Author Report for: Lewis MNo contact information in database for Lewis M
Dudi-Venkata NN, Kroon HM, Bedrikovetski S, Traeger L, Lewis M, Lawrence MJ, Hunter RA, Moore JW, Thomas ML, Sammour T Ref: Colorectal Dis, :, 2021 : PubMed ESTHER: Dudi-Venkata_2021_Colorectal.Dis__ PubMedSearch: Dudi-Venkata 2021 Colorectal.Dis PubMedID: 34021689 Abstract AIM: Postoperative ileus (POI) is a major problem after colorectal surgery. Acetylcholinesterase inhibitors (ACEI) like pyridostigmine increase gastro-intestinal (GI) motility through a cholinergic anti-inflammatory pathway (CAIP). The purpose of this phase II pilot study is to determine the safety of oral pyridostigmine after elective colorectal surgery. METHODS: This is a stage 2b safety study (IDEAL framework). All adult patients undergoing elective colorectal resections or formation or reversal of stoma at the Royal Adelaide Hospital between September 2020 and January 2021 were eligible. The primary outcomes were 30-day postoperative complications, reported adverse events and GI-2: a validated composite outcome measure of recovery of GI function after surgery defined as the interval from surgery until first passage of stool and tolerance of a solid intake for 24 hrs (in whole days) in the absence of vomiting. RESULTS: Fifteen patients were included in the study. The median age was 58 (50-82) years, and seven (47%) were men. Most participants had an ASA grade <= II (53%), and the median BMI was 27 (24-35). There were 13 postoperative complications (seven were Clavien-Dindo (CD) 1, five CD 2, and one CD 3). None appeared directly related to pyridostigmine administration, and none of the patients had any overt symptoms of excessive parasympathetic activity. Median GI-2 was two days (1-4). CONCLUSION: Oral pyridostigmine appears to be safe to use after elective colorectal surgery in a select group of patients. However, considering this is a pilot study with a small sample size, larger controlled studies are needed to confirm this finding and establish efficacy for POI prevention. Title: Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G and Bashir A <7 more author(s)> Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A (- 7) Ref: Antimicrobial Agents & Chemotherapy, 59:7117, 2015 : PubMed ESTHER: Pak_2015_Antimicrob.Agents.Chemother_59_7117 PubMedSearch: Pak 2015 Antimicrob.Agents.Chemother 59 7117 PubMedID: 26324280 Gene_locus related to this paper: stema-a0a0k2iyn7, stema-a0a0m0p330 Abstract Whole-genome sequences for Stenotrophomonas maltophilia serial isolates from a bacteremic patient before and after development of levofloxacin resistance were assembled de novo and differed by one single-nucleotide variant in smeT, a repressor for multidrug efflux operon smeDEF. Along with sequenced isolates from five contemporaneous cases, they displayed considerable diversity compared against all published complete genomes. Whole-genome sequencing and complete assembly can conclusively identify resistance mechanisms emerging in S. maltophilia strains during clinical therapy. Title: Additive Toxicity of beta-Amyloid by a Novel Bioactive Peptide In Vitro: Possible Implications for Alzheimer's Disease Garcia-Rates S, Lewis M, Worrall R, Greenfield SA Ref: PLoS ONE, 8:e54864, 2013 : PubMed ESTHER: Garcia-Rates_2013_PLoS.One_8_e54864 PubMedSearch: Garcia-Rates 2013 PLoS.One 8 e54864 PubMedID: 23390503 Abstract BACKGROUND: beta-amyloid is regarded as a significant factor in Alzheimer's disease: but inefficient therapies based on this rationale suggests that additional signalling molecules or intermediary mechanisms must be involved in the actual initiation of the characteristic degeneration of neurons. One clue could be that acetylcholinesterase, also present in amyloid plaques, is aberrant in peripheral tissues such as blood and adrenal medulla that can be implicated in Alzheimer's disease. The aim of this study was to assess the bioactivity of a fragment of acetylcholinesterase responsible for its non-enzymatic functions, a thirty amino acid peptide ("T30") which has homologies with beta-amyloid. Title: Nonoisotopic assay for the presynaptic choline transporter reveals capacity for allosteric modulation of choline uptake Ruggiero AM, Wright J, Ferguson SM, Lewis M, Emerson KS, Iwamoto H, Ivy MT, Holmstrand EC, Ennis EA and Blakely RD <1 more author(s)> Ruggiero AM, Wright J, Ferguson SM, Lewis M, Emerson KS, Iwamoto H, Ivy MT, Holmstrand EC, Ennis EA, Weaver CD, Blakely RD (- 1) Ref: ACS Chem Neurosci, 3:767, 2012 : PubMed ESTHER: Ruggiero_2012_ACS.Chem.Neurosci_3_767 PubMedSearch: Ruggiero 2012 ACS.Chem.Neurosci 3 767 PubMedID: 23077721 Abstract Current therapies to enhance CNS cholinergic function rely primarily on extracellular acetylcholinesterase AChE inhibition a pharmacotherapeutic strategy that produces dose-limiting side effects The Na(+)-dependent high-affinity choline transporter CHT is an unexplored target for cholinergic medication development Although functional at the plasma membrane CHT at steady-state is localized to synaptic vesicles such that vesicular fusion can support a biosynthetic response to neuronal excitation To identify allosteric potentiators of CHT activity we mapped endocytic sequences in the C-terminus of human CHT identifying transporter mutants that exhibit significantly increased transport function A stable HEK-293 cell line was generated from one of these mutants CHT LV-AA and used to establish a high-throughput screen HTS compatible assay based on the electrogenic nature of the transporter We established that the addition of choline to these cells at concentrations appropriate for high-affinity choline transport at presynaptic terminals generates a hemicholinium-3 HC-3)-sensitive membrane depolarization that can be used for the screening of CHT inhibitors and activators Using this assay we discovered that staurosporine increased CHT LV-AA choline uptake activity an effect mediated by a decrease in choline K(M with no change in V(max As staurosporine did not change surface levels of CHT nor inhibit HC-3 binding we propose that its action is directly or indirectly allosteric in nature Surprisingly staurosporine reduced choline-induced membrane depolarization suggesting that increased substrate coupling to ion gradients arising at the expense of nonstoichiometric ion flow accompanies a shift of CHT to a higher-affinity state Our findings provide a new approach for the identification of CHT modulators that is compatible with high-throughput screening approaches and presents a novel model by which small molecules can enhance substrate flux through enhanced gradient coupling. Title: Modafinil improves rapid shifts of attention Marchant NL, Kamel F, Echlin K, Grice J, Lewis M, Rusted JM Ref: Psychopharmacology (Berl), 202:487, 2009 : PubMed ESTHER: Marchant_2009_Psychopharmacology.(Berl)_202_487 PubMedSearch: Marchant 2009 Psychopharmacology.(Berl) 202 487 PubMedID: 19031073 Abstract RATIONALE: The majority of studies investigating the cognitive effects of modafinil, a wake-promoting compound, demonstrate some improvements in attention. The potential of the drug to selectively benefit distinct components of attention has yet to be fully explored in healthy adults. OBJECTIVE: The present study was conducted to investigate modafinil's effect on specific cognitive tasks that tax components of attention switching. One required the rapid switching of attention between stimuli, and another contained an embedded working memory component on top of the attentional shift requirements. Additionally, prospective memory was examined, which requires the interruption of an ongoing activity to retrieve and act upon a previously formed intention. MATERIALS AND 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: Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J and Jackson S <62 more author(s)> Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, Bera J, Weaver B, Jin S, Johri S, Reardon M, Webb K, Hill J, Moffat K, Tallon L, Van Aken S, Lewis M, Utterback T, Feldblyum T, Zismann V, Iobst S, Hsiao J, de Vazeille AR, Salzberg SL, White O, Fraser C, Yu Y, Kim H, Rambo T, Currie J, Collura K, Kernodle-Thompson S, Wei F, Kudrna K, Ammiraju JS, Luo M, Goicoechea JL, Wing RA, Henry D, Oates R, Palmer M, Pries G, Saski C, Simmons J, Soderlund C, Nelson W, de la Bastide M, Spiegel L, Nascimento L, Huang E, Preston R, Zutavern T, Palmer LE, O'Shaughnessy A, Dike S, McCombie WR, Minx P, Cordum H, Wilson R, Jin W, Lee HR, Jiang J, Jackson S (- 62) Ref: Genome Res, 15:1284, 2005 : PubMed ESTHER: Buell_2005_Genome.Res_15_1284 PubMedSearch: Buell 2005 Genome.Res 15 1284 PubMedID: 16109971 Gene_locus related to this paper: orysa-Q852M6, orysa-Q8S5X5, orysa-Q84QZ6, orysa-Q84QY7, orysa-Q851E3, orysa-q6ave2, orysj-cgep, orysj-q0dud7, orysj-q10j20, orysj-q10ss2 Abstract Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged approximately 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals. 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: Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R and Ward N <25 more author(s)> Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, DeBoy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N (- 25) Ref: Nature, 432:910, 2004 : PubMed ESTHER: Moran_2004_Nature_432_910 PubMedSearch: Moran 2004 Nature 432 910 PubMedID: 15602564 Gene_locus related to this paper: silpo-q5lke5, silpo-q5lke7, silpo-q5lke8, silpo-q5lkk5, silpo-q5lkv2, silpo-q5lln9, silpo-q5llu0, silpo-q5llu2, silpo-q5llx5, silpo-q5lm66, silpo-q5lmb9, silpo-q5lml9, silpo-q5lnp6, silpo-q5lp28, silpo-q5lp48, silpo-q5lp56, silpo-q5lpa5, silpo-q5lpf7, silpo-q5lpy6, silpo-q5lrk1, silpo-q5lsn7, silpo-q5ltb5, silpo-q5ltk0, silpo-q5ltm5, silpo-q5ltw8, silpo-q5ltw9, silpo-q5ltx1, silpo-q5ltx5, silpo-q5lu02, silpo-q5lv12, silpo-q5lv17, silpo-q5lv53, silpo-q5lvg9, silpo-q5lw35, silpo-q5lwk9, silpo-q5lws0 Abstract Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean. 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: Cloning and characterization of a gene cluster for geldanamycin production in Streptomyces hygroscopicus NRRL 3602 Rascher A, Hu Z, Viswanathan N, Schirmer A, Reid R, Nierman WC, Lewis M, Hutchinson CR Ref: FEMS Microbiology Letters, 218:223, 2003 : PubMed ESTHER: Rascher_2003_FEMS.Microbiol.Lett_218_223 PubMedSearch: Rascher 2003 FEMS.Microbiol.Lett 218 223 PubMedID: 12586396 Gene_locus related to this paper: strhy-Q84G29 Abstract We illustrate the use of a PCR-based method by which the genomic DNA of a microorganism can be rapidly queried for the presence of type I modular polyketide synthase genes to clone and characterize, by sequence analysis and gene disruption, a major portion of the geldanamycin production gene cluster from Streptomyces hygroscopicus var. geldanus NRRL 3602. 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: Some observations of levels of plasma cholinesterase activity within an obstetric population Whittaker M, Crawford JS, Lewis M Ref: Anaesthesia, 43:42, 1988 : PubMed ESTHER: Whittaker_1988_Anaesthesia_43_42 PubMedSearch: Whittaker 1988 Anaesthesia 43 42 PubMedID: 3125760 Inhibitor(s) related to this paper: Succinylcholine~Suxamethonium Abstract An account of plasma cholinesterase activity in samples of maternal and cord blood is presented. It is confirmed that plasma exchange markedly reduces the level of activity in maternal blood, and that the level is further reduced during the first 3-4 postnatal days. A particularly marked decrease was found in those cases in which spontaneous mid-trimester abortion occurred. The level of activity in maternal blood (excluding mothers subjected to plasma exchange) at the time of delivery, was higher than that in cord blood in 61% of cases. In 23% of cases the level of activity was appreciably (0.05 units) higher in cord blood, and two-thirds of these cord samples contained the E2+ electrophoretic variant of plasma cholinesterase. The mean levels of activity in maternal and cord blood of Rhesus negative patients were significantly lower than those among Rhesus positive patients but there was no such distinction between Rhesus positive and Rhesus negative males and nonpregnant females. We encountered an incidence of 1:228 abnormal phenotypes in a series of 1593 mothers who underwent Caesarean section under a technique of general anaesthesia which included a suxamethonium infusion. However, probably only two of the seven patients would definitely be sensitive when not pregnant. Title: The Yt blood group system (ISBT No. 011). Genetic studies Lewis M, Kaita H, Philipps S, McAlpine PJ, Wong P, Giblett ER, Anderson J Ref: Vox Sang, 53:52, 1987 : PubMed ESTHER: Lewis_1987_Vox.Sang_53_52 PubMedSearch: Lewis 1987 Vox.Sang 53 52 PubMedID: 3477904 Abstract Allele frequencies of Yta (YT1) and Ytb (YT2) in a series of 659 random Canadian Caucasians are comparable to those in European populations: 0.9469 and 0.0531, respectively. Inheritance of Yt phenotypes in 1,077 children in 286 selected families are in accordance with expectation on the basis of Mendelian codominance. Linkage studies exclude YT from chromosomal segments 1p36-1p22.1, 4q13-4q28, the section of chromosome 9 bounded by AB0 and AK1 and from the chromosome 19 linkage group bounded by LE and SE. Evidence is presented for a possible location of YT on the short arm of chromosome 6 distal to F13A. Title: Refined crystal structure of carboxypeptidase A at 1.54 A resolution Rees DC, Lewis M, Lipscomb WN Ref: Journal of Molecular Biology, 168:367, 1983 : PubMed ESTHER: Rees_1983_J.Mol.Biol_168_367 PubMedSearch: Rees 1983 J.Mol.Biol 168 367 PubMedID: 6887246 Abstract The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981). The crystallographic R factor (formula; see text) for structure factors calculated from the final model is 0.190. Bond lengths and bond angles in the carboxypeptidase A model have root-mean-square deviations from ideal values of 0.025 A and 3.6 degrees, respectively. Four examples of a reverse turn like structure (the "Asx" turn) requiring an aspartic acid or asparagine residue are observed in this structure. The Asx turn has the same number of atoms as a reverse turn, but only one peptide bond, and the hydrogen bond that closes the turn is between the Asx side-chain CO group and a main-chain NH group. The distributions of CO-N and NH-O hydrogen bond angles in the alpha-helices and beta-sheet structures of carboxypeptidase A are centered about 156 degrees. A total of 192 water molecules per molecule of enzyme are included in the final model. Unlike the hydrogen bonding geometry observed in the secondary structure of the enzyme, the CO-O(wat) hydrogen bond angle is distributed about 131 degrees, indicating the role of the lone pair electrons of the carbonyl oxygen in the hydrogen bond interaction. Twenty four solvent molecules are observed buried within the protein. Several of these waters are organized into hydrogen-bonded chains containing up to five waters. The average temperature factor for atoms in carboxypeptidase A is 8 A2, and varies from 5 A2 in the center of the protein, to over 30 A2 at the surface. Title: Zinc environment and cis peptide bonds in carboxypeptidase A at 1.75-A resolution Rees DC, Lewis M, Honzatko RB, Lipscomb WN, Hardman KD Ref: Proceedings of the National Academy of Sciences of the United States of America, 78:3408, 1981 : PubMed ESTHER: Rees_1981_Proc.Natl.Acad.Sci.U.S.A_78_3408 PubMedSearch: Rees 1981 Proc.Natl.Acad.Sci.U.S.A 78 3408 PubMedID: 6943549 Abstract The structure of the metalloenzyme carboxypeptidase A (peptidyl-L-amino-acid hydrolase, EC 3.4.17.1) has been refined at 1.75 A by a restrained least-squares procedure to a conventional crystallographic R factor of 0.162. Significant results of the refined structure relative to the catalytic mechanism are described. In the native enzyme, the zinc coordination number is five (two imidazole N delta 1 nitrogens, the two carboxylate oxygens of glutamate-72, and a water molecule). In the complex (at 2.0-A resolution) of carboxypeptidase A with the dipeptide glycyl-L-tyrosine, however, the water ligand is replaced by both the carbonyl oxygen and the amino nitrogen of the dipeptide. The amino nitrogen also statistically occupies a second position near glutamate-270. Consequently, the coordination number of zinc may vary from five to six in carboxypeptidase A-substrate complexes. Implications of these results for the catalytic mechanism of carboxypeptidase A are discussed. In addition, three cis peptide bonds, none of which involves proline as the amino nitrogen donor, have been located fairly near the active site. | |||||||
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