1.72; P=0.04). However, no significant association between BCHE K variant and AD risk in Caucasians was found (OR=1.14; 95% CI 0.95-1.37; P=0.16). When stratified by the age of AD onset, we found that late-onset AD (LOAD) was significantly associated with BCHE K variant (OR=1.44; 95% CI 1.05-1.97; P=0.02). No significant association between BCHE K variant and early-onset AD (EOAD) risk was observed (OR=1.16; 95% CI 0.89-1.51; P=0.27). Compared with non-APOE epsilon4 and non-BCHE K carriers, no significant association between BCHE K variant and AD risk was found (OR=1.11; 95% CI 0.91-1.35; P=0.30). However, APOE epsilon4 carriers showed increased AD risk in both non-BCHE K carriers (OR=2.81; 95% CI 1.75-4.51; P=0.0001) and BCHE K carriers (OR=3.31; 95% CI 1.82-6.02; P=0.0001). Conclusions The results of this meta-analysis indicate that BCHE K variant might be associated with AD risk. Title: Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L and Haddad GG <17 more author(s)> Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG (- 17) Ref: Genome Biol, 15:R36, 2014 : PubMed ESTHER: Udpa_2014_Genome.Biol_15_R36 PubMedSearch: Udpa 2014 Genome.Biol 15 R36 PubMedID: 24555826 Gene_locus related to this paper: human-LIPE Abstract BACKGROUND: Although it has long been proposed that genetic factors contribute to adaptation to high altitude, such factors remain largely unverified. Recent advances in high-throughput sequencing have made it feasible to analyze genome-wide patterns of genetic variation in human populations. Since traditionally such studies surveyed only a small fraction of the genome, interpretation of the results was limited. Title: Lack of Association between NLGN3, NLGN4, SHANK2 and SHANK3 Gene Variants and Autism Spectrum Disorder in a Chinese Population Liu Y, Du Y, Liu W, Yang C, Wang H, Gong X Ref: PLoS ONE, 8:e56639, 2013 : PubMed ESTHER: Liu_2013_PLoS.One_8_e56639 PubMedSearch: Liu 2013 PLoS.One 8 e56639 PubMedID: 23468870 Abstract Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication, absence or delay in language development, and stereotyped or repetitive behaviors. Genetic studies show that neurexin-neuroligin (NRXN-NLGN) pathway genes contribute susceptibility to ASD, which include cell adhesion molecules , and scaffolding proteins and . Neuroligin proteins play an important role in synaptic function and trans-synaptic signaling by interacting with presynaptic neurexins. Shank proteins are scaffolding molecules of excitatory synapses, which function as central organizers of the postsynaptic density. Sequence level mutations and structural variations in these genes have been identified in ASD cases, while few studies were performed in Chinese population. In this study, we examined the copy numbers of four genes and in 285 ASD cases using multiplex fluorescence competitive polymerase chain reaction (PCR). We also screened the regulatory region including the promoter region and 5'/3' untranslated regions (UTR) and the entire coding region of in a cohort of 285 ASD patients and 384 controls by direct sequencing of genomic DNA using the Sanger method. DNA copy number calculation in four genes showed no deletion or duplication in our cases. No missense mutations in were identified in our cohort. Association analysis of 6 common SNPs in did not find significant difference between ASD cases and controls. These findings showed that these genes may not be major disease genes in Chinese ASD cases. Title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts Du Y, Pattnaik AK, Song C, Yoo D, Li G Ref: Virology, 424:18, 2012 : PubMed ESTHER: Du_2012_Virology_424_18 PubMedSearch: Du 2012 Virology 424 18 PubMedID: 22222209 Abstract The porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 4 (GP4) resembles a typical type I membrane protein in its structure but lacks a hydrophilic tail at the C-terminus, suggesting that GP4 may be a lipid-anchored membrane protein. Using the human decay-accelerating factor (DAF; CD55), a known glycosyl-phosphatidylinositol (GPI) lipid-anchored protein, chimeric constructs were made to substitute the GPI-anchor domain of DAF with the putative lipid-anchor domain of GP4, and their membrane association and lipase cleavage were determined in cells. The DAF-GP4 fusion protein was transported to the plasma membrane and was cleaved by phosphatidylinositol-specific phospholipase C (PI-PLC), indicating that the C-terminal domain of GP4 functions as a GPI anchor. Mutational studies for residues adjacent to the GPI modification site and characterization of respective mutant viruses generated from infectious cDNA clones show that the ability of GP4 for membrane association corresponded to virus viability and growth characteristics. The residues T158 (omega-2, where omega is the GPI moiety at E160), P159 (omega-1), and M162 (omega+2) of GP4 were determined to be important for virus replication, with M162 being of particular importance for virus infectivity. The complete removal of the peptide-anchor domain in GP4 resulted in a complete loss of virus infectivity. The depletion of cholesterol from the plasma membrane of cells reduced the virus production, suggesting a role of lipid rafts in PRRSV infection. Remarkably, GP4 was found to co-localize with CD163 in the lipid rafts on the plasma membrane. Since CD163 has been reported as a cellular receptor for PRRSV and GP4 has been shown to interact with this receptor, our data implicates an important role of lipid rafts during entry of the virus. Title: Sodium aescinate ameliorates liver injury induced by methyl parathion in rats Du Y, Wang T, Jiang N, Ren RT, Li C, Li CK, Fu FH Ref: Exp Ther Med, 3:818, 2012 : PubMed ESTHER: Du_2012_Exp.Ther.Med_3_818 PubMedSearch: Du 2012 Exp.Ther.Med 3 818 PubMedID: 22969975 Abstract Methyl parathion, a highly cytotoxic insecticide, has been used in agricultural pest control for several years. The present study investigated the protective effect of sodium aescinate (SA, the sodium salt of aescin) against liver injury induced by methyl parathion. Forty male Sprague-Dawley rats were randomly divided into 5 groups of 8 animals: the control group; the methyl parathion (15 mg/kg) poisoning (MP) group; and the MP plus SA at doses of 0.45, 0.9 and 1.8 mg/kg groups. Alanine aminotransferase (ALT), aspartate aminotransferase (AST) and acetylcholinesterase (AChE) in the plasma were assayed. Nitric oxide (NO) and antioxidative parameters were measured. Histopathological examination of the liver was also performed. The results revealed that SA had no effect on AChE. Treatment with SA decreased the activities of ALT and AST, and the levels of malondialdehyde and NO. Treatment with SA also increased the level of glutathione and the activities of superoxide dismutase and glutathione peroxidase. SA administration also ameliorated liver injury induced by methyl parathion poisoning. The findings indicate that SA protects against liver injury induced by methyl parathion and that the mechanism of action is related to the antioxidative and anti-inflammatory effects of SA. Title: Steady and fluctuant methods of inhibition of acetylcholinesterase differentially regulate neurotrophic factors in the hippocampus of juvenile mice Li C, Wang T, Jiang N, Yu P, Du Y, Ren R, Fu F Ref: Exp Ther Med, 3:269, 2012 : PubMed ESTHER: Li_2012_Exp.Ther.Med_3_269 PubMedSearch: Li 2012 Exp.Ther.Med 3 269 PubMedID: 22969880 Abstract The present study was designed to evaluate the effects of steady and fluctuant inhibition of acetylcholinesterase (AChE) activity on neurotrophic factors in the hippocampus of juvenile mice. Steady inhibition of AChE activity was induced by an intramuscular injection of huperizine A (HupA) sustained-release microspheres. Fluctuant inhibition of AChE activity was induced by an intragastric administration of HupA tablets. Six days after cessation of steady AChE inhibition, there was a significant increase in the levels of brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF). In contrast, fluctuant AChE inhibition had no effect on BDNF and NGF levels. Additionally, neither steady nor fluctuant inhibition of AChE activity altered the choline acetyltransferase activity or spatial learning in juvenile mice. These findings indicate that steady and fluctuant methods of inhibition of AChE have different effects on the levels of BDNF and NGF in the hippocampus. In addition, the effects of AChE inhibitors may not improve learning in normal juvenile animals. Title: The oyster genome reveals stress adaptation and complexity of shell formation Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X and Yin Y <66 more author(s)> Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, Xiong Z, Que H, Xie Y, Holland PW, Paps J, Zhu Y, Wu F, Chen Y, Wang J, Peng C, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z, Zhu Q, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y, Domazet-Loso T, Du Y, Sun X, Zhang S, Liu B, Cheng P, Jiang X, Li J, Fan D, Wang W, Fu W, Wang T, Wang B, Zhang J, Peng Z, Li Y, Li N, Chen M, He Y, Tan F, Song X, Zheng Q, Huang R, Yang H, Du X, Chen L, Yang M, Gaffney PM, Wang S, Luo L, She Z, Ming Y, Huang W, Huang B, Zhang Y, Qu T, Ni P, Miao G, Wang Q, Steinberg CE, Wang H, Qian L, Liu X, Yin Y (- 66) Ref: Nature, 490:49, 2012 : PubMed ESTHER: Zhang_2012_Nature_490_49 PubMedSearch: Zhang 2012 Nature 490 49 PubMedID: 22992520 Gene_locus related to this paper: cragi-k1qzk7, cragi-k1rad0, cragi-k1p6v9, cragi-k1pa46, cragi-k1pga2, cragi-k1pp63, cragi-k1pwa8, cragi-k1q0b1.1, cragi-k1q0b1.2, cragi-k1q1h2, cragi-k1q2z6, cragi-k1qaj8, cragi-k1qaw5, cragi-k1qhl5, cragi-k1qly1, cragi-k1qqb1.1, cragi-k1qqb1.2, cragi-k1qs61, cragi-k1qs99, cragi-k1qwl6, cragi-k1r068, cragi-k1r0n3.1, cragi-k1r0n3.2, cragi-k1r0r4, cragi-k1r1i9, cragi-k1r8q9, cragi-k1rgi1, cragi-k1rig4, cragi-k1s0a7.1, cragi-k1s0a7.2, cragi-k1s0a7.3, cragi-k1q6q0, cragi-k1rru1, cragi-k1qfi4, cragi-k1qvm5, cragi-k1qq58, cragi-k1qdc0, cragi-k1r754, cragi-k1pje5, cragi-k1qca6, cragi-k1qdt5, cragi-k1qkz7, cragi-k1rgd2, cragi-k1puh6, cragi-k1raz4, cragi-k1qqj4, cragi-k1rbs1 Abstract The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. Title: Biosynthesis of the Apoptolidins in Nocardiopsis sp. FU 40 Du Y, Derewacz DK, Deguire SM, Teske J, Ravel J, Sulikowski GA, Bachmann BO Ref: Tetrahedron, 67:6568, 2011 : PubMed ESTHER: Du_2011_Tetrahedron_67_6568 PubMedSearch: Du 2011 Tetrahedron 67 6568 PubMedID: 21869849 Abstract The apoptolidins are 20/21-membered macrolides produced by Nocardiopsis sp. FU40. Several members of this family are potent and remarkably selective inducers of apoptosis in cancer cell lines, likely via a distinct mitochondria associated target. To investigate the biosynthesis of this natural product, the complete genome of the apoptolidin producer Nocardiopsis sp. FU40 was sequenced and a 116 Kb region was identified containing a putative apoptolidin biosynthetic gene cluster. The apoptolidin gene cluster comprises a type I polyketide synthase, with 13 homologating modules, apparently initiated in an unprecedented fashion via transfer from a methoxymalonyl-acyl carrier protein loading module. Spanning approximately 39 open reading frames, the gene cluster was cloned into a series of overlapping cosmids and functionally validated by targeted gene disruption experiments in the producing organism. Disruption of putative PKS and P(450) genes delineated the roles of these genes in apoptolidin biosynthesis and chemical complementation studies demonstrated intact biosynthesis peripheral to the disrupted genes. This work provides insight into details of the biosynthesis of this biologically significant natural product and provides a basis for future mutasynthetic methods for the generation of non-natural apopotolidins. Title: Protective effect of sodium aescinate on lung injury induced by methyl parathion Du Y, Wang T, Jiang N, Ren RT, Zhao DL, Li C, Fu FH Ref: Hum Exp Toxicol, 30:1584, 2011 : PubMed ESTHER: Du_2011_Hum.Exp.Toxicol_30_1584 PubMedSearch: Du 2011 Hum.Exp.Toxicol 30 1584 PubMedID: 21177729 Abstract Methyl parathion (MP) is a high venenosus insecticide. It has been used in pest control of agriculture for several years. The present study is performed to investigate the protective effect of sodium aescinate (SA) on lung injury induced by MP. Forty male Sprague-Dawley rats are randomly divided into five groups, with 8 animals in each group: control group, MP administration group, MP plus SA at doses of 0.45 mg/kg, 0.9 mg/kg and 1.8 mg/kg groups. Acetylcholinesterase (AChE) activity and nitric oxide (NO) level in plasma, myeloperoxidase (MPO) activity, NO level, and antioxidative parameters in lung tissue are assayed. Histopathological examination of lung is also performed. The results show that SA has no effect on AChE. Treatment with SA decreases the activity of MPO in lung and the level of NO in plasma and lung. The level of malondialdehyde in lung is decreased after SA treatments. SA increases the activities of superoxide dismutase, glutathione peroxidase and the content of glutathione in lung. SA administration also ameliorates lung injury induced by MP. The findings indicate that SA could protect lung injury induced by MP and the mechanism of action is related to the anti-inflammatory and anti-oxidative effect of SA. Title: Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-gamma-glutamic acid Geng W, Cao M, Song C, Xie H, Liu L, Yang C, Feng J, Zhang W, Jin Y and Wang S <1 more author(s)> Geng W, Cao M, Song C, Xie H, Liu L, Yang C, Feng J, Zhang W, Jin Y, Du Y, Wang S (- 1) Ref: Journal of Bacteriology, 193:3393, 2011 : PubMed ESTHER: Geng_2011_J.Bacteriol_193_3393 PubMedSearch: Geng 2011 J.Bacteriol 193 3393 PubMedID: 21551302 Gene_locus related to this paper: baca2-a7z811 Abstract Bacillus amyloliquefaciens is one of most prevalent Gram-positive aerobic spore-forming bacteria with the ability to synthesize polysaccharides and polypeptides. Here, we report the complete genome sequence of B. amyloliquefaciens LL3, which was isolated from fermented food and presents the glutamic acid-independent production of poly-gamma-glutamic acid. Title: The genome of the mesopolyploid crop species Brassica rapa Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I and Zhang Z <88 more author(s)> Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Yu J, Meng J, Min J, Poulain J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Z, Li Z, Xiong Z, Zhang Z (- 88) Ref: Nat Genet, 43:1035, 2011 : PubMed ESTHER: Wang_2011_Nat.Genet_43_1035 PubMedSearch: Wang 2011 Nat.Genet 43 1035 PubMedID: 21873998 Gene_locus related to this paper: braol-Q8GTM3, braol-Q8GTM4, brarp-m4ei94, brarp-m4c988, brana-a0a078j4a9, brana-a0a078e1m0, brana-a0a078cd75, brarp-m4dwa6, brana-a0a078j4f0, brana-a0a078cus4, brana-a0a078f8c2, brana-a0a078jql1, brana-a0a078dgj3, brana-a0a078hw50, brana-a0a078cuu0, brana-a0a078dfa9, brana-a0a078ic91, brarp-m4ctw3, brana-a0a078ca65, brana-a0a078ctc8, brana-a0a078h021, brana-a0a078jx23, brarp-m4da84, brarp-m4dwr7, brana-a0a078dh94, brana-a0a078h612, brana-a0a078j2t3, braol-a0a0d3dpb2, braol-a0a0d3dx76, brana-a0a078jxa8, brana-a0a078i2k3, brarp-m4cwq4, brarp-m4dcj8, brarp-m4eh17, brarp-m4eey4, brarp-m4dnj8, brarp-m4ey83, brarp-m4ey84 Abstract We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops. Title: Genome sequence and analysis of the tuber crop potato Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R and Visser RG <87 more author(s)> Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejia N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sonderkaer M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, De Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert B, Goverse A, van Ham RC, Visser RG (- 87) Ref: Nature, 475:189, 2011 : PubMed ESTHER: Xu_2011_Nature_475_189 PubMedSearch: Xu 2011 Nature 475 189 PubMedID: 21743474 Gene_locus related to this paper: soltu-q2tqv0, soltu-q4h433, soltu-m0zl00, soltu-m1aw23, soltu-m0zxh5, soltu-m1d3q4, soltu-m1bz14, soltu-m1d3q6, sollc-k4b1g3, soltu-m0zzn8, soltu-m1ba60, sollc-k4bf33, soltu-m1c8d8, soltu-m1ced9, soltu-m1a385, soltu-m1bz15, soltu-m1a7s9, soltu-m1bc84, soltu-m1bpd1, sollc-k4bm34, soltu-m1a487, soltu-m1a5u0, soltu-m1cjx7, soltu-m1bvq8, soltu-m1baq1, soltu-m1cfh4, soltu-m1azl4, soltu-m0ztj0, soltu-m1d6d0 Abstract Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. Title: Flavonoids from Radix Astragali induce the expression of erythropoietin in cultured cells: a signaling mediated via the accumulation of hypoxia-inducible factor-1alpha Zheng KY, Choi RC, Cheung AW, Guo AJ, Bi CWC, Zhu KY, Fu Q, Du Y, Zhang WL and Tsim KWK <4 more author(s)> Zheng KY, Choi RC, Cheung AW, Guo AJ, Bi CWC, Zhu KY, Fu Q, Du Y, Zhang WL, Zhan JY, Duan R, Lau DT, Dong TTX, Tsim KWK (- 4) Ref: Journal of Agricultural and Food Chemistry, 59:1697, 2011 : PubMed ESTHER: Zheng_2011_J.Agric.Food.Chem_59_1697 PubMedSearch: Zheng 2011 J.Agric.Food.Chem 59 1697 PubMedID: 21309574 Abstract Radix Astragali (RA) is commonly used as a health food supplement to reinforce the body vital energy. Flavonoids, including formononetin, ononin, calycosin, and calycosin-7-O-beta-d-glucoside, are considered to be the major active ingredients within RA. Here, we provided different lines of evidence that the RA flavonoids stimulated the expression of erythropoietin (EPO), the central regulator of red blood cell mass, in cultured human embryonic kidney fibroblasts (HEK293T). A plasmid containing hypoxia response element (HRE), a critical regulator for EPO transcription, was tagged upstream of a firefly luciferase gene, namely, pHRE-Luc, which was being transfected into fibroblasts. The application of RA flavonoids onto the transfected cells induced the transcriptional activity of HRE. To account for the transcriptional activation after the treatment of flavonoids, the expression of hypoxia-inducible factor-1alpha (HIF-1alpha) was markedly increased: The increase was in both mRNA and protein levels. In addition, the degradation of HIF-1alpha was reduced under the effect of flavonoids. The regulation of HIF-1alpha therefore could account for the activation of EPO expression mediated by the RA flavonoids. The current results therefore reveal the function of this herb in enhancing hematopoietic functions. Title: The genome of the cucumber, Cucumis sativus L Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B and Du Y <77 more 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 (- 77) Ref: Nat Genet, 41:1275, 2009 : PubMed 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 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. Title: An integrated genetic and cytogenetic map of the cucumber genome Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H and Huang S <6 more 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 (- 6) Ref: PLoS ONE, 4:e5795, 2009 : PubMed 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 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. Title: Requirement of nicotinic acetylcholine receptor subunit beta2 in the maintenance of spiral ganglion neurons during aging Bao J, Lei D, Du Y, Ohlemiller KK, Beaudet AL, Role LW Ref: Journal of Neuroscience, 25:3041, 2005 : PubMed ESTHER: Bao_2005_J.Neurosci_25_3041 PubMedSearch: Bao 2005 J.Neurosci 25 3041 PubMedID: 15788760 Abstract Age-related hearing loss (presbycusis) is a major health concern for the elderly. Loss of spiral ganglion neurons (SGNs), the primary sensory relay of the auditory system, is associated consistently with presbycusis. The causative molecular events responsible for age-related loss of SGNs are unknown. Recent reports directly link age-related neuronal loss in cerebral cortex with the loss of high-affinity nicotine acetylcholine receptors (nAChRs). In cochlea, cholinergic synapses are made by olivocochlear efferent fibers on the outer hair cells that express alpha9 nAChR subunits and on the peripheral projections of SGNs that express alpha2, alpha4-7, and beta2-3 nAChR subunits. A significantly decreased expression of the beta2 nAChR subunit in SGNs was found specifically in mice susceptible to presbycusis. Furthermore, mice lacking the beta2 nAChR subunit (beta2-/-), but not mice lacking the alpha5 nAChR subunit (alpha5-/-), have dramatic hearing loss and significant reduction in the number of SGNs. Our findings clearly established a requirement for beta2 nAChR subunit in the maintenance of SGNs during aging. Title: [A gene analysis of familial lipoprotein lipase deficiency in China] Shen J, Chen R, Hu W, Bingshen KE, Li L, Du Y, Liu Y Ref: Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 16:233, 1999 : PubMed ESTHER: Shen_1999_Zhonghua.Yi.Xue.Yi.Chuan.Xue.Za.Zhi_16_233 PubMedSearch: Shen 1999 Zhonghua.Yi.Xue.Yi.Chuan.Xue.Za.Zhi 16 233 PubMedID: 10431049 Abstract OBJECTIVE: To investigate the gene mutation of lipoprotein lipase(LPL) of familial LPL deficiency in China. | |||||||
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