Author Report for: Wu MNo contact information in database for Wu M
Hu D, Jin Y, Hou X, Zhu Y, Chen D, Tai J, Chen Q, Shi C, Ye J and Lu Y <2 more author(s)> Hu D, Jin Y, Hou X, Zhu Y, Chen D, Tai J, Chen Q, Shi C, Ye J, Wu M, Zhang H, Lu Y (- 2) Ref: Mar Drugs, 21:, 2023 : PubMed ESTHER: Hu_2023_Mar.Drugs_21_ PubMedSearch: Hu 2023 Mar.Drugs 21 PubMedID: 36662216 Abstract Alzheimer's disease (AD), a neurodegenerative disease, is one of the most intractable illnesses which affects the elderly. Clinically manifested as various impairments in memory, language, cognition, visuospatial skills, executive function, etc., the symptoms gradually aggravated over time. The drugs currently used clinically can slow down the deterioration of AD and relieve symptoms but cannot completely cure them. The drugs are mainly acetylcholinesterase inhibitors (AChEI) and non-competitive N-methyl-D-aspartate receptor (NDMAR) antagonists. The pathogenesis of AD is inconclusive, but it is often associated with the expression of beta-amyloid. Abnormal deposition of amyloid and hyperphosphorylation of tau protein in the brain have been key targets for past, current, and future drug development for the disease. At present, researchers are paying more and more attention to excavate natural compounds which can be effective against Alzheimer's disease and other neurodegenerative pathologies. Marine natural products have been demonstrated to be the most prospective candidates of these compounds, and some have presented significant neuroprotection functions. Consequently, we intend to describe the potential effect of bioactive compounds derived from marine organisms, including polysaccharides, carotenoids, polyphenols, sterols and alkaloids as drug candidates, to further discover novel and efficacious drug compounds which are effective against AD. Title: Impact of Donepezil Supplementation on Alzheimer's Disease-like Pathology and Gut Microbiome in APP/PS1 Mice Li Y, Wu M, Kong M, Sui S, Wang Q, He Y, Gu J Ref: Microorganisms, 11:, 2023 : PubMed ESTHER: Li_2023_Microorganisms_11_ PubMedSearch: Li 2023 Microorganisms 11 PubMedID: 37764150 Abstract Based on published information, the occurrence and development of Alzheimer's disease (AD) are potentially related to gut microbiota changes. Donepezil hydrochloride (DH), which enhances cholinergic activity by blocking acetylcholinesterase (AChE), is one of the first-line drugs for AD treatment approved by the Food and Drug Administration (FDA) of the USA. However, the potential link between the effects of DH on the pathophysiological processes of AD and the gut microbiota remains unclear. In this study, pathological changes in the brain and colon, the activities of superoxide dismutase (SOD) and AChE, and changes in intestinal flora were observed. The results showed that Abeta deposition in the prefrontal cortex and hippocampus of AD mice was significantly decreased, while colonic inflammation was significantly alleviated by DH treatment. Concomitantly, SOD activity was significantly improved, while AChE was significantly reduced after DH administration. In addition, the gut microbiota community composition of AD mice was significantly altered after DH treatment. The relative abundance of Akkermansia in the AD group was 54.8% higher than that in the N group. The relative abundance of Akkermansia was increased by 18.3% and 53.8% in the AD_G group and the N_G group, respectively. Interestingly, Akkermansia showed a potential predictive value and might be a biomarker for AD. Molecular docking revealed the binding mode and major forces between DH and membrane proteins of Akkermansia. The overall results suggest a novel therapeutic mechanism for treating AD and highlight the critical role of gut microbiota in AD pathology. Title: Exogenous methyl jasmonate induced cassava defense response and enhanced resistance to Tetranychus urticae Zhang Y, Liu Y, Liang X, Wu C, Liu X, Wu M, Yao X, Qiao Y, Zhan X, Chen Q Ref: Exp Appl Acarol, :, 2023 : PubMed ESTHER: Zhang_2023_Exp.Appl.Acarol__ PubMedSearch: Zhang 2023 Exp.Appl.Acarol PubMedID: 36635606 Abstract Exogenous application of methyl jasmonate (MeJA) could activate plant defense response against the two-spotted spider mite (TSSM), Tetranychus urticae Koch,sin different plants. However, whether MeJA can also serve as an elicitor in cassava (Manihot esculenta Crantz) remains unknown. In this study, induced defense responses were investigated in TSSM-resistant cassava variety C1115 and TSSM-susceptible cassava variety KU50 when applied with MeJA. The performance of TSSM feeding on cassava plants that werespre-treated with various concentrations of MeJA was first evaluated. Subsequently, the activities of antioxidative enzymes (superoxide dismutase and catalase), detoxification enzymes (glutathione S-transferase, cytochrome P450 and carboxylesterase) and digestive enzymes (protease, amylase and invertase) in TSSM were analyzed at days 1, 2, 4 and 8 post-feeding. The results showed that MeJA treatment can induce cassava defense responses to TSSM in terms of reducing egg production and adult longevity as well as slowing development and prolonging thesegg stage. Noticeably, C1115 exhibited stronger inhibition of TSSM development and reproduction than KU50. In addition, the activities of all the tested enzymes were induced in both C1115 and KU50, the most in C1115. We conclude that exogenous methyl jasmonate can induce cassava defense responses and enhance resistance to TSSM. Title: Defining the Chemical Additives Driving In Vitro Toxicities of Plastics Chen W, Gong Y, McKie M, Almuhtaram H, Sun J, Barrett H, Yang D, Wu M, Andrews RC, Peng H Ref: Environ Sci Technol, :, 2022 : PubMed ESTHER: Chen_2022_Environ.Sci.Technol__ PubMedSearch: Chen 2022 Environ.Sci.Technol PubMedID: 36173153 Abstract Increases in the global use of plastics have caused concerns regarding potential adverse effects on human health. Plastic products contain hundreds of potentially toxic chemical additives, yet the exact chemicals which drive toxicity currently remain unknown. In this study, we employed nontargeted analysis and in vitro bioassays to identify the toxicity drivers in plastics. A total of 56 chemical additives were tentatively identified in five commonly used plastic polymer pellets (i.e., PP, LDPE, HDPE, PET, and PVC) by employing suspect screening and nontargeted analysis. Phthalates and organophosphates were found to be dominant in PVC pellets. Triphenyl phosphate and 2-ethylhexyl diphenyl phosphate accounted for a high amount (53.6%) of the inhibition effect of PVC pellet extract on human carboxylesterase 1 (hCES1) activity. Inspired by the high abundances of chemical additives in PVC pellets, six different end-user PVC-based products including three widely used PVC water pipes were further examined. Among them, extracts of PVC pipe exerted the strongest PPARgamma activity and cell viability suppression. Organotins were identified as the primary drivers to these in vitro toxicities induced by the PVC pipe extracts. This study clearly delineates specific chemical additives responsible for hCES1 inhibition, PPARgamma activity, and cell viability suppression associated with plastic. Title: The Composition and Anti-Aging Activities of Polyphenol Extract from Phyllanthus emblica L. Fruit Wu M, Cai J, Fang Z, Li S, Huang Z, Tang Z, Luo Q, Chen H Ref: Nutrients, 14:, 2022 : PubMed ESTHER: Wu_2022_Nutrients_14_ PubMedSearch: Wu 2022 Nutrients 14 PubMedID: 35215512 Abstract Phyllanthus emblica L. (PE) is commonly known as a medicine and food homologous plant, which is abundant in natural products polyphenols. In the present study, polyphenols were extracted from PE fruit by response surface method, and the anti-aging ability was determined. PE fruit polyphenols exhibited strong antioxidant capacities in scavenging free radicals, and anti-cholinesterase ability by inhibition of AChE (IC(50) 0.2186 +/- 0.0416 mg/mL) and BuChE (IC(50) 0.0542 +/- 0.0054 mg/mL) in vitro. Moreover, PE fruit polyphenols showed strong protective effect against the aging process in Caenorhabditis elegans model, including increased thermal resistance, extended lifespan by 18.53% (p < 0.05), reduced activity of AChE by 34.71% and BuChE by 45.38% (p < 0.01). This was accompanied by the enhancement in antioxidant enzymes activity of SOD by 30.74% (p < 0.05) and CAT by 8.42% (p > 0.05), while decrease in MDA level by 36.25% (p < 0.05). These properties might be interrelated with the presence of abundant flavonols and phenolic acids identified by UPLC-ESI-QTOF-MS, such as quercetin, myricetin, ellagic, gallic, and chlorogenic acids, together with their glycosides. The remarkable antioxidant and anti-aging potential of PE fruit polyphenols could be implemented in the food and pharmaceutical industry. Title: The inhibition mechanism of polyphenols from Phyllanthus emblica Linn. fruit on acetylcholinesterase: A interaction, kinetic, spectroscopic, and molecular simulation study Wu M, Liu M, Wang F, Cai J, Luo Q, Li S, Zhu J, Tang Z, Fang Z and Chen H <1 more author(s)> Wu M, Liu M, Wang F, Cai J, Luo Q, Li S, Zhu J, Tang Z, Fang Z, Wang C, Chen H (- 1) Ref: Food Res Int, 158:111497, 2022 : PubMed ESTHER: Wu_2022_Food.Res.Int_158_111497 PubMedSearch: Wu 2022 Food.Res.Int 158 111497 PubMedID: 35840206 Abstract The present study aimed to investigate the inhibition mechanism of polyphenols from Phyllanthus emblica Linn. fruit (PEF, family Euphorbiaceous) on acetylcholinesterase (AChE). Interaction assay, enzyme kinetics, spectroscopic methods, and molecular simulations were performed. Results showed that myricetin, quercetin, fisetin, and gallic acid were the most active components in PEF, because of their low docking scores and strong inhibition ability on AChE with IC(50) values of 0.1974 +/- 0.0047, 0.2589 +/- 0.0131, 1.0905 +/- 0.0598 and 1.503 +/- 0.0728 mM, respectively. Among them, the results of kinetic study showed that myricetin, quercetin, and fisetin reversibly inhibited AChE in a competitive manner, while gallic acid inhibited it through a noncompetition type. The interaction assay implied that a combination of the four polyphenols at the selected concentrations manifested a synergistic inhibition effect on AChE in a mixed inhibition type. Fluorescence and UV-vis spectrophotometry revealed that the active PEF polyphenols could strongly quench the intrinsic fluorescence of AChE via a static quenching mechanism. Circular dichroism spectroscopy analysis indicated that the active PEF polyphenols gave rise to the secondary structure changes of AChE by increasing the content of alpha-helix and reducing beta-sheet and random coil conformation. The molecular dynamics simulation results validated that all the four docked polyphenol-AChE complexes were relatively stable according to their root-mean-square distance, root-mean-square fluctuations, solvent accessible surface area, radius of gyration values and hydrogen bonds evaluations during the whole simulation process. Overall, our study provides a creative insight into the further utilization of PEF polyphenols as functional components in exploring natural AChE inhibitors. Title: In Vitro and in Silico Analysis of Phytochemicals From Fallopia dentatoalata as Dual Functional Cholinesterase Inhibitors for the Treatment of Alzheimer's Disease Wu Y, Su X, Lu J, Wu M, Yang SY, Mai Y, Deng W, Xue Y Ref: Front Pharmacol, 13:905708, 2022 : PubMed ESTHER: Wu_2022_Front.Pharmacol_13_905708 PubMedSearch: Wu 2022 Front.Pharmacol 13 905708 PubMedID: 35899116 Abstract Current studies have found that butyrylcholinesterase (BuChE) replaces the biological function of acetylcholinesterase (AChE) in the late stage of Alzheimer's disease. Species in the genus of Fallopia, rich in polyphenols with diverse chemical structures and significant biological activities, are considered as an important resource for screening natural products to against AD. In this study, thirty-four compounds (1-34) were isolated from Fallopia dentatoalata (Fr. Schm.) Holub, and their inhibitory effects against AChE and BuChE were assessed. Compounds of the phenylpropanoid sucrose ester class emerged as the most promising members of the group, with 31-33 displaying moderate AChE inhibition (IC50 values ranging from 30.6 +/- 4.7 to 56.0 +/- 2.4 microM) and 30-34 showing potential inhibitory effects against BuChE (IC50 values ranging from 2.7 +/- 1.7 to 17.1 +/- 3.4 microM). Tacrine was used as a positive control (IC50: 126.7 +/- 1.1 in AChE and 5.5 +/- 1.7 nM in BuChE). Kinetic analysis highlighted compounds 31 and 32 as non-competitive inhibitors of AChE with Ki values of -30.0 and -34.4 microM, whilst 30-34 were revealed to competitively inhibit BuChE with Ki values ranging from -1.8 to -17.5 microM. Molecular binding studies demonstrated that 30-34 bound to the catalytic sites of BuChE with negative binding energies. The strong agreement between both in vitro and in silico studies highlights the phenylpropanoid sucrose esters 30-34 as promising candidates for use in future anti-cholinesterase therapeutics against Alzheimer's disease. Title: Gram-Scale Synthesis of (R)-P-Chlorophenyl-1,2-Ethanediol at High Concentration by a Pair of Epoxide Hydrolases Zhang D, Lei Y, Wang T, Lin W, Chen X, Wu M Ref: Front Bioeng Biotechnol, 10:824300, 2022 : PubMed ESTHER: Zhang_2022_Front.Bioeng.Biotechnol_10_824300 PubMedSearch: Zhang 2022 Front.Bioeng.Biotechnol 10 824300 PubMedID: 35295651 Abstract (R)-p-chlorophenyl-1,2-ethanediol (pCPED) is an important intermediate for the synthesis of (R)-eliprodil that is widely applied in the treatment of ischemic stroke. To prepare (R)-pCPED with high enantiomeric excess (ee (p)) and yield via the enantioconvergent hydrolysis of racemic styrene oxide (rac-pCSO) at high concentration, the bi-enzymatic catalysis was designed and investigated by a pair of epoxide hydrolases, a mutant (PvEH1(Z4X4-59)) of Phaseolus vulgaris EH1 and a mutant (RpEH(F361V)) of Rhodotorula paludigena RpEH. Firstly, the maximum allowable concentration of rac-pCSO was confirmed. Subsequently, the addition mode and the weight ratio of two Escherichia coli cells were optimized. Finally, under the optimized reaction conditions-the cell weight ratio 20:1 of E. coli/pveh1(z4x4-59) to E. coli/rpeh (F361V), a simultaneous addition mode, and reaction temperature at 25 degreesC-300 mM rac-pCSO in the 100 ml 4% (v/v) Tween-20/phosphate buffer system (100 mM, pH 7.0) was completely hydrolyzed within 5 h, affording (R)-pCPED with 87.8% ee (p), 93.4% yield, and 8.63 g/L/h space-time yield (STY). This work would be an efficient technical strategy for the preparation of chiral vicinal diols at industrial scale. Title: Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9 Zhou X, Lei D, Tang J, Wu M, Ye H, Zhang Q Ref: AMB Express, 12:51, 2022 : PubMed ESTHER: Zhou_2022_AMB.Express_12_51 PubMedSearch: Zhou 2022 AMB.Express 12 51 PubMedID: 35523901 Abstract Citrobacter freundii CD-9 is a Gram-negative bacteria sourced from factory sludge that can use fenvalerate as its sole carbon source and has a broad degradation spectrum for pyrethroid pesticides. The whole genome of CD-9 sequenced using Illumina HiSeq PE150 was reported in this study. The CD-9 genome size was 5.33 Mb and the G + C content was 51.55%. A total of 5291 coding genes, 9 5s-rRNA, and 79 tRNA were predicted bioinformatically. 3586 genes annotated to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database that can be involved in 173 metabolic pathways, including various microbial metabolic pathways that degrade exogenous chemicals, especially those that degrade aromatic compounds, and also produce a variety of bioactive substances. Fifty genes related to pyrethroid degradation were identified in the C. freundii CD-9 genome, including 9 dioxygenase, 25 hydrolase, and 16 esterase genes. Notably, RT-qPCR results showed that from the predicted 13 genes related to fenvalerate degradation, the expression of six genes, including esterase, HAD family hydrolase, lipolytic enzyme, and gentisic acid dioxygenase, was induced in the presence of fenvalerate. In this study, the key genes and degradation mechanism of C. freundii CD-9 were analyzed and the results provide scientific evidence to support its application in environmental bioremediation. It can establish application models for different environmental pollution management by constructing genetically engineered bacteria for efficient fenvalerate or developing enzyme formulations that can be industrially produced. Title: Impacts of chronic exposure to sublethal diazepam on behavioral traits of female and male zebrafish (Danio rerio) Chen K, Wu M, Chen C, Xu H, Wu X, Qiu X Ref: Ecotoxicology & Environmental Safety, 208:111747, 2021 : PubMed ESTHER: Chen_2021_Ecotoxicol.Environ.Saf_208_111747 PubMedSearch: Chen 2021 Ecotoxicol.Environ.Saf 208 111747 PubMedID: 33396073 Abstract Residues of the psychoactive drug diazepam (DZP) may pose potential risks to fish in aquatic environments, especially by disrupting their behavioral traits. In this study, female and male zebrafish were subjected to chronic exposure (21 days) to sublethal doses (120 and 12 microg/L) of DZP, aimed to compare the characteristics of their behavioral responses to DZP exposure, and to investigate the possible links between those behavioral responses and variations in their brain gamma-aminobutyric acid (GABA) and acetylcholinesterase (AChE) levels. Chronic exposure to DZP significantly decreased the swimming velocity and locomotor activity of both genders, indicating a typical sedative effect. Compared with males, whose locomotor activity was only significantly decreased by exposure to DZP for 21 days, females became hypoactive on day 14 (i.e., more sensitive), and they developed tolerance to the hypoactive effect induced by 120 microg/L DZP by day 21. Exposure to DZP significantly disturbed the behavioral traits related to social interactions in females but not in males. Those results indicate that DZP exhibits sex-dependent effects on the behaviors of fish. Moreover, exposure to DZP for 21 days significantly disturbed almost all of the tested behavioral traits associated with courtship when both genders were put together. Sex-dependent responses in brain GABA and AChE levels due to DZP exposure were also identified. Significant relationships between the brain GABA/AChE levels and some behavioral parameters related to locomotor activity were detected in females, but not in males. Title: Safety and pharmacokinetic interaction between fotagliptin, a dipeptidyl peptidase-4 inhibitor, and metformin in healthy subjects Ding Y, Zhang H, Li C, Zheng W, Wang M, Li Y, Sun H, Wu M Ref: Expert Opin Drug Metab Toxicol, 17:725, 2021 : PubMed ESTHER: Ding_2021_Expert.Opin.Drug.Metab.Toxicol_17_725 PubMedSearch: Ding 2021 Expert.Opin.Drug.Metab.Toxicol 17 725 PubMedID: 33899649 Inhibitor(s) related to this paper: Fotagliptin Abstract BACKGROUND: Dipeptidyl peptidase-4 (DPP-4) inhibitors have significant clinical efficacy for type 2 diabetes mellitus (T2DM). The combination of fotagliptin (FOT) with metformin (MET) is a promising therapeutic approach in MET-resistant patients. The aim of the present study was to evaluate the pharmacokinetic (PK) interaction between FOT and MET in healthy subjects after multiple-dose administration. METHODS: Eighteen participants received a randomized open-label, three period treatment that included MET 1000 mg alone, co-administration of FOT 24 mg and MET, followed by FOT 24 mg alone. Serial blood samples were collected for PK analysis, which included geometric mean ratios (GMRs) with 90% confidence intervals (CIs), area under the concentration-time curve (AUC), and maximum plasma concentration (C(max)). RESULTS: Analysis results showed that for FOT alone or combination therapy, the 90% CIs of the GMR for AUC(0-24,ss) and C(max,ss) were 102.08% (98.9%, 105.36%) and 110.65% (102.19%, 119.82%), respectively. For MET, they were 113.41% (100.32%, 128.22%) and 97.11% (83.80%, 112.55%) for AUC(0-12,ss) and C(max,ss), respectively. FOT or MET monotherapy and the combination therapy with both drugs were well tolerated. CONCLUSIONS: No PK drug-drug interactions were found in the combination therapy with FOT and MET. Therefore, FOT can be co-administered with MET without dose adjustment. TRIAL REGISTRATION: The trial is registered at http://www.chinadrugtrials.org.cn/(Registration No. CTR20190221). Title: Acorenone C: A New Spiro-Sesquiterpene from a Mangrove-Associated Fungus, Pseudofusicoccum sp. J003 Jia S, Su X, Yan W, Wu M, Wu Y, Lu J, He X, Ding X, Xue Y Ref: Front Chem, 9:780304, 2021 : PubMed ESTHER: Jia_2021_Front.Chem_9_780304 PubMedSearch: Jia 2021 Front.Chem 9 780304 PubMedID: 34900941 Abstract Mangrove-derived endophytes are rich in bioactive secondary metabolites with a variety of biological activities. Recently, a fungus Pseudofusicoccum sp. J003 was first isolated by our research group from mangrove species Sonneratia apetala Buch.-Ham. The subsequent chemical investigation of the methanol extract of the culture broth of this strain has led to the isolation of a new sesquiterpenoid named acorenone C (1), two alkaloids (2-3), four phenolic compounds (4-7), and four steroid derivatives (8-11). The new structure of 1 was established by extensive spectroscopic analysis, including 1D, 2D NMR spectroscopy, and HRESIMS. Its absolute configuration was elucidated by experimental ECD and ECD calculation. The in vitro AChE inhibitory, anti-inflammatory, and cytotoxic activities of the selected compounds were evaluated. The results showed that compound 1 showed mild AChE inhibitory activity, with an inhibition rate of 23.34% at the concentration of 50 microM. Compound 9 exerted a significant inhibitory effect against nitric oxide (NO) production in LPS-stimulated RAW 264.7 mouse macrophages, with an inhibition rate of 72.89% at the concentration of 25 microM, better than that of positive control L-NMMA. Compound 9 also displayed obvious inhibition effects on the growth of two human tumor cell lines, HL-60 and SW480 (inhibition rates 98.68 +/- 0.97% and 60.40 +/- 4.51%, respectively). The antimicrobial activities of the compounds (1-11) against Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Pseudomonas aeruginosa were also tested; however, none of them showed antimicrobial activities. Title: Degradation and toxicity of the antidepressant fluoxetine in an aqueous system by UV irradiation Pan C, Zhu F, Wu M, Jiang L, Zhao X, Yang M Ref: Chemosphere, :132434, 2021 : PubMed ESTHER: Pan_2021_Chemosphere__132434 PubMedSearch: Pan 2021 Chemosphere 132434 PubMedID: 34606890 Abstract Fluoxetine (FLU), a selective serotonin reuptake inhibitor, is commonly found in aquatic environments. Ultraviolet (UV) photolysis is widely used to remove certain pharmaceuticals from water and wastewater. The present study aimed to investigate the toxicity of FLU and its transformed products formed during UV photolysis by using zebrafish embryos (Danio rerio) as a model. The degradation rates of FLU for five days were approximately 63.6% +/- 2.14%, 84.6% +/- 0.99%, and 97.5% +/- 0.25% after 15, 30, and 60 min of UV irradiation, respectively. Furthermore, the degradation mechanism was explored using LC-MS measurements and density flooding theory (DFT) theoretical calculations. Comprehensive toxicity preassessment of FLU and its degradation products was carried out using the T.E.S.T. software. The effects of physiological and biochemical parameters and neuron- and apoptosis-related gene expression were examined in zebrafish embryos exposed to non-irradiated (0-min) and irradiated (15, 30- and 60-min) solutions from 4 h post-fertilization (hpf) to 120 hpf. The hatching time of zebrafish embryos exposed to the non-irradiated solution (0-min) and irradiated solution (60-min) was delayed, their heart rate at 48 and 72 hpf increased, and their body length at 120 hpf decreased. Significant differences were found between the non-irradiated (0-min) and UV-irradiated (15- or 30-min) groups. A dynamic response involving acetylcholinesterase (AChE) and superoxide dismutase (SOD) activity was also observed in the non-irradiated and UV-irradiated groups. During the UV treatment experiments, the expression levels of neuron-related and apoptosis-related genes were significantly reduced over time alongside the formation of FLU degradation products. Overall, this study provides new concepts to remove and assess the toxicity of emerging contaminants in aquatic environments and highlights the need to consider the formation and persistence of toxic transformation products. Title: An efficient phthalate ester-degrading Bacillus subtilis: Degradation kinetics, metabolic pathway, and catalytic mechanism of the key enzyme Xu Y, Liu X, Zhao J, Huang H, Wu M, Li X, Li W, Sun X, Sun B Ref: Environ Pollut, 273:116461, 2021 : PubMed ESTHER: Xu_2021_Environ.Pollut_273_116461 PubMedSearch: Xu 2021 Environ.Pollut 273 116461 PubMedID: 33485001 Gene_locus related to this paper: bacsu-pnbae Abstract Phthalate ester pollution in the environment and food chain is frequently reported. Microbial treatment is a green and efficient method for solving this problem. The isolation and systematic investigation of microorganisms generally recognized as safe (GRAS) will provide useful resources. A GRAS Bacillus subtilis strain, BJQ0005, was isolated from Baijiu fermentation starter and efficiently degraded phthalate esters (PAEs). The half-lives for di-isobutyl phthalate, di-butyl phthalate and di-(2-ethylhexyl) phthalate were 3.93, 4.28, and 25.49 h, respectively, from the initial amount of 10 mg per 10 mL reaction mixture, which are records using wild-type strains. Genome sequencing and metabolic intermediate analysis generated the whole metabolic pathway. Eighteen enzymes from the alpha/beta hydrolase family were expressed. Enzymes GTW28_09400 and GTW28_13725 were capable of single ester bond hydrolysis of PAEs, while GTW28_17760 hydrolyzed di-ester bonds of PAEs. Using molecular docking, a possible mechanism affecting enzymatic ester bond hydrolysis of mono-butyl phthalate was proposed of GTW28_17760. The carboxyl group generated by the first hydrolysis step interacted with histidine in the catalytic active center, which negatively affected enzymatic hydrolysis. Isolation and systematic investigation of the PAE degradation characteristics of B. subtilis will promote the green and safe treatment of PAEs in the environment and food industry. Title: Huperzine A ameliorates obesity-related cognitive performance impairments involving neuronal insulin signaling pathway in mice Wang HY, Wu M, Diao JL, Li JB, Sun YX, Xiao XQ Ref: Acta Pharmacol Sin, 41:145, 2020 : PubMed ESTHER: Wang_2020_Acta.Pharmacol.Sin_41_145 PubMedSearch: Wang 2020 Acta.Pharmacol.Sin 41 145 PubMedID: 31213670 Abstract Type 2 diabetes (T2D) and Alzheimer's disease (AD) share several common pathophysiological features. Huperzine A (Hup A), a Lycopodium alkaloid extracted from the Chinese herb moss Huperzia serrata, is a specific and reversible inhibitor of acetylcholinesterase, which is clinically used for the treatment of AD. In this study, we investigated whether Hup A improved the metabolic and cognitive functions in the high fat-induced (HFD) obese mice and genetic ob/ob mice. HFD and ob/ob mice were treated with Hup A (0.1, 0.3 mg . kg(-1) . d(-1), ig) for 3 months. Body weight was monitored and glucose tolerance tests were performed. Novel object recognition test and Morris water maze assay were conducted to evaluate the cognitive functions. We found that the Hup A treatment had no significant effect on peripheral metabolism of obese mice, whereas Hup A (0.1, mg . kg(-1) . d(-1)) improved both the abilities of object recognition and spatial memory in HFD-fed mice, but not in ob/ob mice. Furthermore, Hup A treatment significantly upregulated the insulin and phosphorylated Akt levels in the cortex of HFD-fed mice, but not ob/ob mice. In addition, Hup A (0.3, mg . kg(-1) . d(-1)) significantly decreased cortical beta-secretase (BACE1) expression. In conclusion, these results demonstrate that treatment with Hup A (0.1, mg . kg(-1) . d(-1)) can effectively improve the cognitive functions, at least in diet-induced obese mice. Title: Biological evaluation of 7-O-amide hesperetin derivatives as multitarget-directed ligands for the treatment of Alzheimer's disease Wu M, Zhu X, Zhang Y, Wang M, Liu T, Han J, Li J, Li Z Ref: Chemico-Biological Interactions, 334:109350, 2020 : PubMed ESTHER: Wu_2020_Chem.Biol.Interact_334_109350 PubMedSearch: Wu 2020 Chem.Biol.Interact 334 109350 PubMedID: 33307048 Abstract A series of 7-O-amide hesperetin derivatives were subjected to multi-target biological evaluation of anti-Alzheimer's disease. Most of the compounds showed good in vitro inhibitory activity against cholinesterase, of which compound 7c (7-O-(4-(morpholinoethyl)-acetamide) hesperetin) was the most effective anti-eqBuChE derivative (IC(50) = 0.28 +/- 0.05 M) and exerted neuroprotective effects. Further biological evaluation found that compounds 4d, 4e and 7c showed strong antioxidant, anti-Abeta self-aggregation and anti-neuroinflammatory activities. Compound 7c could inhibit the expression of iNOS and COX-2 proteins and prevent LPS-induced inflammatory response in BV2 cells. In addition, compound 7c could chelate biometal ions such as Cu(2+) and Zn(2+). In the vivo study, the MWM test confirmed that compound 7c could improve the cognitive impairment caused by scopolamine. In summary, the above studies have shown that the optimized compound 7c has great development potential as MTDL for the treatment of AD. Title: Significant improvement in catalytic activity and enantioselectivity of a Phaseolus vulgaris epoxide hydrolase, PvEH3, towards ortho-cresyl glycidyl ether based on the semi-rational design Zhang C, Liu Y, Li C, Xu Y, Su Y, Li J, Zhao J, Wu M Ref: Sci Rep, 10:1680, 2020 : PubMed ESTHER: Zhang_2020_Sci.Rep_10_1680 PubMedSearch: Zhang 2020 Sci.Rep 10 1680 PubMedID: 32015448 Gene_locus related to this paper: phavu-PvEH3 Abstract The investigation of substrate spectrum towards five racemic (rac-) aryl glycidyl ethers (1a-5a) indicated that E. coli/pveh3, an E. coli BL21(DE3) transformant harboring a PvEH3-encoding gene pveh3, showed the highest EH activity and enantiomeric ratio (E) towards rac-3a. For efficiently catalyzing the kinetic resolution of rac-3a, the activity and E value of PvEH3 were further improved by site-directed mutagenesis of selected residues. Based on the semi-rational design of an NC-loop in PvEH3, four single-site variants of pveh3 were amplified by PCR, and intracellularly expressed in E. coli BL21(DE3), respectively. E. coli/pveh3(E134K) and /pveh3(T137P) had the enhanced EH activities of 15.3 +/- 0.4 and 16.1 +/- 0.5 U/g wet cell as well as E values of 21.7 +/- 1.0 and 21.2 +/- 1.1 towards rac-3a. Subsequently, E. coli/pveh3(E134K/T137P) harboring a double-site variant gene was also constructed, having the highest EH activity of 22.4 +/- 0.6 U/g wet cell and E value of 24.1 +/- 1.2. The specific activity of the purified PvEH3(E134K/T137P) (14.5 +/- 0.5 U/mg protein) towards rac-3a and its catalytic efficiency (k(cat)/K(m) of 5.67 mM(-1) s(-1)) for (S)-3a were 1.7- and 3.54-fold those (8.4 +/- 0.3 U/mg and 1.60 mM(-1) s(-1)) of PvEH3. The gram-scale kinetic resolution of rac-3a using whole wet cells of E. coli/pveh3(E134K/T137P) was performed at 20 degC for 7.0 h, producing (R)-3a with 99.4% ee(s) and 38.5 +/- 1.2% yield. Additionally, the mechanism of PvEH3(E134K/T137P) with remarkably improved E value was analyzed by molecular docking simulation. Title: Design, synthesis, and biological evaluation of rutacecarpine derivatives as multitarget-directed ligands for the treatment of Alzheimer's disease Wu M, Ma J, Ji L, Wang M, Han J, Li Z Ref: Eur Journal of Medicinal Chemistry, 177:198, 2019 : PubMed ESTHER: Wu_2019_Eur.J.Med.Chem_177_198 PubMedSearch: Wu 2019 Eur.J.Med.Chem 177 198 PubMedID: 31136894 Abstract A series of 3-amino-substituted rutacecarpine derivatives were synthesized to identify novel multitarget-directed ligands (MTDLs) for the treatment of Alzheimer's disease (AD). Biological evaluation showed that most of the synthesized compounds inhibited butyrylcholinesterase (BuChE) and exerted antioxidant effects. Among the synthesized compounds, 6n was subjected to further biological evaluation. Lineweaver-Burk plotting and molecular modeling illustrated that 6n bound simultaneously to the peripheral anionic site (PAS) and catalytic sites (CAS) of BuChE. Furthermore, 6n modulated Abeta aggregation; chelated biometals; presented good absorption, distribution, metabolism, excretion, and toxicity properties; and showed remarkable neuroprotective activity. Previous research has shown that the optimized compound 6n has considerable potential for development as an MTDL for the treatment of AD. Title: Safety, efficacy, and pharmacokinetics of pradefovir for the treatment of chronic hepatitis B infection Zhang H, Liu J, Zhu X, Li X, Jin W, Chen H, Wu M, Li C, Liu C and Ding Y <1 more author(s)> Zhang H, Liu J, Zhu X, Li X, Jin W, Chen H, Wu M, Li C, Liu C, JunqiNiu, Ding Y (- 1) Ref: Antiviral Res, :104693, 2019 : PubMed ESTHER: Zhang_2019_Antiviral.Res__104693 PubMedSearch: Zhang 2019 Antiviral.Res 104693 PubMedID: 31838002 Abstract BACKGROUND & AIMS: Pradefovir is a liver targeted novel prodrug of adefovir (PMEA) developed to provide higher antiviral activity with reduced systemic toxicities. This study evaluated the tolerability, pharmacokinetics, and antiviral activity of pradefovir in patients with chronic hepatitis B (CHB) virus infection. METHODS: Non-cirrhotic, treatment-naive subjects with CHB were divided into five groups (10 patients each) and randomized within each group in a ratio of 6:2:2 to receive an ascending dose of 30, 60, 75, 90, or 120mg pradefovir, 10mg adefovir dipivoxil (ADV), or 300mg tenofovir disoproxil fumarate (TDF) once a day for 28 days. RESULTS: A total of 51 subjects were randomized and 49 subjects completed the study. The groups were well matched and included 39 males, of whom 71% were hepatitis B e-antigen-negative with a mean hepatitis B virus (HBV) DNA level of 6.4-7.16 log10 IU/mL. No subject experienced a serious adverse event or nephrotoxicity. The most frequently reported adverse event was asymptomatic reduction in blood cholinesterase levels in the pradefovir group which recovered without any treatment about 13+/-7 days after drug discontinuation. This adverse event was not observed in the ADV and TDF groups. The mean changes in serum HBV DNA were -2.78, -2.77, -3.08, -3.18, -3.44, -2.34, and -3.07 log10 IU/mL at 30, 60, 75, 90, and 120mg pradefovir, 10mg ADV and 300mg TDF, respectively, with plateau levels reached with 60mg pradefovir. Pradefovir and its metabolite PMEA showed linear pharmacokinetics proportional to the dose. The half-life of PMEA in the pradefovir group was 11.47-17.63h. CONCLUSIONS: Short-term use of pradefovir was well tolerated. A decline in HBV DNA levels was superior to TDF at higher doses of pradefovir. 30-60mg pradefovir is recommended for CHB treatment. CLINICAL TRIAL NUMBER: CTR20150224. Title: Tissue bioconcentration and effects of fluoxetine in zebrafish (Danio rerio) and red crucian cap (Carassius auratus) after short-term and long-term exposure Pan C, Yang M, Xu H, Xu B, Jiang L, Wu M Ref: Chemosphere, 205:8, 2018 : PubMed ESTHER: Pan_2018_Chemosphere_205_8 PubMedSearch: Pan 2018 Chemosphere 205 8 PubMedID: 29679789 Abstract Fluoxetion (FLU) is an antidepressant pharmaceutical most commonly detected in the aquatic environment. The present study aims to elucidate the tissue accumulation and effects of FLU using two different fish models. First, the multiple effects and the FLU levels in fish, were examined in zebrafish (Danio rerio) embryos exposed to FLU concentrations (0, 0.1, 1, 10, 100, 1000mug/L) from 4h post-fertilization (hpf) until 120 hpf. Exposure to FLU accelerated heart rates, postponed hatching time, and increased swimming speed of fish. A dynamic response of acetylcholinesterase (AChE) activity was also displayed in the fish. Second, a 30-day exposure experiment using red crucian carp (Carassius auratus) was performed, and it found that the concentration of FLU in fish organs increased with increasing water concentrations, but the highest FLU bioconcentration was present in the lowest FLU exposure group (0.1mug/L). Finally, 6 days of exposure to 0.1mug/L of FLU followed by a 6-day clearance experiment was performed with both adult zebrafish and red crucian carp. The FLU levels in different fish organs increased as exposure time increased, but they sharply declined following the 6-day clearance. Correspondingly, the changes in brain AChE activity and in antioxidant parameters in the liver were consistent with the FLU levels in the fish organs. Our study provides fundamental data on the tissue accumulation and concentration-dependent effects in fish exposed to fluoxetine. Title: Response of detoxification and immune genes and of transcriptome expression in Mythimna separata following chlorantraniliprole exposure Wang JD, Wang WZ, Wang YR, Gao SJ, Elzaki M, Wang R, Wu M Ref: Comparative Biochemistry & Physiology Part D Genomics Proteomics, 28:90, 2018 : PubMed ESTHER: Wang_2018_Comp.Biochem.Physiol.Part.D.Genomics.Proteomics_28_90 PubMedSearch: Wang 2018 Comp.Biochem.Physiol.Part.D.Genomics.Proteomics 28 90 PubMedID: 30005390 Abstract The oriental armyworm Mythimna separata is a serious polyphagous pest in China and there are major efforts to control this pest. In the present study, an RNA-Seq method was used to explore transcriptome data of M. separata and identify the responses of genes to chlorantraniliprole. Sequencing and de novo assembly yielded 134,533 transcripts that were further assembled into 77,628 unigenes with an N50 length of 2165bp. A total of 76 unigenes encoding insecticide targets were identified. Furthermore, 62 cytochrome P450s, 34 glutathione S-transferase (GSTs)and 64 carboxylesterase (CCEs) were curated to construct phylogenetic trees. In addition, we identified 647 the differentially expressed genes following treatment with chlorantraniliprole. The pathways of calcium signaling was identified as response to the pesticide The transcriptome data we generated represents a comprehensive genomic resource for further studies focused on control of M. separata. The response of genes to chlorantraniliprole treatment will elucidate the molecular mechanisms of insecticide resistance and allow for the development of new chemical pesticides to control this pest. Title: Impairment of Inhibitory Synapse Formation and Motor Behavior in Mice Lacking the NL2 Binding Partner LHFPL4/GARLH4 Wu M, Tian HL, Liu X, Lai JHC, Du S, Xia J Ref: Cell Rep, 23:1691, 2018 : PubMed ESTHER: Wu_2018_Cell.Rep_23_1691 PubMedSearch: Wu 2018 Cell.Rep 23 1691 PubMedID: 29742426 Abstract Normal brain functions depend on the balanced development of excitatory and inhibitory synapses. Our knowledge of the molecular mechanisms underlying inhibitory synapse formation is limited. Neuroligin-2 (NL2), a transmembrane protein at inhibitory postsynaptic sites, is capable of initiating inhibitory synapse formation. In an effort to search for NL2 binding proteins and the downstream mechanisms responsible for inhibitory synapse development, we identify LHFPL4/GARLH4 as a major NL2 binding partner that is specifically enriched at inhibitory postsynaptic sites. LHFPL4/GARLH4 and NL2 regulate the protein levels and synaptic clustering of each other in the cerebellum. Lhfpl4/Garlh4(-/-) mice display profound impairment of inhibitory synapse formation as well as prominent motor behavioral deficits and premature death. Our findings highlight the essential role of LHFPL4/GARLH4 in brain functions by regulating inhibitory synapse formation as a major NL2 binding partner. Title: Stereoselective Hydrolysis of Epoxides by reVrEH3, a Novel Vigna radiata Epoxide Hydrolase with High Enantioselectivity or High and Complementary Regioselectivity Hu D, Tang C, Li C, Kan T, Shi X, Feng L, Wu M Ref: Journal of Agricultural and Food Chemistry, 65:9861, 2017 : PubMed ESTHER: Hu_2017_J.Agric.Food.Chem_65_9861 PubMedSearch: Hu 2017 J.Agric.Food.Chem 65 9861 PubMedID: 29058432 Gene_locus related to this paper: vigra-Vreh3 Abstract To provide more options for the stereoselective hydrolysis of epoxides, an epoxide hydrolase (VrEH3) gene from Vigna radiata was cloned and expressed in Escherichia coli. Recombinant VrEH3 displayed the maximum activity at pH 7.0 and 45 degrees C and high stability at pH 4.5-7.5 and 55 degrees C. Notably, reVrEH3 exhibited high and complementary regioselectivity toward styrene oxides 1a-3a and high enantioselectivity (E = 48.7) toward o-cresyl glycidyl ether 9a. To elucidate these interesting phenomena, the interactions of the three-dimensional structure between VrEH3 and enantiomers of 1a and 9a were analyzed by molecular docking simulation. Using E. coli/vreh3 whole cells, gram-scale preparations of (R)-1b and (R)-9a were performed by enantioconvergent hydrolysis of 100 mM rac-1a and kinetic resolution of 200 mM rac-9a in the buffer-free water system at 25 degrees C. These afforded (R)-1b with >99% eep and 78.7% overall yield after recrystallization and (R)-9a with >99% ees, 38.7% overall yield, and 12.7 g/L/h space-time yield. Title: Enantioconvergent hydrolysis of racemic styrene oxide at high concentration by a pair of novel epoxide hydrolases into (R)-phenyl-1,2-ethanediol Wang R, Hu D, Zong X, Li J, Ding L, Wu M Ref: Biotechnol Lett, 39:1917, 2017 : PubMed ESTHER: Wang_2017_Biotechnol.Lett_39_1917 PubMedSearch: Wang 2017 Biotechnol.Lett 39 1917 PubMedID: 28875350 Gene_locus related to this paper: vigra-Vreh3, aspng-q1ktb5 Inhibitor(s) related to this paper: Styrene-glycol Abstract OBJECTIVES: To prepare (R)-phenyl-1,2-ethanediol ((R)-PED) with high enantiomeric excess (ee p) and yield from racemic styrene oxide (rac-SO) at high concentration by bi-enzymatic catalysis. Title: Effects of the antidepressant, mianserin, on early development of fish embryos at low environmentally relevant concentrations Yang M, Liu S, Hu L, Zhan J, Lei P, Wu M Ref: Ecotoxicology & Environmental Safety, 150:144, 2017 : PubMed ESTHER: Yang_2017_Ecotoxicol.Environ.Saf_150_144 PubMedSearch: Yang 2017 Ecotoxicol.Environ.Saf 150 144 PubMedID: 29272719 Abstract Pharmaceuticals have been considered as emerging organic contaminants in the environment that might pose huge risk to the non-target aquatic organisms. Mianserin, a tetracyclic antidepressant, is present at low detectable concentrations in the aquatic environment; however, limited attention has been devoted to its potential adverse effects on the aquatic animals. In the present study, we first performed an acute toxicity test for mianserin exposure using zebrafish (Danio rerio) embryos during 4-124h post fertilization (hpf). Time-dependent lethal concentrations of mianserin exposure on the zebrafish embryos were firstly determined at mg/L levels. Then, a series of sublethal concentrations of 0.01, 0.1, 1, 10, 100, and 1000mug/L of mianserin were prepared for the short-term exposure of zebrafish embryos for 120h. The results showed that mianserin exposure reduced the body length of zebrafish larvae, in addition to altering multiple physiological and biochemical parameters in the exposed embryos/larvae. A dose-dependent inhibition of the total antioxidant capacity and total cholinesterase activity was revealed in the exposed fish larvae upon increasing the concentrations of mianserin exposure. A U-shaped concentration-dependent response curve was observed for the adrenocorticotropic hormone; however, an inversed U-shaped response curve was obtained for the monoamine oxidase level in response to mianserin exposure. Activities of the total adenosine triphosphatase (T-ATPase), Na(+)/K(+)-ATPase, and Ca(2+)/Mg(2+)-ATPase were significantly increased in the fish larvae exposed to relatively high doses of mianserin; interestingly however, low dose of mianserin at 10ng/L inhibited their Na(+)/K(+)-ATPase and T-ATPase activities. Additionally, the coordinated regulation of cyclic adenosine monophosphate and protein kinase A was observed in the mianserin-exposed fish larvae, implying a reserved signaling pathway involved in the fish response to the antidepressant. Therefore, our study demonstrated that mianserin exposure significantly affected the early development of fish embryos at environmentally relevant concentrations, and suggested that the risk of pharmaceutical contamination of the aquatic environment, even at low doses, should receive more attention. Title: Identification and Characterization of ML352: A Novel, Noncompetitive Inhibitor of the Presynaptic Choline Transporter Ennis EA, Wright J, Retzlaff CL, McManus OB, Lin Z, Huang X, Wu M, Li M, Daniels JS and Blakely RD <2 more author(s)> Ennis EA, Wright J, Retzlaff CL, McManus OB, Lin Z, Huang X, Wu M, Li M, Daniels JS, Lindsley CW, Hopkins CR, Blakely RD (- 2) Ref: ACS Chem Neurosci, 6:417, 2015 : PubMed ESTHER: Ennis_2015_ACS.Chem.Neurosci_6_417 PubMedSearch: Ennis 2015 ACS.Chem.Neurosci 6 417 PubMedID: 25560927 Abstract The high-affinity choline transporter (CHT) is the rate-limiting determinant of acetylcholine (ACh) synthesis, yet the transporter remains a largely undeveloped target for the detection and manipulation of synaptic cholinergic signaling. To expand CHT pharmacology, we pursued a high-throughput screen for novel CHT-targeted small molecules based on the electrogenic properties of transporter-mediated choline transport. In this effort, we identified five novel, structural classes of CHT-specific inhibitors. Chemical diversification and functional analysis of one of these classes identified ML352 as a high-affinity (Ki = 92 nM) and selective CHT inhibitor. At concentrations that fully antagonized CHT in transfected cells and nerve terminal preparations, ML352 exhibited no inhibition of acetylcholinesterase (AChE) or cholineacetyltransferase (ChAT) and also lacked activity at dopamine, serotonin, and norepinephrine transporters, as well as many receptors and ion channels. ML352 exhibited noncompetitive choline uptake inhibition in intact cells and synaptosomes and reduced the apparent density of hemicholinium-3 (HC-3) binding sites in membrane assays, suggesting allosteric transporter interactions. Pharmacokinetic studies revealed limited in vitro metabolism and significant CNS penetration, with features predicting rapid clearance. ML352 represents a novel, potent, and specific tool for the manipulation of CHT, providing a possible platform for the development of cholinergic imaging and therapeutic agents. Title: Encapsulation of enzyme via one-step template-free formation of stable organic-inorganic capsules: A simple and efficient method for immobilizing enzyme with high activity and recyclability Huang R, Wu M, Goldman MJ, Li Z Ref: Biotechnol Bioeng, 112:1092, 2015 : PubMed ESTHER: Huang_2015_Biotechnol.Bioeng_112_1092 PubMedSearch: Huang 2015 Biotechnol.Bioeng 112 1092 PubMedID: 25580912 Abstract Enzyme encapsulation is a simple, gentle, and general method for immobilizing enzyme, but it often suffers from one or more problems regarding enzyme loading efficiency, enzyme leakage, mechanical stability, and recyclability. Here we report a novel, simple, and efficient method for enzyme encapsulation to overcome these problems by forming stable organic-inorganic hybrid capsules. A new, facile, one-step, and template-free synthesis of organic-inorganic capsules in aqueous phase were developed based on PEI-induced simultaneous interfacial self-assembly of Fmoc-FF and polycondensation of silicate. Addition of an aqueous solution of Fmoc-FF and sodium silicate into an aqueous solution of PEI gave a new class of organic-inorganic hybrid capsules (FPSi) with multi-layered structure in high yield. The capsules are mechanically stable due to the incorporation of inorganic silica. Direct encapsulation of enzyme such as epoxide hydrolase SpEH and BSA along with the formation of the organic-inorganic capsules gave high yield of enzyme-containing capsules ( approximately 1.2 mm in diameter), >90% enzyme loading efficiency, high specific enzyme loading (158 mg protein g(-1) carrier), and low enzyme leakage (<3% after 48 h incubation). FPSi-SpEH capsules catalyzed the hydrolysis of cyclohexene oxide to give (1R, 2R)-cyclohexane-1,2-diol in high yield and concentration, with high specific activity (6.94 U mg(-1) protein) and the same high enantioselectivity as the free enzyme. The immobilized SpEH demonstrated also excellent operational stability and recyclability: retaining 87% productivity after 20 cycles with a total reaction time of 80 h. The new enzyme encapsulation method is efficient, practical, and also better than other reported encapsulation methods. Biotechnol. Bioeng. 2015;112: 1092-1101. (c) 2015 Wiley Periodicals, Inc. Title: Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N and Gordon JI <2 more author(s)> Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N, Henrissat B, Osterman AL, Gordon JI (- 2) Ref: Science, 350:aac5992, 2015 : PubMed ESTHER: Wu_2015_Science_350_AAC5992 PubMedSearch: Wu 2015 Science 350 AAC5992 PubMedID: 26430127 Gene_locus related to this paper: bactn-BT2379, 9bace-a0a0p0g3y7 Abstract Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness. Title: Characterization of a tannin acyl hydrolase from Streptomyces sviceus with substrate preference for digalloyl ester bonds Wu M, Wang Q, McKinstry WJ, Ren B Ref: Applied Microbiology & Biotechnology, 99:2663, 2015 : PubMed ESTHER: Wu_2015_Appl.Microbiol.Biotechnol_99_2663 PubMedSearch: Wu 2015 Appl.Microbiol.Biotechnol 99 2663 PubMedID: 25246309 Abstract The search for new tannases with novel enzymatic properties suitable for industrial applications has been a continuous effort since the first discovery of the enzyme more than a century ago. A tannase gene (Ss-Tan) from the Gram-positive bacterium Streptomyces sviceus was identified, chemically synthesized, and cloned into a C-terminal His-tagged vector for expression in Escherichia coli. The tannase possesses the active site motif of GXSXG that is conserved for serine hydrolases. The residues that constitute the catalytic triad and galloyl binding site in bacterial tannases are found conserved in Ss-Tan, which include Ser209, Asp452, His484 and Lys370, Glu384, Asp454, respectively. Ss-Tan was overexpressed in E. coli BL21-AI cells with high productivity. Enzymatic assay revealed that the enzyme displays tannase activities to hydrolyze both the ester bonds and depside bonds in hydrolyzable tannins. Kinetic analysis indicated that the enzyme preferentially acts on depside bonds with considerably higher substrate affinity and catalytic efficiency. The enzyme showed maximum activity around pH 8.0 and at 50 degrees C with the highest melting temperature close to 70 degrees C. The high depsidase activity and thermostablility of Ss-Tan may make the enzyme suitable for potential industrial applications to achieve complete digestion of hydrolyzable tannins. Title: Epoxyeicosatrienoic acids mediate insulin-mediated augmentation in skeletal muscle perfusion and blood volume Shim CY, Kim S, Chadderdon S, Wu M, Qi Y, Xie A, Alkayed N, Davidson BP, Lindner JR Ref: American Journal of Physiology Endocrinol Metab, :ajpendo 00216 2014, 2014 : PubMed ESTHER: Shim_2014_Am.J.Physiol.Endocrinol.Metab__ajpendo 00216 2014 PubMedSearch: Shim 2014 Am.J.Physiol.Endocrinol.Metab ajpendo 00216 2014 PubMedID: 25336524 Abstract Skeletal muscle microvascular blood flow (MBF) increases in response to physiologic hyperinsulinemia. This vascular action of insulin may facilitate glucose uptake. We hypothesized that epoxyeicosatrienoic acids (EETs), a family of arachadonic acid-derived endothelium-derived hyperpolarizing factors, is a mediator of insulin's microvascular effects. Contrast-enhanced ultrasound (CEU) was performed to quantify skeletal muscle capillary blood volume (CBV) and MBF in wild-type and obese insulin-resistant (db/db) mice after administration of vehicle or tAUCB, an inhibitor of soluble epoxide hydrolase which converts EETs to less active dihydroxyeicosatrienoic acids. Similar studies were performed in rats pre-treated with L-NAME. CEU was also performed in rats undergoing a euglycemic hyperinsulinemic clamp, half of which were pre-treated with the epoxygenase inhibitor MS-PPOH to inhibit EET synthesis. In both wild type and db/db mice, intravenous tAUCB produced an increase in CBV (65-100% increase at 30 min, p<0.05) and in MBF. In db/db/ mice tAUCB also reduced plasma glucose by approximately 15%. In rats pretreated with L-NAME, tAUCB after produced a significant approximately 20% increase in CBV indicating a component of vascular response independent of nitric oxide (NO) production. Hyperinsulinemic clamp produced a time-dependent increase in MBF (19+/-36 and 76+/-49% at 90 min, p=0.026) mediated in part by an increase in CBV. Insulin-mediated changes in both CBV and MBF during the clamp were entirely blocked MS-PPOH. We conclude that EETs are a mediator of insulin-mediated augmentation in skeletal muscle perfusion and are involved in regulating changes in CBV during hyperinsulinemia. Title: Enhancing the Thermostability of a Cold-Active Lipase from Penicillium cyclopium by In Silico Design of a Disulfide Bridge Tan Z, Li J, Wu M, Wang J Ref: Appl Biochem Biotechnol, 173:1752, 2014 : PubMed ESTHER: Tan_2014_Appl.Biochem.Biotechnol_173_1752 PubMedSearch: Tan 2014 Appl.Biochem.Biotechnol 173 1752 PubMedID: 24867629 Abstract Cysteine mutants of a cold-active lipase (PcLipI) from Penicillium cyclopium were designed by the software Disulfide by Design Ver. 1.20 in an effort to improve enzyme thermostability by addition of a disulfide bridge. Those mutants predicted by molecular dynamics simulation to have better thermostability than the wild type were first expressed in Escherichia coli BL21(DE3) and then, for further investigation, in Pichia pastoris GS115. By replacing Val(248) and Thr(251) with cysteines to create a disulfide bridge, the recombinant lipases reE-PcLip(V248C-T251C) (expressed in E. coli) and reP-PcLip(V248C-T251C) (expressed in P. pastoris) were obtained. Both had enhanced thermostability with half-lives at 35 degrees C about 4.5- and 12.8-fold longer than that of the parent PcLipI expressed in E. coli and P. pastoris, respectively. The temperature optima of reE-PcLip(V248C-T251C) and reP-PcLip(V248C-T251C) were 35 and 30 degrees C, which were each 5 degrees C higher than those of the parent PcLipI expressed in E. coli and P. pastoris. The K ms of reE-PcLip(V248C-T251C) and reP-PcLip(V248C-T251C) toward tributyrin were 53.2 and 39.5 mM, while their V maxs were 1,460 and 3,800 U/mg, respectively. PcLip(V248C-T251C) had better thermostability and catalytic efficiency than the other mutants and the parent PcLipI. Title: SLEEPLESS Is a Bifunctional Regulator of Excitability and Cholinergic Synaptic Transmission Wu M, Robinson JE, Joiner WJ Ref: Current Biology, 24:621, 2014 : PubMed ESTHER: Wu_2014_Curr.Biol_24_621 PubMedSearch: Wu 2014 Curr.Biol 24 621 PubMedID: 24613312 Abstract BACKGROUND: Although sleep is conserved throughout evolution, the molecular basis of its control is still largely a mystery. We previously showed that the quiver/sleepless (qvr/sss) gene encodes a membrane-tethered protein that is required for normal sleep in Drosophila. SLEEPLESS (SSS) protein functions, at least in part, by upregulating the levels and open probability of Shaker (Sh) potassium channels to suppress neuronal excitability and enable sleep. Consistent with this proposed mechanism, loss-of-function mutations in Sh phenocopy qvr/sss-null mutants. However, sleep is more genetically modifiable in Sh than in qvr/sss mutants, suggesting that SSS may regulate additional molecules to influence sleep. Title: Biochemical and molecular characterisation and cross-resistance in field and laboratory chlorpyrifos-resistant strains of Laodelphax striatellus (Hemiptera: Delphacidae) from eastern China Xu L, Wu M, Han Z Ref: Pest Manag Sci, 70:1118, 2014 : PubMed ESTHER: Xu_2014_Pest.Manag.Sci_70_1118 PubMedSearch: Xu 2014 Pest.Manag.Sci 70 1118 PubMedID: 24115461 Abstract BACKGROUND: Laboratory selection is often employed in resistance mechanism studies because field-derived populations commonly do not have high enough resistance for such studies. In the present study, a field-collected Laodelphax striatellus population from eastern China was laboratory selected for chlorpyrifos resistance and susceptibility, and the developed strains, along with a field population, were studied for cross-resistance and resistance mechanisms at biochemical and molecular levels. Title: Crystal structure of tannase from lactobacillusplantarum Ren B, Wu M, Wang Q, Peng X, Wen H, McKinstry WJ, Chen Q Ref: Journal of Molecular Biology, 425:2737, 2013 : PubMed ESTHER: Ren_2013_J.Mol.Biol_425_2737 PubMedSearch: Ren 2013 J.Mol.Biol 425 2737 PubMedID: 23648840 Gene_locus related to this paper: lacpl-tanL Inhibitor(s) related to this paper: 3,4-dihydroxybenzoate, Gallate Abstract Tannins are water-soluble polyphenolic compounds in plants. Hydrolyzable tannins are derivatives of gallic acid (3,4,5-trihydroxybenzoic acid) or its meta-depsidic forms that are esterified to polyol, catechin, or triterpenoid units. Tannases are a family of esterases that catalyze the hydrolysis of the galloyl ester bond in hydrolyzable tannins to release gallic acid. The enzymes have found wide applications in food, feed, beverage, pharmaceutical, and chemical industries since their discovery more than a century ago, although little is known about them at the molecular level, including the details of the catalytic and substrate binding sites. Here, we report the first three-dimensional structure of a tannase from Lactobacillus plantarum. The enzyme displays an alpha/beta structure, featured by a large cap domain inserted into the classical serine hydrolase fold. A catalytic triad was identified in the structure, which is composed of Ser163, His451, and Asp419. During the binding of gallic acid, the carboxyl group of the molecule forges hydrogen-bonding interactions with the catalytic triad of the enzyme while the three hydroxyl groups make contacts with Asp421, Lys343, and Glu357 to form another hydrogen-bonding network. Mutagenesis studies demonstrated that these residues are indispensable for the activity of the enzyme. Structural studies of the enzyme in complex with a number of substrates indicated that the interactions at the galloyl binding site are the determinant force for the binding of substrates. The single galloyl binding site is responsible for the esterase and depsidase activities of the enzyme. Title: Cloning, expression and characterization of a new enantioselective esterase from a marine bacterium Pelagibacterium halotolerans B2T Wei X, Jiang X, Ye L, Yuan S, Chen Z, Wu M, Yu H Ref: J Mol Catal B Enzym, 97:270, 2013 : PubMed ESTHER: Wei_2013_J.Mol.Catal.B.Enzym_97_270 PubMedSearch: Wei 2013 J.Mol.Catal.B.Enzym 97 270 Gene_locus related to this paper: pelhb-g4rfi7 Abstract An esterase, designated as PE8 (219 aa, 23.19 kDa), was cloned from a marine bacterium Pelagibacterium halotolerans B2T and overexpressed in Escherichia coli Rosetta, resulting an active, soluble protein which constituted 23.1% of the total cell protein content. Phylogenetic analysis of the protein showed it was a new member of family VI lipolytic enzymes. Biochemical characterization analysis showed that PE8 preferred short chain p-nitrophenyl esters (C2-C6), exhibited maximum activity toward p-nitrophenyl acetate, and was not a metalloenzyme. PE8 was an alkaline esterase with an optimal pH of 9.5 and an optimal temperature of 45 C toward p-nitrophenyl acetate. Furthermore, it was found that PE8 exhibited activity and enantioselectivity in the synthesis of methyl (R)-3-(4-fluorophenyl)glutarate ((R)-3-MFG) from the prochiral dimethyl 3-(4-fluorophenyl)glutarate (3-DFG). (R)-3-MFG was obtained in 71.6% ee and 73.2% yield after 36 h reaction under optimized conditions (0.6 M phosphate buffer (pH 8.0) containing 17.5% 1,4-dioxane under 30C). In addition, PE8 was tolerant to extremely strong basic and high ionic strength solutions as it exhibited high activity even at pH 11.0 in 1 M phosphate buffer. Given its highly soluble expression, alkalitolerance, halotolerance and enantioselectivity, PE8 could be a promising candidate for the production of (R)-3-MFG in industry. The results also demonstrate the potential of the marine environment as a source of useful biocatalysts. Title: Expression, purification, crystallization and preliminary X-ray analysis of tannase from Lactobacillus plantarum. Wu M, Peng X, Wen H, Wang Q, Chen Q, McKinstry WJ, Ren B Ref: Acta Crystallographica Sect F Struct Biol Cryst Commun, 69:456, 2013 : PubMed ESTHER: Wu_2013_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_69_456 PubMedSearch: Wu 2013 Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun 69 456 PubMedID: 23545659 Gene_locus related to this paper: lacpl-tanL Inhibitor(s) related to this paper: 3,4-dihydroxybenzoate, Gallate Abstract Tannase catalyses the hydrolysis of the galloyl ester bond of tannins to release gallic acid. It belongs to the serine esterases and has wide applications in the food, feed, beverage, pharmaceutical and chemical industries. The tannase from Lactobacillus plantarum was cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method with microseeding. The crystals belonged to space group P1, with unit-cell paramters a = 46.5, b = 62.8, c = 83.8 A, alpha = 70.4, beta = 86.0, gamma = 79.4degre. Although the enzyme exists mainly as a monomer in solution, it forms a dimer in the asymmetric unit of the crystal. The crystals diffracted to beyond 1.60A resolution using synchrotron radiation and a complete data set was collected to 1.65A resolution. Title: Complete genome sequence of Pelagibacterium halotolerans B2(T) Huo YY, Cheng H, Han XF, Jiang XW, Sun C, Zhang XQ, Zhu XF, Liu YF, Li PF and Wu M <1 more author(s)> Huo YY, Cheng H, Han XF, Jiang XW, Sun C, Zhang XQ, Zhu XF, Liu YF, Li PF, Ni PX, Wu M (- 1) Ref: Journal of Bacteriology, 194:197, 2012 : PubMed ESTHER: Huo_2012_J.Bacteriol_194_197 PubMedSearch: Huo 2012 J.Bacteriol 194 197 PubMedID: 22156395 Gene_locus related to this paper: pelhb-g4red0, pelhb-g4rch3, pelhb-g4rd19, pelhb-g4rgf4 Abstract Pelagibacterium halotolerans B2(T) is a marine halotolerant bacterium that was isolated from a seawater sample collected from the East China Sea. Here, we present the complete genome sequence of the type strain P. halotolerans B2(T), which consists of one chromosome (3,944,837 bp; 61.4% G+C content) and one plasmid (4,050 bp; 56.1% G+C content). This is the first complete genome of a member of the Pelagibacterium genus. Title: Identification and characterization of novel esterases from a deep-sea sediment metagenome Jiang X, Xu X, Huo Y, Wu Y, Zhu X, Zhang X, Wu M Ref: Arch Microbiol, 194:207, 2012 : PubMed ESTHER: Jiang_2012_Arch.Microbiol_194_207 PubMedSearch: Jiang 2012 Arch.Microbiol 194 207 PubMedID: 21861153 Gene_locus related to this paper: 9bact-H6BDX1, 9bact-h6bdx2 Abstract A deep-sea sediment metagenomic library was constructed and screened for lipolytic enzymes by activity-based approach. Nine novel lipolytic enzymes were identified, and the amino acid sequences shared 56% to 84% identity to other lipolytic enzymes in the database. Phylogenetic analysis showed that these enzymes belonged to family IV lipolytic enzymes. One of the lipolytic enzymes, Est6, was successfully cloned and expressed in Escherichia coli Rosetta in a soluble form. The recombinant protein was purified by Ni-nitrilotriacetic affinity chromatography column and characterized using p-nitrophenyl esters with various chain lengths. The est6 gene consisted of 909 bp that encoded 302 amino acid residues. Est6 was most similar to a lipolytic enzyme from uncultured bacterium (ACL67845, 61% identity) isolated from the South China Sea marine sediment metagenome. The characterization of Est6 revealed that it was a cold-active esterase and exhibited the highest activity toward p-nitrophenyl butyrate (C4) at 20 degrees C and pH 7.5. Title: Cloning, expression and characterization of a halotolerant esterase from a marine bacterium Pelagibacterium halotolerans B2T Jiang X, Huo Y, Cheng H, Zhang X, Zhu X, Wu M Ref: Extremophiles, 16:427, 2012 : PubMed ESTHER: Jiang_2012_Extremophiles_16_427 PubMedSearch: Jiang 2012 Extremophiles 16 427 PubMedID: 22481638 Gene_locus related to this paper: pelhb-g4rec9 Abstract An esterase PE10 (279 aa) from Pelagibacterium halotolerans B2(T) was cloned and overexpressed in Escherichia coli Rosetta in a soluble form. The deduced protein was 29.91 kDa and the phylogenetic analysis of the deduced amino acids sequence showed it represented a new family of lipolytic enzymes. The recombinant protein was purified by Ni-NTA affinity chromatography column and the characterization showed its optimal temperature and pH were 45 degrees C and pH 7.5, respectively. Substrate specificity study showed PE10 preferred short chain p-nitrophenyl esters and exhibited maximum activity toward p-nitrophenyl acetate. In addition, PE10 was a halotolerant esterase as it was still active under 4 M NaCl. Three-dimensional modeling of PE10 suggested that the high negative electrostatic potential on the surface may relevant to its tolerance to high salt environment. With this halotolerance property, PE10 could be a candidate for industrial use. Title: New feruloyl esterases to access phenolic acids from grass biomass Wu M, Abokitse K, Grosse S, Leisch H, Lau PC Ref: Appl Biochem Biotechnol, 168:129, 2012 : PubMed ESTHER: Wu_2012_Appl.Biochem.Biotechnol_168_129 PubMedSearch: Wu 2012 Appl.Biochem.Biotechnol 168 129 PubMedID: 21927859 Abstract In the Sorangium cellulosum strain So ce56 genome two putative esterase-encoding genes loci sce1896 and sce8927 were cloned expressed in Escherichia coli and the resulting enzymes designated ScFAE1 and ScFAE2 were used to assess the possible release of ferulic acid FA from triticale and wheat brans and an aqueous fraction of steam-exploded wheat straw The two polypeptides sharing only 30 sequence identity exhibit a typical catalytic Ser-Asp-His triad a characteristic of alpha/beta-hydrolase fold proteins Both ScFAE1 35 kDa and ScFAE2 34 kDa were purified to apparent homogeneity and comparison of their kinetic parameters indicated an apparent higher affinity of ScFAE2 than ScFAE1 towards the various feruloyl substrates This property was reflected by the observation that ScFAE2 was capable of yielding up to 85 of FA from destarched triticale bran In the steam-exploded wheat sample more than 85 yield of FA or p-coumaric acid was also effected by ScFAE2 without the decomposition of valuable chemical such as furfural The two cloned FAEs represent the first of myxobacterial origin to be characterized and they are classified as new members of the type D family of FAEs. Title: Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13 Wang Z, Kadouri DE, Wu M Ref: BMC Genomics, 12:453, 2011 : PubMed ESTHER: Wang_2011_BMC.Genomics_12_453 PubMedSearch: Wang 2011 BMC.Genomics 12 453 PubMedID: 21936919 Gene_locus related to this paper: micaa-g2kq08 Abstract BACKGROUND: Although bacterial predators play important roles in the dynamics of natural microbial communities, little is known about the molecular mechanism of bacterial predation and the evolution of diverse predatory lifestyles. Title: Thermostable feruloyl esterase for the bioproduction of ferulic acid from triticale bran Abokitse K, Wu M, Bergeron H, Grosse S, Lau PC Ref: Applied Microbiology & Biotechnology, 87:195, 2010 : PubMed ESTHER: Abokitse_2010_Appl.Microbiol.Biotechnol_87_195 PubMedSearch: Abokitse 2010 Appl.Microbiol.Biotechnol 87 195 PubMedID: 20127235 Abstract A putative alpha/beta hydrolase fold-encoding gene (locus tag TTE1809) from the genome of Thermoanaerobacter tengcongensis was cloned and expressed in Escherichia coli as a possible source of thermostable feruloyl esterase (FAE) for the production of antioxidant phenolic acids from biomass. Designated as TtFAE, the 33-kDa protein was purified to apparent homogeneity. The lipase-like sequence characteristics of TtFAE and its substrate specificity towards methyl ferulate, methyl sinapate, and methyl p-coumarate classify it as a new member of the type A FAEs. At 75 degrees C, the enzyme retained at least 95% of its original activity for over 80 min; at 80 degrees C, its half-life was found to be 50 min, rendering TtFAE a highly thermostable protein. Under different hydrolytic conditions, ferulic acid (FA) was shown to be released from feruloylated oligosaccharides prepared from triticale bran. An estimated recovery of 68 mg FA/100 g triticale bran was demonstrated by a 30% release of the total FA from triticale bran within a 5-h incubation period. Both the oxygen radical absorbing capacity values of the feruloylated oligosaccharides and free FA were also determined. Overall, this work introduces a new bacterial member to the growing family of plant cell wall degrading FAEs that at present is largely of fungal origin, and it benchmarks the bioproduction of FA from triticale bran. Title: Characterization of the polyoxin biosynthetic gene cluster from Streptomyces cacaoi and engineered production of polyoxin H Chen W, Huang T, He X, Meng Q, You D, Bai L, Li J, Wu M, Li R and Deng Z <4 more author(s)> Chen W, Huang T, He X, Meng Q, You D, Bai L, Li J, Wu M, Li R, Xie Z, Zhou H, Zhou X, Tan H, Deng Z (- 4) Ref: Journal of Biological Chemistry, 284:10627, 2009 : PubMed ESTHER: Chen_2009_J.Biol.Chem_284_10627 PubMedSearch: Chen 2009 J.Biol.Chem 284 10627 PubMedID: 19233844 Gene_locus related to this paper: strci-c1ic18 Abstract A gene cluster (pol) essential for the biosynthesis of polyoxin, a nucleoside antibiotic widely used for the control of phytopathogenic fungi, was cloned from Streptomyces cacaoi. A 46,066-bp region was sequenced, and 20 of 39 of the putative open reading frames were defined as necessary for polyoxin biosynthesis as evidenced by its production in a heterologous host, Streptomyces lividans TK24. The role of PolO and PolA in polyoxin synthesis was demonstrated by in vivo experiments, and their functions were unambiguously characterized as O-carbamoyltransferase and UMP-enolpyruvyltransferase, respectively, by in vitro experiments, which enabled the production of a modified compound differing slightly from that proposed earlier. These studies should provide a solid foundation for the elucidation of the molecular mechanisms for polyoxin biosynthesis, and set the stage for combinatorial biosynthesis using genes encoding different pathways for nucleoside antibiotics. Title: The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans Saccone NL, Wang JC, Breslau N, Johnson EO, Hatsukami D, Saccone SF, Grucza RA, Sun L, Duan W and Bierut LJ <8 more author(s)> Saccone NL, Wang JC, Breslau N, Johnson EO, Hatsukami D, Saccone SF, Grucza RA, Sun L, Duan W, Budde J, Culverhouse RC, Fox L, Hinrichs AL, Steinbach JH, Wu M, Rice JP, Goate AM, Bierut LJ (- 8) Ref: Cancer Research, 69:6848, 2009 : PubMed ESTHER: Saccone_2009_Cancer.Res_69_6848 PubMedSearch: Saccone 2009 Cancer.Res 69 6848 PubMedID: 19706762 Abstract Genetic association studies have shown the importance of variants in the CHRNA5-CHRNA3-CHRNB4 cholinergic nicotinic receptor subunit gene cluster on chromosome 15q24-25.1 for the risk of nicotine dependence, smoking, and lung cancer in populations of European descent. We have carried out a detailed study of this region using dense genotyping in both European-Americans and African-Americans. We genotyped 75 known single nucleotide polymorphisms (SNPs) and one sequencing-discovered SNP in an African-American sample (N = 710) and in a European-American sample (N = 2,062). Cases were nicotine-dependent and controls were nondependent smokers. The nonsynonymous CHRNA5 SNP rs16969968 is the most significant SNP associated with nicotine dependence in the full sample of 2,772 subjects [P = 4.49 x 10(-8); odds ratio (OR), 1.42; 95% confidence interval (CI), 1.25-1.61] as well as in African-Americans only (P = 0.015; OR, 2.04; 1.15-3.62) and in European-Americans only (P = 4.14 x 10(-7); OR, 1.40; 1.23-1.59). Other SNPs that have been shown to affect the mRNA levels of CHRNA5 in European-Americans are associated with nicotine dependence in African-Americans but not in European-Americans. The CHRNA3 SNP rs578776, which has a low correlation with rs16969968, is associated with nicotine dependence in European-Americans but not in African-Americans. Less common SNPs (frequency <or= 5%) are also associated with nicotine dependence. In summary, multiple variants in this gene cluster contribute to nicotine dependence risk, and some are also associated with functional effects on CHRNA5. The nonsynonymous SNP rs16969968, a known risk variant in populations of European-descent, is also significantly associated with risk in African-Americans. Additional SNPs contribute to risk in distinct ways in these two populations. Title: Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M and Kuske CR <36 more author(s)> Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR (- 36) Ref: Applied Environmental Microbiology, 75:2046, 2009 : PubMed ESTHER: Ward_2009_Appl.Environ.Microbiol_75_2046 PubMedSearch: Ward 2009 Appl.Environ.Microbiol 75 2046 PubMedID: 19201974 Gene_locus related to this paper: korve-q1ihr9, korve-q1ii02, korve-q1iit0, korve-q1ilk4, korve-q1imj9, korve-q1ims4, korve-q1iqj0, korve-q1isy7, korve-q1itj5, korve-q1itz6, korve-q1ivc8, acic5-c1f1u6, acic5-c1f2i7, acic5-c1f4m6, acic5-c1f4y4, acic5-c1f5a7, acic5-c1f5u2, acic5-c1f7a9, acic5-c1f7x6, acic5-c1f8y9, acic5-c1f9m2, acic5-c1f594, acic5-c1f609, acic5-c1f692, acic5-c1f970, acic5-c1fa52, korve-q1iiw2, korve-q1ivn9, solue-q01nb0, solue-q01qj6, solue-q01r37, solue-q01rq8, solue-q01rz0, solue-q01t44, solue-q01t57, solue-q01ts5, solue-q01tv4, solue-q01vd8, solue-q01vr3, solue-q01vw5, solue-q01w12, solue-q01wt9, solue-q01y40, solue-q01ym8, solue-q01z24, solue-q01z97, solue-q01zl4, solue-q01zm0, solue-q01zm5, solue-q01zm7, solue-q02aa4, solue-q02ab9, solue-q02b72, solue-q02bs8, solue-q02bt7, solue-q02cp0, solue-q02d61, solue-q020h3, solue-q020i8, solue-q021i6, solue-q022b1, solue-q022p8, solue-q022q2, solue-q022q3, solue-q022x2, solue-q022x5, solue-q022x6, solue-q022x8, solue-q023e7, solue-q024d9, solue-q025c1, solue-q026j1, solue-q026k6, solue-q026r6, solue-q027p2, solue-q027r8, solue-q01zt5, korve-q1itw6, solue-q01yh7, solue-q02ad6, korve-q1imj6, korve-q1iuf6, acic5-c1f891, solue-q026h7 Abstract The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration. Title: Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A and Eisen JA <4 more author(s)> Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA (- 4) Ref: PLoS ONE, 4:e4207, 2009 : PubMed ESTHER: Wu_2009_PLoS.ONE_4_E4207 PubMedSearch: Wu 2009 PLoS.ONE 4 E4207 PubMedID: 19148287 Gene_locus related to this paper: therp-b9kxz7, therp-b9l2i8, therp-b9l396 Abstract In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced. Title: cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism Freeman RM, Jr., Wu M, Cordonnier-Pratt MM, Pratt LH, Gruber CE, Smith M, Lander ES, Stange-Thomann N, Lowe CJ and Kirschner M <1 more author(s)> Freeman RM, Jr., Wu M, Cordonnier-Pratt MM, Pratt LH, Gruber CE, Smith M, Lander ES, Stange-Thomann N, Lowe CJ, Gerhart J, Kirschner M (- 1) Ref: Biol Bull, 214:284, 2008 : PubMed ESTHER: Freeman_2008_Biological.Bulletin_214_284 PubMedSearch: Freeman 2008 Biological.Bulletin 214 284 PubMedID: 18574105 Gene_locus related to this paper: sacko-a0a1l7h7f0, sacko-a0a1l7h7f2 Abstract We describe a collection of expressed sequence tags (ESTs) for Saccoglossus kowalevskii, a direct-developing hemichordate valuable for evolutionary comparisons with chordates. The 202,175 ESTs represent 163,633 arrayed clones carrying cDNAs prepared from embryonic libraries, and they assemble into 13,677 continuous sequences (contigs), leaving 10,896 singletons (excluding mitochondrial sequences). Of the contigs, 53% had significant matches when BLAST was used to query the NCBI databases (< or = 10(-10)), as did 51% of the singletons. Contigs most frequently matched sequences from amphioxus (29%), chordates (67%), and deuterostomes (87%). From the clone array, we isolated 400 full-length sequences for transcription factors and signaling proteins of use for evolutionary and developmental studies. The set includes sequences for fox, pax, tbx, hox, and other homeobox-containing factors, and for ligands and receptors of the TGFbeta, Wnt, Hh, Delta/Notch, and RTK pathways. At least 80% of key sequences have been obtained, when judged against gene lists of model organisms. The median length of these cDNAs is 2.3 kb, including 1.05 kb of 3' untranslated region (UTR). Only 30% are entirely matched by single contigs assembled from ESTs. We conclude that an EST collection based on 150,000 clones is a rich source of sequences for molecular developmental work, and that the EST approach is an efficient way to initiate comparative studies of a new organism. Title: Efficacy and tolerability of the dipeptidyl peptidase-4 inhibitor sitagliptin as monotherapy over 12 weeks in patients with type 2 diabetes Scott R, Wu M, Sanchez M, Stein P Ref: Int J Clin Pract, 61:171, 2007 : PubMed ESTHER: Scott_2007_Int.J.Clin.Pract_61_171 PubMedSearch: Scott 2007 Int.J.Clin.Pract 61 171 PubMedID: 17156104 Inhibitor(s) related to this paper: Sitagliptin Abstract The aim of this study was to assess the efficacy and tolerability of the dipeptidyl peptidase-4 inhibitor, sitagliptin, in patients with type 2 diabetes who have inadequate glycaemic control on diet and exercise. In a randomised, double-blind, placebo- and active-controlled study, 743 patients with type 2 diabetes and a mean baseline HbA(1c) of 7.9% were randomised to receive one of six treatments for 12 weeks: placebo, sitagliptin 5, 12.5, 25 or 50 mg b.i.d., or glipizide 5 mg/day (electively titrated up to 20 mg/day). At week 12, treatment with sitagliptin at all doses tested led to a significant (p < 0.001) reduction in HbA(1c) relative to placebo, with the largest reductions occurring in the 50-mg b.i.d. group. The placebo-subtracted differences in HbA(1c) for the sitagliptin dose groups ranged from -0.38% to -0.77% in a dose-dependent manner, and -1.00% in the glipizide group. Sitagliptin also produced significant reductions in fasting plasma glucose and mean daily glucose across the dose range studied. Sitagliptin treatment was well tolerated and resulted in no significant weight change relative to placebo. There was a modest weight gain observed with glipizide treatment relative to placebo. Hypoglycaemia adverse experiences were reported with the highest incidence in the glipizide group (17%) compared with the placebo (2%) or sitagliptin groups (0-4%, not dose-dependent). In summary, in this study sitagliptin improved glycaemic control, with 50 mg b.i.d. being the most effective dose, and was generally well-tolerated in patients with type 2 diabetes. Title: Comparative genomics of emerging human ehrlichiosis agents Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M and Tettelin H <30 more author(s)> Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H (- 30) Ref: PLoS Genet, 2:e21, 2006 : PubMed ESTHER: Dunning Hotopp_2006_PLoS.Genet_2_e21 PubMedSearch: Dunning Hotopp 2006 PLoS.Genet 2 e21 PubMedID: 16482227 Gene_locus related to this paper: anapz-q2gj80, anapz-q2gle9, anapz-q2glf0, anapz-q2gln7, ehrch-q40iu0, ehrch-q40jj7, ehrcr-q2gfq9, neosm-q2gcq8, neosm-q2gdf2, neosm-q2gcn8, anapz-q2gk48, ehrcr-q2ggj6 Abstract Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. Title: Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P and Orias E <43 more author(s)> Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Jr., Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E (- 43) Ref: PLoS Biol, 4:e286, 2006 : PubMed ESTHER: Eisen_2006_PLoS.Biol_4_e286 PubMedSearch: Eisen 2006 PLoS.Biol 4 e286 PubMedID: 16933976 Gene_locus related to this paper: tetts-i7mam3, tetts-i7ml33 Abstract The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance. Title: Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q and Heidelberg JF <9 more author(s)> Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, Madupu R, Tallon L, Kim M, Jin S, Vuong H, Stine OC, Ali A, Horneman AJ, Heidelberg JF (- 9) Ref: Journal of Bacteriology, 188:8272, 2006 : PubMed ESTHER: Seshadri_2006_J.Bacteriol_188_8272 PubMedSearch: Seshadri 2006 J.Bacteriol 188 8272 PubMedID: 16980456 Gene_locus related to this paper: aerhh-a0kes5, aerhh-a0keu7, aerhh-a0kf11, aerhh-a0kfl9, aerhh-a0kfn7, aerhh-a0kgz2, aerhh-a0khk1, aerhh-a0kin3, aerhh-a0kiv7, aerhh-a0kkc6, aerhh-a0kkj8, aerhh-a0klc3, aerhh-a0kme3, aerhh-a0knr1, aerhh-a0knu8, aerhh-a0kp50, aerhh-a0kpk1, aerhh-a0kr22, aerhy-PHAC, aerpu-PEP, aerhh-a0khd8, aerhh-a0kle4, aerhy-a0a028v5g9 Abstract The complete genome of Aeromonas hydrophila ATCC 7966(T) was sequenced. Aeromonas, a ubiquitous waterborne bacterium, has been placed by the Environmental Protection Agency on the Contaminant Candidate List because of its potential to cause human disease. The 4.7-Mb genome of this emerging pathogen shows a physiologically adroit organism with broad metabolic capabilities and considerable virulence potential. A large array of virulence genes, including some identified in clinical isolates of Aeromonas spp. or Vibrio spp., may confer upon this organism the ability to infect a wide range of hosts. However, two recognized virulence markers, a type III secretion system and a lateral flagellum, that are reported in other A. hydrophila strains are not identified in the sequenced isolate, ATCC 7966(T). Given the ubiquity and free-living lifestyle of this organism, there is relatively little evidence of fluidity in terms of mobile elements in the genome of this particular strain. Notable aspects of the metabolic repertoire of A. hydrophila include dissimilatory sulfate reduction and resistance mechanisms (such as thiopurine reductase, arsenate reductase, and phosphonate degradation enzymes) against toxic compounds encountered in polluted waters. These enzymes may have bioremediative as well as industrial potential. Thus, the A. hydrophila genome sequence provides valuable insights into its ability to flourish in both aquatic and host environments. Title: The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC and Fraser CM <17 more author(s)> Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM (- 17) Ref: Proc Natl Acad Sci U S A, 102:10913, 2005 : PubMed ESTHER: Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913 PubMedSearch: Methe 2005 Proc.Natl.Acad.Sci.U.S.A 102 10913 PubMedID: 16043709 Gene_locus related to this paper: colp3-q47uc4, colp3-q47uc7, colp3-q47ut6, colp3-q47ut7, colp3-q47v81, colp3-q47vk3, colp3-q47vy9, colp3-q47w94, colp3-q47wj4, colp3-q47wr2, colp3-q47ws7, colp3-q47ws9, colp3-q47x08, colp3-q47x48, colp3-q47yd5, colp3-q47ye2, colp3-q47yq1, colp3-q47yv1, colp3-q47za7, colp3-q47zp5, colp3-q48ac9, colp3-q48aj8, colp3-q48aq9, colp3-q480e1, colp3-q481z4, colp3-q482y8, colp3-q484d8, colp3-q484k3, colp3-q485e4, colp3-q485t4, colp3-q486t5, colp3-q487b7, colp3-q487s5, colp3-q488a3, colp3-q488d2, colp3-q488d8, colp3-q488e7, colp3-q488f8, colp3-q488p2, colp3-q489b1, colp3-q489i6, colp3-q47ya3 Abstract The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition. Title: Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF and Eisen JA <8 more author(s)> Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA (- 8) Ref: PLoS Genet, 1:e65, 2005 : PubMed ESTHER: Wu_2005_PLoS.Genet_1_e65 PubMedSearch: Wu 2005 PLoS.Genet 1 e65 PubMedID: 16311624 Gene_locus related to this paper: carhz-metx, carhz-q3abd5, carhz-q3adp4 Abstract We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously. Title: Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath) Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D and Eisen JA <28 more author(s)> Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA (- 28) Ref: PLoS Biol, 2:e303, 2004 : PubMed ESTHER: Ward_2004_PLoS.Biol_2_e303 PubMedSearch: Ward 2004 PLoS.Biol 2 e303 PubMedID: 15383840 Gene_locus related to this paper: metca-q60a38, metca-q60bu6, metca-q60cn0, metca-q605j8, metca-q606x9, metca-q607f7, metca-q607m2, metca-q609v0 Abstract Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential. Title: Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C and Eisen JA <20 more author(s)> Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA (- 20) Ref: PLoS Biol, 2:E69, 2004 : PubMed ESTHER: Wu_2004_PLoS.Biol_2_E69 PubMedSearch: Wu 2004 PLoS.Biol 2 E69 PubMedID: 15024419 Gene_locus related to this paper: wolpm-q73gf0, wolpm-q73gx7 Abstract The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections. Title: Hypocretin/orexin innervation and excitation of identified septohippocampal cholinergic neurons Wu M, Zaborszky L, Hajszan T, van den Pol AN, Alreja M Ref: Journal of Neuroscience, 24:3527, 2004 : PubMed ESTHER: Wu_2004_J.Neurosci_24_3527 PubMedSearch: Wu 2004 J.Neurosci 24 3527 PubMedID: 15071100 Abstract Hypothalamic fibers containing the wake-promoting peptides, hypocretins (Hcrts) or orexins, provide a dense innervation to the medial septum-diagonal band of Broca (MSDB), a sleep-associated brain region that has been suggested to show intense axonal degeneration in canine narcoleptics. The MSDB, via its cholinergic and GABAergic projections to the hippocampus, controls the hippocampal theta rhythm and associated learning and memory functions. Neurons of the MSDB express very high levels of the Hcrt receptor 2, which is mutated in canine narcoleptics. In the present study, we investigated the electrophysiological effects of Hcrt peptides on septohippocampal cholinergic neurons that were identified in living brain slices of the MSDB using a selective fluorescent marker. Hcrt activation of septohippocampal cholinergic neurons was reversible, reproducible, and concentration dependent and mediated via a direct postsynaptic mechanism. Both Hcrt1 and Hcrt2 activated septohippocampal cholinergic neurons with similar EC(50) values. The Hcrt effect was dependent on external Na(+), reduced by external Ba(2+), and also reduced in recordings with CsCl-containing electrodes, suggesting a dual underlying ionic mechanism that involved inhibition of a K(+) current, presumably an inward rectifier, and a Na(+)-dependent component. The Na(+) component was dependent on internal Ca(2+), blocked by replacing external Na(+) with Li(+), and also blocked by bath-applied Ni(2+) and KB-R7943, suggesting involvement of the Na(+)-Ca(2+) exchanger. Using double-immunolabeling studies at light and ultrastructural levels, we also provide definitive evidence for a hypocretin innervation of cholinergic neurons. Thus Hcrt effects within the septum should increase hippocampal acetylcholine release and thereby promote hippocampal arousal. Title: Histamine innervation and activation of septohippocampal GABAergic neurones: involvement of local ACh release Xu C, Michelsen KA, Wu M, Morozova E, Panula P, Alreja M Ref: Journal of Physiology, 561:657, 2004 : PubMed ESTHER: Xu_2004_J.Physiol_561_657 PubMedSearch: Xu 2004 J.Physiol 561 657 PubMedID: 15486020 Abstract Recent studies indicate that the histaminergic system, which is critical for wakefulness, also influences learning and memory by interacting with cholinergic systems in the brain. Histamine-containing neurones of the tuberomammillary nucleus densely innervate the cholinergic and GABAergic nucleus of the medial septum/diagonal band of Broca (MSDB) which projects to the hippocampus and sustains hippocampal theta rhythm and associated learning and memory functions. Here we demonstrate that histamine, acting via H(1) and/or H(2) receptor subtypes, utilizes direct and indirect mechanisms to excite septohippocampal GABA-type neurones in a reversible, reproducible and concentration-dependent manner. The indirect mechanism involves local ACh release, is potentiated by acetylcholinesterase inhibitors and blocked by atropine methylbromide and 4-DAMP mustard, an M(3) muscarinic receptor selective antagonist. This indirect effect, presumably, results from a direct histamine-induced activation of septohippocampal cholinergic neurones and a subsequent indirect activation of the septohippocampal GABAergic neurones. In double-immunolabelling studies, histamine fibres were found in the vicinity of both septohippocampal cholinergic and GABAergic cell types. These findings have significance for Alzheimer's disease and other neurodegenerative disorders involving a loss of septohippocampal cholinergic neurones as such a loss would also obtund histamine effects on septohippocampal cholinergic and GABAergic functions and further compromise hippocampal arousal and associated cognitive functions. Title: Genome of Geobacter sulfurreducens: metal reduction in subsurface environments Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N and Fraser CM <24 more author(s)> Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM (- 24) Ref: Science, 302:1967, 2003 : PubMed ESTHER: Methe_2003_Science_302_1967 PubMedSearch: Methe 2003 Science 302 1967 PubMedID: 14671304 Gene_locus related to this paper: geosl-q74a54, geosl-q74ac8, geosl-q74eb1, geosl-q747u4, geosl-q747v8, geosl-q749w4 Abstract The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity. Title: The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA and Fraser CM <42 more author(s)> Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM (- 42) Ref: Nature, 423:81, 2003 : PubMed ESTHER: Read_2003_Nature_423_81 PubMedSearch: Read 2003 Nature 423 81 PubMedID: 12721629 Gene_locus related to this paper: bacan-BA0160, bacan-BA0950, bacan-BA0954, bacan-BA1019, bacan-BA1242, bacan-BA1727, bacan-BA1747, bacan-BA1866, bacan-BA1914, bacan-BA2015, bacan-BA2392, bacan-BA2417, bacan-BA2557, bacan-BA2607, bacan-BA2687, bacan-BA2694, bacan-BA2738, bacan-BA2865, bacan-BA3068, bacan-BA3165, bacan-BA3178, bacan-BA3187, bacan-BA3343, bacan-BA3372, bacan-BA3703, bacan-BA3805, bacan-BA3863, bacan-BA3877, bacan-BA3887, bacan-BA4324, bacan-BA4328, bacan-BA4338, bacan-BA4577, bacan-BA4983, bacan-BA5009, bacan-BA5110, bacan-BA5136, bacan-DHBF, bacan-q81tt2, bacce-BC0192, bacce-BC1788, bacce-BC1954, bacce-BC2141, bacce-BC2171, bacce-BC4730, bacce-BC4862, bacce-BC5130, bacce-PHAC, bacce-q72yu1, baccr-pepx Abstract Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity--including haemolysins, phospholipases and iron acquisition functions--and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis. Title: Acetylcholinesterase inhibitors activate septohippocampal GABAergic neurons via muscarinic but not nicotinic receptors Wu M, Newton SS, Atkins JB, Xu C, Duman RS, Alreja M Ref: Journal of Pharmacology & Experimental Therapeutics, 307:535, 2003 : PubMed ESTHER: Wu_2003_J.Pharmacol.Exp.Ther_307_535 PubMedSearch: Wu 2003 J.Pharmacol.Exp.Ther 307 535 PubMedID: 12966162 Abstract Acetylcholinesterase (AChE) inhibitors, which increase synaptic levels of available acetylcholine (ACh) by preventing its degradation, are the most extensively prescribed drugs for the treatment of Alzheimer's disease. In animals, AChE inhibitors improve learning and memory, reverse scopolamine-induced amnesia, and produce hippocampal theta rhythm. The medial septum/diagonal band of Broca (MSDB), which maintains hippocampal theta rhythm and associated mnemonic functions via the septohippocampal pathway, is considered a critical locus for mediating the effects of AChE inhibitors. Using electrophysiological recordings and fluorescent labeling techniques to identify living septohippocampal neurons in rat brain slices, we report that AChE inhibitors, in the absence of exogenous ACh, produce a profound excitation in 94% of septohippocampal GABAergic neurons and an inhibition in 24% of septohippocampal cholinergic neurons. The inhibitory and excitatory effects of AChE inhibitors, presumably, occur due to accumulation of ACh that is released locally within the MSDB via axon collaterals of septohippocampal cholinergic neurons. The excitatory effects of AChE inhibitors on septohippocampal GABAergic neurons were blocked by muscarinic but not nicotinic receptor antagonists, especially by the M3 receptor antagonist, 4-diphenylacetoxy-N-methylpiperidine mustard, and not by M1 or M2/M4 muscarinic receptor antagonists. M3 muscarinic receptor mRNA colocalized with the calcium-binding protein, parvalbumin, a marker of septohippocampal GABAergic neurons. These findings may be useful in designing therapeutic strategies that do not depend on endogenous ACh and may therefore be effective in situations where AChE inhibitors cease to be effective, such as in progressive neurodegeneration. Title: Cloning of an alkaline lipase gene from Penicillium cyclopium and its expression in Escherichia coli Wu M, Qian Z, Jiang P, Min T, Sun C, Huang W Ref: Lipids, 38:191, 2003 : PubMed ESTHER: Wu_2003_Lipids_38_191 PubMedSearch: Wu 2003 Lipids 38 191 PubMedID: 12784858 Gene_locus related to this paper: penex-Q9HFW6 Abstract The gene encoding an alkaline lipase of Penicillium cyclopium PG37 was cloned with four steps of PCR amplification based on different principles. The cloned gene was 1,480 nucleotides in length, consisted of 94 bp of promoter region, and had 6 exons and 5 short introns ranging from 50 to 70 nucleotides. The open reading frame encoded a protein of 285 amino acid residues consisting of a 27-AA signal peptide and a 258-AA mature peptide, with a conserved motif of Gly-X-Ser-X-Gly shared by all types of alkaline lipases. However, this protein had a low homology with lipases of P. camembertii (22.9%), Humicola lanuginosa (25.6%), and Rhizomucor miehei (22.3%) at the amino acid level. The mature peptide-encoding cDNA was cloned and expressed in Escherichia coli on pET-30a for confirmation. A distinct band with a M.W. of 33 kDa was detected on SDS-PAGE. Results of a Western blot analysis and an enzyme activity assay verified the recombinant 33-kDa protein as an alkaline lipase. Its catalytic properties were not changed when compared with its natural counterpart. Title: The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC and Fraser CM <25 more author(s)> Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM (- 25) Ref: Proceedings of the National Academy of Sciences of the United States of America, 99:9509, 2002 : PubMed ESTHER: Eisen_2002_Proc.Natl.Acad.Sci.U.S.A_99_9509 PubMedSearch: Eisen 2002 Proc.Natl.Acad.Sci.U.S.A 99 9509 PubMedID: 12093901 Gene_locus related to this paper: chlte-CT0177, chlte-CT0524, chlte-CT0717, chlte-CT0947, chlte-CT1208, chlte-CT1253, chlte-CT1301, chlte-CT1312, chlte-CT1856, chlte-CT1908, chlte-CT2087, chlte-CT2271, chlte-MENH, chlte-MET2, chlte-q4w546, chlte-q8kgb8 Abstract The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are highly conserved among photosynthetic species. Many of these have no assigned function and may play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species. Title: Sequence and analysis of rice chromosome 4 Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y and Han B <61 more author(s)> Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (- 61) Ref: Nature, 420:316, 2002 : PubMed ESTHER: Feng_2002_Nature_420_316 PubMedSearch: Feng 2002 Nature 420 316 PubMedID: 12447439 Gene_locus related to this paper: orysa-Q7XTC5, orysa-Q7F959, orysa-q7f9i3, orysa-q7x7y5, orysa-q7xkj9, orysa-q7xr62, orysa-q7xr63, orysa-q7xr64, orysa-q7xsg1, orysa-q7xsq2, orysa-Q7XTM8, orysa-q7xts6, orysa-q7xue7, orysa-q7xv53, orysa-Q7XVB5, orysa-Q7XVG5, orysj-q0jaf0, orysj-q7f8x1 Abstract Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis. Title: The genome sequence of the malaria mosquito Anopheles gambiae Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM and Hoffman SL <113 more author(s)> Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL (- 113) Ref: Science, 298:129, 2002 : PubMed ESTHER: Holt_2002_Science_298_129 PubMedSearch: Holt 2002 Science 298 129 PubMedID: 12364791 Gene_locus related to this paper: anoga-a0nb77, anoga-a0nbp6, anoga-a0neb7, anoga-a0nei9, anoga-a0nej0, anoga-a0ngj1, anoga-a7ut12, anoga-a7uuz9, anoga-ACHE1, anoga-ACHE2, anoga-agCG44620, anoga-agCG44666, anoga-agCG45273, anoga-agCG45279, anoga-agCG45511, anoga-agCG46741, anoga-agCG47651, anoga-agCG47655, anoga-agCG47661, anoga-agCG47690, anoga-agCG48797, anoga-AGCG49362, anoga-agCG49462, anoga-agCG49870, anoga-agCG49872, anoga-agCG49876, anoga-agCG50851, anoga-agCG51879, anoga-agCG52383, anoga-agCG54954, anoga-AGCG55021, anoga-agCG55401, anoga-agCG55408, anoga-agCG56978, anoga-ebiG239, anoga-ebiG2660, anoga-ebiG5718, anoga-ebiG5974, anoga-ebiG8504, anoga-ebiG8742, anoga-glita, anoga-nrtac, anoga-q5tpv0, anoga-Q5TVS6, anoga-q7pm39, anoga-q7ppw9, anoga-q7pq17, anoga-Q7PQT0, anoga-q7q8m4, anoga-q7q626, anoga-q7qa14, anoga-q7qa52, anoga-q7qal7, anoga-q7qbj0, anoga-f5hl20, anoga-q7qkh2, anoga-a0a1s4h1y7, anoga-q7q887 Abstract Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect. Title: The sequence of the human genome Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA and Zhu X <264 more author(s)> Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (- 264) Ref: Science, 291:1304, 2001 : PubMed ESTHER: Venter_2001_Science_291_1304 PubMedSearch: Venter 2001 Science 291 1304 PubMedID: 11181995 Gene_locus related to this paper: human-AADAC, human-ABHD1, human-ABHD10, human-ABHD11, human-ACHE, human-BCHE, human-LDAH, human-ABHD18, human-CMBL, human-ABHD17A, human-KANSL3, human-LIPA, human-LYPLAL1, human-NDRG2, human-NLGN3, human-NLGN4X, human-NLGN4Y, human-PAFAH2, human-PREPL, human-RBBP9, human-SPG21 Abstract A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge. Title: Differential development of cholinergic-like neurons in the superior olive: a light microscopic study Simmons DD, Bertolotto C, Typpo K, Clay A, Wu M Ref: Anatomy & Embryology (Berl), 200:585, 1999 : PubMed ESTHER: Simmons_1999_Anat.Embryol.(Berl)_200_585 PubMedSearch: Simmons 1999 Anat.Embryol.(Berl) 200 585 PubMedID: 10592062 Abstract To better understand the development of cholinergic-like neurons within the superior olivary complex, we investigated the onset and distribution of two well-known markers of cholinergic-like neurons in hamsters: choline acetyltransferase (ChAT) and acetylcholinesterase (AChE). From embryonic day (E) 14 through postnatal day (P) 0, olivary cells immunopositive for ChAT were restricted to the rostral periolivary (RPO) area. Between P0 and P3, ChAT-positive cells are found in progressively more caudal and ventral periolivary locations. Although rostral and ventral periolivary cells exhibited an early onset of ChAT expression, stable numbers were not reached until P4. In contrast, ChAT expression within the lateral superior olive (LSO) is not visible until after P0 and higher numbers of ChAT-positive cells are obtained by P5. The AChE expression lags several days but follows roughly the same pattern of onset as for ChAT. Additionally in rostral and ventral periolivary regions as well as in the LSO, there were fewer AChE-labeled cells than ChAT-labeled cells. The observed temporal relationships in cholinergic-like expression within olivary cells suggest that different cholinergic-like populations may be defined on the basis of the onset of neurotransmitter-related enzymes: RPO cells are first, cells in ventral periolivary regions are second, and cells associated with the LSO are last. The differences observed in the onset of ChAT and AChE expression may reflect differences in the timing of target innervation as well as differences in synaptogenesis. Title: Subpallidal outputs to the nucleus accumbens and the ventral tegmental area: anatomical and electrophysiological studies Wu M, Hrycyshyn AW, Brudzynski SM Ref: Brain Research, 740:151, 1996 : PubMed ESTHER: Wu_1996_Brain.Res_740_151 PubMedSearch: Wu 1996 Brain.Res 740 151 PubMedID: 8973809 Abstract The goal of this study was to investigate the functional organization of the subpallidal-->accumbens direct and indirect feedback loops by both anatomical and electrophysiological methods. The results of the dextran-conjugated rhodamine injections into the subpallidal area has shown three distinct projections: (1) a substantial pathway from the subpallidal area to the ventral tegmental area, (2) a more diffuse rostral projection from the subpallidal area to the core area of the nucleus accumbens, and (3) a sparse pathway projecting rostrodorsally from the subpallidal area toward the thalamic regions. Electrical or chemical stimulation of the subpallidal region, which was studied by the axonal tracer, evoked inhibitory responses in the majority (60 and 80%, respectively) of the accumbens and ventral tegmental area neurons in a standard extracellular recording study. Less than 1/3 of the accumbens or ventral tegmental area cells showed an increase in the mean firing rate. The majority (77.5%) of all responded neurons had a latency of less than 10 ms. Furthermore, injection of glutamate into the subpallidal area not only altered the firing pattern of the accumbens neurons, but also attenuated their excitatory responses elicited by the electrical stimulation of the ventral subiculum. Our results indicate that the subpallidal area plays a predominantly inhibitory role in the ventral tegmental area-accumbens-subpallidal circuitry, presumably by its GABAergic projections, and may also modulate subicular input into the nucleus accumbens. Title: Mesolimbic dopamine terminals and locomotor activity induced from the subiculum Wu M, Brudzynski SM Ref: Neuroreport, 6:1601, 1995 : PubMed ESTHER: Wu_1995_Neuroreport_6_1601 PubMedSearch: Wu 1995 Neuroreport 6 1601 PubMedID: 8527723 Abstract The role of the mesolimbic dopamine terminals in the nucleus accumbens in the initiation of locomotion in rats was studied. Locomotor activity was initiated by activation of the excitatory input from the ventral subiculum to the nucleus accumbens with NMDA. Measurements of locomotor activity, induced by unilateral administration of NMDA into the ventral subiculum, were compared before and after destruction of the mesolimbic dopamine terminals in the nucleus accumbens. The dopamine terminals were destroyed by injection of 6-OHDA into the ventral tegmental area which projects to the nucleus accumbens. Injection of NMDA into the ventral subiculum caused an almost four-fold increase in locomotor activity. However, this increase was abolished after the destruction of the mesolimbic dopamine terminals in the nucleus accumbens. The results suggest that the mesolimbic dopamine terminals are essential in transmitting subicular signals to the output neurones within the nucleus accumbens. Title: Decreases in rat locomotor activity as a result of changes in synaptic transmission to neurons within the mesencephalic locomotor region Brudzynski SM, Wu M, Mogenson GJ Ref: Canadian Journal of Physiology & Pharmacology, 71:394, 1993 : PubMed ESTHER: Brudzynski_1993_Can.J.Physiol.Pharmacol_71_394 PubMedSearch: Brudzynski 1993 Can.J.Physiol.Pharmacol 71 394 PubMedID: 8402406 Abstract The mesencephalic locomotor region is defined as a functional region sending signals to the spinal cord generators of rhythmical limb movements for locomotion. It has been shown that the mesencephalic locomotor region plays a critical role in locomotion initiated from the nucleus accumbens or from the subpallidal region. However, there are conflicting data on whether synaptic input from the nucleus accumbens--subpallidal region to the mesencephalic locomotor region mediates locomotion. The purpose of the study was to determine the role of synaptic input to different subregions of the mesencephalic locomotor region in locomotion induced by injecting dopamine into the nucleus accumbens or by injecting picrotoxin into the subpallidal region in freely behaving rats. Synaptic transmission in the mesencephalic locomotor region was eliminated by excitotoxic lesions or was reversibly interrupted by injecting cobalt chloride, which can block synaptic transmission. Excitotoxic lesions or injections of cobalt into subregions of the mesencephalic locomotor region significantly decreased, although did not completely block, locomotion. The most effective sites for cobalt- and lesion-induced reduction in locomotion were consistent with localization of the mesencephalic locomotor region. Effective sites for cobalt and lesions markedly overlapped but were not identical. The results indicate that synaptic transmission within the mesencephalic locomotor region contributes to dopamine- or picrotoxin-induced locomotion. Title: Differential effects of quinpirole in the nucleus accumbens depending on the initial level of locomotor activity Wu M, Brudzynski SM, Mogenson GJ Ref: Brain Research Bulletin, 32:395, 1993 : PubMed ESTHER: Wu_1993_Brain.Res.Bull_32_395 PubMedSearch: Wu 1993 Brain.Res.Bull 32 395 PubMedID: 8106125 Abstract Effects of dopamine D1 and D2 receptor agonists (SKF 38393 and quinpirole, respectively) on locomotion were studied in two behavioural situations characterized by low and high level of exploratory locomotor activity. Administration of quinpirole bilaterally into the nucleus accumbens increased locomotor activity at the low initial level of activity and decreased locomotor activity at the high activity level, while the administration of SKF 38393 increased locomotor activity in both behavioural situations. It was concluded that quinpirole has differential effects on locomotion, depending on the initial level of activity. Title: Functional interaction of dopamine and glutamate in the nucleus accumbens in the regulation of locomotion Wu M, Brudzynski SM, Mogenson GJ Ref: Canadian Journal of Physiology & Pharmacology, 71:407, 1993 : PubMed ESTHER: Wu_1993_Can.J.Physiol.Pharmacol_71_407 PubMedSearch: Wu 1993 Can.J.Physiol.Pharmacol 71 407 PubMedID: 7691389 Abstract The interaction of dopamine and glutamate in the nucleus accumbens in the regulation of locomotion was investigated. Microinjection of N-methyl-D-aspartic acid (NMDA, a glutamatergic NMDA receptor agonist) or alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA, a quisqualic receptor agonist which is a glutamatergic non-NMDA receptor agonist) into the nucleus accumbens caused a substantial increase in locomotor activity. This increase in locomotor activity was significantly reduced by prior administration of the dopamine D2 agonist quinpirole, but not the D1 agonist, SKF 38393, into the same brain sites. The reduction in locomotion produced by quinpirole was dose dependent. Eight days after the ventral tegmental area was lesioned with 6-hydroxydopamine to destroy the dopamine projection and the axon terminals of the mesolimbic dopamine neurons in nucleus accumbens, the hyperkinetic effects produced by injections of NMDA and AMPA into the nucleus accumbens were substantially reduced. These results suggested that the glutamate agonist induced locomotion is mediated by dopamine. Thus, it appears that NMDA- or AMPA-induced locomotion is due to the activation of glutamate receptors on the mesolimbic dopamine terminals in the nucleus accumbens which release dopamine and subsequently increase locomotion. Title: Modulation of locomotor activity induced by injections of carbachol into the tegmental pedunculopontine nucleus and adjacent areas in the rat Brudzynski SM, Wu M, Mogenson GJ Ref: Brain Research, 451:119, 1988 : PubMed ESTHER: Brudzynski_1988_Brain.Res_451_119 PubMedSearch: Brudzynski 1988 Brain.Res 451 119 PubMedID: 3251577 Abstract The pedunculopontine nucleus (PPN) is a major component of the mesencephalic locomotor region. There is little known, however, about neurotransmitters in the PPN associated with locomotor activity. The purpose of the present study was to investigate a possible modulatory effect of the cholinergic system on locomotion. The effects of application of carbachol (CCh) into the PPN on locomotor activity of freely moving rats were studied. Unilateral injections of CCh into the PPN decreased spontaneous locomotor activity of rats. On the other hand, an increase in locomotor activity resulted from CCh injections into sites surrounding the PPN. These CCh-induced changes in locomotion were no longer observed after pretreatment of the PPN with atropine. Locomotor activity induced by injections of amphetamine into the nucleus accumbens was also reduced to control levels by ipsilateral injections of CCh into the PPn, whereas contralateral injections of CCh were ineffective. The results suggest that the muscarinic cholinergic system has a modulatory influence on locomotor activity presumably by affecting PPN cells involved in relaying locomotion-associated signals. The PPN receives signals from higher structures involved in initiation of locomotion while the muscarinic system seems to play a role in attenuation or inhibition of locomotor behaviour. | |||||||
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