Author Report for: Martinez DNo contact information in database for Martinez D
Skomal AE, Zhang J, Yang K, Yen J, Tu X, Suarez-Torres J, Lopez-Paredes D, Calafat AM, Ospina M and Suarez-Lopez JR <1 more author(s)> Skomal AE, Zhang J, Yang K, Yen J, Tu X, Suarez-Torres J, Lopez-Paredes D, Calafat AM, Ospina M, Martinez D, Suarez-Lopez JR (- 1) Ref: Environ Research, :112163, 2021 : PubMed ESTHER: Skomal_2021_Environ.Res__112163 PubMedSearch: Skomal 2021 Environ.Res 112163 PubMedID: 34627797 Abstract BACKGROUND: Organophosphates are insecticides that inhibit the enzymatic activity of acetylcholinesterase (AChE). Because of this, AChE is considered a physiological marker of organophosphate exposure in agricultural settings. However, limited research exists on the associations between urinary organophosphate metabolites and AChE activity in children. METHODS: This study included 526 participants from 2 exams (April and July-October 2016) of ages 12-17 years living in agricultural communities in Ecuador. AChE activity was measured at both examinations, and organophosphate metabolites, including para-nitrophenol (PNP), 3,5,6-trichloro-2-pyridinol (TCPy), and malathion dicarboxylic acid (MDA) were measured in urine collected in July-October. We used generalized estimating equation generalized linear model (GEEGLM), adjusting for hemoglobin, creatinine, and other demographic and anthropometric covariates, to estimate associations of urinary metabolite concentrations with AChE activity (July-October) and AChE % change between April and July-October. RESULTS: The mean (SD) of AChE and AChE % change (April vs July-October) were 3.67 U/mL (0.54) and -2.5 % (15.4 %), respectively. AChE activity was inversely associated with PNP concentration, whereas AChE % change was inversely associated with PNP and MDA. There was evidence of a threshold: difference was only significant above the 80th percentile of PNP concentration (AChE difference per SD increase of metabolite = -0.12 U/mL [95 %CI: 0.20, -0.04]). Likewise, associations with AChE % change were significant only above the 80th percentile of TCPy (AChE % change per SD increase of metabolite = -1.38 % [95 %CI: 2.43 %, -0.32 %]) and PNP -2.47 % [95 %CI: 4.45 %, -0.50 %]). PNP concentration at <=80th percentile was associated with elevated ORs for low AChE activity of 2.9 (95 % CI: 1.5, 5.7) and for AChE inhibition of >= -10 % of 3.7 (95 % CI: 1.4, 9.8). CONCLUSIONS: Urinary organophosphate metabolites, including PNP, TCPy and MDA, particularly at concentrations above the 80th percentile, were associated with lower AChE activity among adolescents. These findings bring attention to the value of using multiple constructs of pesticide exposure in epidemiologic studies. Title: Transcriptional activation of genes involved in oxidative stress in Salmo salar challenged with Piscirickettsia salmonis Pedro AVF, Martinez D, Pontigo JP, Vargas-Lagos C, Hawes C, Wadsworth S, Morera FJ, Vargas-Chacoff L, Yanez AJ Ref: Comparative Biochemistry & Physiology B Biochem Mol Biol, 229:18, 2018 : PubMed ESTHER: Pedro_2018_Comp.Biochem.Physiol.B.Biochem.Mol.Biol_229_18 PubMedSearch: Pedro 2018 Comp.Biochem.Physiol.B.Biochem.Mol.Biol 229 18 PubMedID: 30590175 Abstract Piscirickettsiosis caused by Piscirickettsia salmonis constitutes one of the main problems in farmed salmonid and marine fishes. The objective of this study was to evaluate the modulation of genes involved in the oxidative stress in the liver and muscle of Salmo salar challenge with low dosage of P. salmonis. The treatment (in duplicate) were as follows: Control injection (culture medium) and P. salmonis injection (1x10(2) PFU/mL) with sampling (liver and muscle) at several time-points during the 42-days experimental period (dpi). In liver, the gene expression of superoxide dismutase (SOD) and acetylcholinesterase (AChE) had differences with the control group only at 7dpi, compared with glutathione-S-transferase (GST) and heat shock protein 70 (HSP70) that presented increases at 7 and 21dpi. The glutathione peroxidase (GPx) and catalase (CAT) mRNAs were elevated at 13 and 21dpi, respectively. While glutathione reductase (GR) and cytochrome P450 (P450) did not show variations in their expression during the experimental course. In muscle, the expression of CAT and AChE was higher than in the control condition at 2 and 42dpi, respectively. While the number of transcripts SOD, GPx, GR, GST, P450 and HSP70 showed increases at 7- and 42-days post injection. The results suggest a transcriptional activation of genes involved in oxidative stress in both liver and muscle, with expression profiles that were tissue-specific and dependent on the time. This is the first study that reveals the transcriptional participation of all these genes associated with oxidative stress in response to the injection of P. salmonis. Title: Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R and Baker SE <37 more author(s)> Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE (- 37) Ref: Genome Res, 21:885, 2011 : PubMed ESTHER: Andersen_2011_Genome.Res_21_885 PubMedSearch: Andersen 2011 Genome.Res 21 885 PubMedID: 21543515 Gene_locus related to this paper: aspna-g3y4g9, aspna-g3yal2, aspna-g3ycq2, aspnc-a2qbh3, aspnc-a2qe77, aspnc-a2qf54, aspnc-a2qfe9, aspnc-a2qg33, aspnc-a2qh76, aspnc-a2qhe2, aspnc-a2qi32, aspnc-a2ql89, aspnc-a2ql90, aspnc-a2qla0, aspnc-a2qmk5, aspnc-a2qn56, aspnc-a2qs22, aspnc-a2qti9, aspnc-a2qtz0, aspnc-a2quc1, aspnc-a2qx92, aspnc-a2qyf0, aspnc-a2qys7, aspnc-a2qz72, aspnc-a2qzn6, aspnc-a2qzr0, aspnc-a2qzx0, aspnc-a2qzx4, aspnc-a2r0p4, aspnc-a2r1r5, aspnc-a2r2i5, aspnc-a2r5r4, aspnc-a2r6h5, aspnc-a2r8r3, aspnc-a2r8z3, aspnc-a2r273, aspnc-a2r496, aspnc-a2r502, aspnc-a5abe5, aspnc-a5abe8, aspnc-a5abh9, aspnc-a5abk1, aspnc-axe1, aspnc-cuti1, aspnc-cuti2, aspng-a2qs46, aspng-a2qv27, aspni-EstA, aspkw-g7y0v7, aspnc-a2qt47, aspnc-a2qt66, aspna-g3xpq9, aspnc-a2qqa1, aspna-g3xsl3, aspna-g3y5a6, aspna-g3xpw9, aspaw-a0a401kpx5, aspnc-a2qw57, aspaw-a0a401kcz4, aspna-alba, aspna-azac Abstract The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi. Title: Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C and Tsang A <29 more author(s)> Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan MC, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LD, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A (- 29) Ref: Nat Biotechnol, 29:922, 2011 : PubMed ESTHER: Berka_2011_Nat.Biotechnol_29_922 PubMedSearch: Berka 2011 Nat.Biotechnol 29 922 PubMedID: 21964414 Gene_locus related to this paper: thiha-cip2, thite-g2r8b5, thite-g2rcm8, thite-g2r192, thiha-g2qdy2, thiha-g2qh51, thite-g2rae6, thite-g2r5h0, thiha-g2qj94, thiha-g2qnb2, thite-g2rg14, myctt-g2q973, thite-g2qtu3, myctt-g2qpr0, thite-g2rhm0, 9pezi-a0a3s4b069, myctt-g2qmb4, thett-g2qur2 Abstract Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics. Title: Genome sequence and analysis of the tuber crop potato Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R and Visser RG <87 more author(s)> Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejia N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sonderkaer M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, De Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert B, Goverse A, van Ham RC, Visser RG (- 87) Ref: Nature, 475:189, 2011 : PubMed ESTHER: Xu_2011_Nature_475_189 PubMedSearch: Xu 2011 Nature 475 189 PubMedID: 21743474 Gene_locus related to this paper: soltu-q2tqv0, soltu-q4h433, soltu-m0zl00, soltu-m1aw23, soltu-m0zxh5, soltu-m1d3q4, soltu-m1bz14, soltu-m1d3q6, sollc-k4b1g3, soltu-m0zzn8, soltu-m1ba60, sollc-k4bf33, soltu-m1c8d8, soltu-m1ced9, soltu-m1a385, soltu-m1bz15, soltu-m1a7s9, soltu-m1bc84, soltu-m1bpd1, sollc-k4bm34, soltu-m1a487, soltu-m1a5u0, soltu-m1cjx7, soltu-m1bvq8, soltu-m1baq1, soltu-m1cfh4, soltu-m1azl4, soltu-m0ztj0, soltu-m1d6d0 Abstract Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. Title: Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT and Cullen D <43 more author(s)> Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavin JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kues U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D (- 43) Ref: Proc Natl Acad Sci U S A, 106:1954, 2009 : PubMed ESTHER: Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954 PubMedSearch: Martinez 2009 Proc.Natl.Acad.Sci.U.S.A 106 1954 PubMedID: 19193860 Gene_locus related to this paper: pospm-b8p1f3, pospm-b8p2q7, pospm-b8p4n0, pospm-b8p4n9, pospm-b8p5g9, pospm-b8p5r9, pospm-b8p6h2, pospm-b8p7b1, pospm-b8p7c4, pospm-b8p8w7, pospm-b8p9j1, pospm-b8p164, pospm-b8p280, pospm-b8p423.1, pospm-b8p423.2, pospm-b8p858, pospm-b8pam2, pospm-b8pam5, pospm-b8pb68, pospm-b8pbm3, pospm-b8pc54, pospm-b8pc56, pospm-b8pce4, pospm-b8pd91, pospm-b8pdk6, pospm-b8ph32, pospm-b8ph43, pospm-b8phc9, pospm-b8php7, pospm-b8phy5, pospm-b8pjg8, pospm-b8pji9, pospm-b8plr5, pospm-b8pmk3, pospm-b8pfg0, pospm-b8pg35, pospm-b8pa20.1, pospm-b8pa20.2, pospm-b8p4g8, pospm-b8phn6 Abstract Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost. Title: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM and Brettin TS <35 more author(s)> Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS (- 35) Ref: Nat Biotechnol, 26:553, 2008 : PubMed ESTHER: Martinez_2008_Nat.Biotechnol_26_553 PubMedSearch: Martinez 2008 Nat.Biotechnol 26 553 PubMedID: 18454138 Gene_locus related to this paper: hypjq-g0rh85, hypjq-cip2, hypjq-g0r9d1, hypjq-g0r810, hypjq-g0rbm4, hypjq-g0rez4, hypjq-g0rfr3, hypjq-g0rg60, hypjq-g0rij9, hypjq-g0riu1, hypjq-g0rl87, hypjq-g0rlh4, hypjq-g0rme5, hypjq-g0rwy5, hypje-axylest, hypje-q7z9m3, hypjq-g0r6x2, hypje-a0a024s1b8, hypjr-a0a024s1s9, hypjq-g0rxi5 Abstract Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production. Title: The complete genome sequence of Bacillus thuringiensis Al Hakam Challacombe JF, Altherr MR, Xie G, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J and Brettin TS <38 more author(s)> Challacombe JF, Altherr MR, Xie G, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, Cleland C, Dimitrijevic M, Doggett NA, Fawcett JJ, Glavina T, Goodwin LA, Green LD, Han CS, Hill KK, Hitchcock P, Jackson PJ, Keim P, Kewalramani AR, Longmire J, Lucas S, Malfatti S, Martinez D, McMurry K, Meincke LJ, Misra M, Moseman BL, Mundt M, Munk AC, Okinaka RT, Parson-Quintana B, Reilly LP, Richardson P, Robinson DL, Saunders E, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Ticknor LO, Wills PL, Gilna P, Brettin TS (- 38) Ref: Journal of Bacteriology, 189:3680, 2007 : PubMed ESTHER: Challacombe_2007_J.Bacteriol_189_3680 PubMedSearch: Challacombe 2007 J.Bacteriol 189 3680 PubMedID: 17337577 Gene_locus related to this paper: bacah-a0rcd1, bacah-a0rer5, bacah-a0rev7, bacan-BA1019, bacan-BA1242, bacan-BA2392, bacan-BA2607, bacan-BA3343, bacan-BA3863, bacan-BA3877, bacan-BA4324, bacan-BA4338, bacan-BA4577, bacan-BA5009, bacan-BA5110, bacan-BA5136, bacan-DHBF, bacc1-q73a27, bacc1-q73c93, bacce-BC0192, bacce-BC1788, bacce-BC1954, bacce-BC2141, bacce-BC2171, bacce-BC4730, bacce-BC4862, bacce-BC5130, bacce-PHAC, bacce-q72yu1, baccr-pepx, bachk-q6hcl3, bachk-q6hgn4, bachk-q6hgp9, bachk-q6hig3, bachk-q6hit8 Abstract Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003). Title: The Chlamydomonas genome reveals the evolution of key animal and plant functions Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK and Grossman AR <107 more author(s)> Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR (- 107) Ref: Science, 318:245, 2007 : PubMed ESTHER: Merchant_2007_Science_318_245 PubMedSearch: Merchant 2007 Science 318 245 PubMedID: 17932292 Gene_locus related to this paper: chlre-a0a2k3e2k6, chlre-a8hmd4, chlre-a8hqa9, chlre-a8htq0, chlre-a8hus6.1, chlre-a8hus6.2, chlre-a8icg4, chlre-a8iwm0, chlre-a8ize5, chlre-a8j2s9, chlre-a8j5w6, chlre-a8j7f8, chlre-a8j8u9, chlre-a8j8v0, chlre-a8j9u6, chlre-a8j143, chlre-a8j248, chlre-a8jd32, chlre-a8jd42, chlre-a8jgj2, chlre-a8jhc8, chlre-a8jhe5, chlre-a8iwj1, chlre-a8j7d5, chlre-a0a2k3dii0 Abstract Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella. Title: Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity Frutos R, Viari A, Ferraz C, Morgat A, Eychenie S, Kandassamy Y, Chantal I, Bensaid A, Coissac E and Martinez D <2 more author(s)> Frutos R, Viari A, Ferraz C, Morgat A, Eychenie S, Kandassamy Y, Chantal I, Bensaid A, Coissac E, Vachiery N, Demaille J, Martinez D (- 2) Ref: Journal of Bacteriology, 188:2533, 2006 : PubMed ESTHER: Frutos_2006_J.Bacteriol_188_2533 PubMedSearch: Frutos 2006 J.Bacteriol 188 2533 PubMedID: 16547041 Gene_locus related to this paper: ehrrw-a0a0h3m645 Abstract Ehrlichia ruminantium is the causative agent of heartwater, a major tick-borne disease of livestock in Africa that has been introduced in the Caribbean and is threatening to emerge and spread on the American mainland. We sequenced the complete genomes of two strains of E. ruminantium of differing phenotypes, strains Gardel (Erga; 1,499,920 bp), from the island of Guadeloupe, and Welgevonden (Erwe; 1,512,977 bp), originating in South Africa and maintained in Guadeloupe in a different cell environment. Comparative genomic analysis of these two strains was performed with the recently published parent strain of Erwe (Erwo) and other Rickettsiales (Anaplasma, Wolbachia, and Rickettsia spp.). Gene order is highly conserved between the E. ruminantium strains and with A. marginale. In contrast, there is very little conservation of gene order with members of the Rickettsiaceae. However, gene order may be locally conserved, as illustrated by the tuf operons. Eighteen truncated protein-encoding sequences (CDSs) differentiate Erga from Erwe/Erwo, whereas four other truncated CDSs differentiate Erwe from Erwo. Moreover, E. ruminantium displays the lowest coding ratio observed among bacteria due to unusually long intergenic regions. This is related to an active process of genome expansion/contraction targeted at tandem repeats in noncoding regions and based on the addition or removal of ca. 150-bp tandem units. This process seems to be specific to E. ruminantium and is not observed in the other Rickettsiales. Title: The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE and Rokhsar DS <35 more author(s)> Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (- 35) Ref: Science, 306:79, 2004 : PubMed ESTHER: Armbrust_2004_Science_306_79 PubMedSearch: Armbrust 2004 Science 306 79 PubMedID: 15459382 Gene_locus related to this paper: thaps-b5ymy7, thaps-b5yn04, thaps-b5ynz7, thaps-b8bq57, thaps-b8bsn5, thaps-b8bsy4, thaps-b8bv00, thaps-b8bxb3, thaps-b8byx0, thaps-b8bzg5, thaps-b8c0a3, thaps-b8c2d8, thaps-b8c2k9, thaps-b8c2s5, thaps-b8c3p0, thaps-b8c5l7, thaps-b8c6y7, thaps-b8c9k8, thaps-b8c9t6, thaps-b8c345, thaps-b8c584, thaps-b8c885, thaps-b8c954, thaps-b8cdd7, thaps-b8cdt3, thaps-b8cf07, thaps-b8cfn8, thaps-b8c079 Abstract Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments. Title: The DNA sequence and biology of human chromosome 19 Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O and Lucas SM <88 more author(s)> Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM (- 88) Ref: Nature, 428:529, 2004 : PubMed ESTHER: Grimwood_2004_Nature_428_529 PubMedSearch: Grimwood 2004 Nature 428 529 PubMedID: 15057824 Abstract Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu. Title: The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M and Rokhsar DS <77 more author(s)> Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-I T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS (- 77) Ref: Science, 298:2157, 2002 : PubMed ESTHER: Dehal_2002_Science_298_2157 PubMedSearch: Dehal 2002 Science 298 2157 PubMedID: 12481130 Gene_locus related to this paper: cioin-141645, cioin-147959, cioin-150181, cioin-154370, cioin-ACHE1, cioin-ACHE2, cioin-cxest, cioin-f6qcp0, cioin-f6r8z1, cioin-f6u176, cioin-f6vac9, cioin-f6x584, cioin-f6xa69, cioin-f6y403, cioin-h2xqb4, cioin-H2XTI0, cioin-F6T1M3, cioin-H2XUP7, cioin-CIN.7233, cioin-F6V269, cioin-Cin16330, cioin-h2xua2, cioin-f6vaa5, cioin-f6v9x6, cioin-f6swc9, cioin-f7amz2, cioin-f6s021, cioin-h2xxq9, cioin-h2xne6, cioin-f6ynr2 Abstract The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi. Title: Tricompartmental kinetics of the organophosphorous pesticide dimethoate Garcia-Repetto R, Martinez D, Repetto M Ref: Vet Hum Toxicol, 39:201, 1997 : PubMed ESTHER: Garcia-Repetto_1997_Vet.Hum.Toxicol_39_201 PubMedSearch: Garcia-Repetto 1997 Vet.Hum.Toxicol 39 201 PubMedID: 9251166 Abstract We present a study on the distribution and persistence of the organophosphorous pesticide, dimethoate, in the Wistar rat. Dimethoate's levels in blood and tissues were determined using gas chromatography with a NPD detector. The toxicokinetic profile was estimated by non-linear regression using the software program PCNONLIN, which concluded that a tricompartmental model best described dimethoate's behavior in the rat body. Title: Biodisposition study of the organophosphorus pesticide, methyl- parathion Garcia-Repetto R, Martinez D, Repetto M Ref: Bulletin of Environmental Contamination & Toxicology, 59:901, 1997 : PubMed ESTHER: Garcia-Repetto_1997_Bull.Environ.Contam.Toxicol_59_901 PubMedSearch: Garcia-Repetto 1997 Bull.Environ.Contam.Toxicol 59 901 PubMedID: 9400660 | |||||||
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