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CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0 Nature Precedings
Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5887/version/3
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Coliform density in oyster culture waters and its relationship with environmental factors PAB
Mignani,Luciene; Barbieri,Edison; Marques,Helcio Luis de Almeida; Oliveira,Ana Julia Fernandes Cardoso de.
The objective of this work was to evaluate the total and thermotolerant coliform densities in the oyster culture water of Cananeia, SP, Brazil, correlating these densities with environmental variables and tidal variations. Superficial water samples were collected in two tide conditions (spring and neap) from three areas of Cananéia municipality (Mandira, Itapitangui and Cooperostra). The three studied areas showed good conditions for the culture regarding coliform densities. The two tidal conditions differed significantly as to total coliform concentration; however, the same procedure was not performed for thermotolerant coliforms. No correlation was observed between water temperature, pH, and concentrations of total and thermotolerant coliforms. Coliform...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Crassostrea; Contamination; Microbiology; Principal component analysis; Total and thermotolerant coliforms.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2013000800007
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Comment to "Endogenous Viral Etiology of Prion Diseases" Nature Precedings
Claudiu Bandea.
This note is intended as a comment to a paper in Nature Precedings entitled "Endogenous viral etiology of prion diseases":http://precedings.nature.com/documents/3887/version/1 . Because it contains illustrations that could not be displayed in the comments section of that paper, I’m posting this comment here as a PDF document.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Neuroscience; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/4101/version/1
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Community Outreach through Genomics Education Partnership Nature Precedings
Ramana Madupu; Anne G. Rosenwald; A. Malcolm Campbell; Satish C. Bhalla; Granger Sutton.
The J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID’s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience. Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the...
Tipo: Poster Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3149/version/1
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Comparison of histopathologicalfeatures of Vibrio cholerae O1 El Tor andO139 Bengal infections in rabbit intestinal mucosa Nature Precedings
Atif A. Baig.
Vibrio cholerae is the causative agent of the infectious disease, cholera. The bacteria adhere to the mucosal membrane and release cholera toxin, leading to watery diarrhea. There are >100 serovars of V. cholerae, but the O1 and O139 serovars are the main causative agents of cholera. The present study aimed to compare the severity of intestinal mucosal infection caused by O1 El Tor and O139 V. cholerae in a rabbit ileal loop model.
The results showed that although the fluid accumulation was similar in the loops inoculated with O1 and O139 V. cholerae, the presence of blood was detected only in the loops inoculated with the O139 serovar. Serosal hemorrhage was confirmed by histopathological examination and the loops inoculated with...
Tipo: Presentation Palavras-chave: Microbiology.
Ano: 2011 URL: http://precedings.nature.com/documents/6418/version/1
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Comportamento de dois genótipos de milho sob diferentes doses e formas de nitrogênio e inoculação com Azospirillum amazonense em um ensaio de casa-de-vegetação. Infoteca-e
REIS JÚNIOR, F. B.; MACHADO, C. T. T.; MACHADO, A. T.; ROLIM, L.; SODEK, L..
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Tipo: Fôlder / Folheto / Cartilha (INFOTECA-E) Palavras-chave: Microbiologia do solo; Inoculação; Milho; Zea mays; Bactéria; Azospirillum amazonense; Microbiology; Soil; Inoculation methods; Maize.
URL: http://www.infoteca.cnptia.embrapa.br/handle/doc/569425
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Comportamento de duas variedades de milho sob diferentes níveis de fósforo e inoculação com Azospirillum amazonense em um ensaio de casa-de-vegetação. Infoteca-e
REIS JÚNIOR, F. B.; MACHADO, C. T. T.; ROLIM, L.; VILELA, A. L.; SANTOS, A. B. dos; MENDES, I. C.; MACHADO, A. T..
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Tipo: Fôlder / Folheto / Cartilha (INFOTECA-E) Palavras-chave: Microbiologia do solo; Inoculação; Milho; Zea mays; Bactéria; Azospirillum amazonense; Microbiology; Soil; Inoculation methods; Maize.
URL: http://www.infoteca.cnptia.embrapa.br/handle/doc/569494
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Computational binding mechanism of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (MurA) with inhibitors fosfomycin, cyclic disulfide analog RWJ-3981, pyrazolopyrimidine analog RWJ-110192, purine analog RWJ-140998, 5-sulfonoxy-anthranilic aci Nature Precedings
C. M. Anuradha; B. Babajan; M. Chaitanaya; C. Rajasekhar; Suresh Kumar Chitta.
Worldwide, tuberculosis (TB) remains the most frequent and important infectious disease causing morbidity and death. One-third of the world's population is infected with Mycobacterium tuberculosis (Mtb), the etiologic agent of TB. In this context, TB is in the top three, with malaria and HIV being the leading causes of death from a single infectious agent, and about two million deaths are attributable to TB annually. The bacterial enzyme MurA catalyzes the transfer of enolpyruvate from phosphoenolpyruvate (PEP) to uridine diphospho-N-acetylglucosamine (UNAG), which is the first committed step of bacterial cell wall biosynthesis. In this work, 3D structural model of Mtb-MurA enzyme has been developed, for the first time, by homology modeling and...
Tipo: Manuscript Palavras-chave: Biotechnology; Microbiology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3731/version/1
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Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades Nature Precedings
Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1,2. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60% 3. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases 4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the...
Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/459/version/1
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Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades Nature Precedings
Henry Niman; Mona M. Aly; Abdel-Satar Arafa; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1,2. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 3. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases 4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, Kuwait, and Ghana. These changes are not easily...
Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/459/version/4
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Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades Nature Precedings
Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current...
Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/459/version/2
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Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades Nature Precedings
Henry L. Niman; Magdi D. Saad; Mona M. Aly; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics & Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/459/version/3
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Contaminação, conservação e alteração da carne. Infoteca-e
FEITOSA, T..
Transformacao do musculo em carne; contaminacao; fatores que influenciam a multiplicacao da flora inicial; atividade da agua; pH; potencial redox; temperatura; alteracao; alteracoes em temperaturas elevadas; aleracoes em temperaturas intermediarias; alteracoes em temperaturas baixas; conservacao; assepsia; emprego de temperaturas baixas; refrigeracao; congelamento; emprego do calor; radiacao; desidratacao; emprego deconservantes; cura; defumacao; condimentos; antibioticos...
Tipo: Documentos (INFOTECA-E) Palavras-chave: Carne; Contaminacao; Conservacao; Microbiologia; Qualidade; Meat; Contamination; Conservation; Microbiology; Quality.
Ano: 1999 URL: http://www.infoteca.cnptia.embrapa.br/handle/doc/421977
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Controlling sap-sucking insect pests with recombinant endophytes expressing plant lectin Nature Precedings
Xiuyun Zhao; Gaofu Qi; Xianfang Zhang; Nan Lan; Xinrong Ma.
We developed a novel pest management strategy, which uses endophytes to express anti-pest plant lectins. Fungal endophyte of Chaetomium globosum YY-11 with anti-fungi activities was isolated from rape seedlings, and bacterial endophytes of SJ-10 (Enterobacter sp.) and WB (Bacillus subtilis) were isolated from rice seedlings. Pinellia ternate agglutinin gene was cloned into SJ-10 and WB for expression by a shuttle vector, and YY-11 was mediated by Agrobacterium tumefaciens. Positive transformants were evaluated using PCR and Western blot assay. Recombinant endophytes colonized most of crops, and resistance of rice seedlings, which were inoculated with the recombinant endophytic bacteria, to white backed planthoppers was dramatically enhanced by decreasing...
Tipo: Manuscript Palavras-chave: Biotechnology; Microbiology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4862/version/1
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Critical Concentration Gradient Model of Bacterial Cell Division Nature Precedings
Aijaz A. Rashid; Perminder P. Sing.
Critical concentration gradient model is helpful in understanding the mechanism of Z-ring formation. The distribution of positive and negative regulators of Z-ring formation in cell is not random but well programmed. The positive and negative regulators in cell lead to a critical concentration gradient from mid cell to the poles. The critical concentration of FtsZ required for Z-ring assembly at the centre of cell is less than that at the poles. So FtsZ starts polymerizing at cell centre and afterwards by cooperative association of more and more monomers leads to the Z-ring formation. Simultaneously during Z-ring formation the recruitment of other accessory proteins takes place, leading to the formation of a stable divisome complex.
Tipo: Manuscript Palavras-chave: Biotechnology; Microbiology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/4659/version/1
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Cutaneous mycobiota of boid snakes kept in captivity Arq. Bras. Med. Vet. Zootec.
Freire,B.C.; Garcia,V.C.; Quadrini,A.E.; Bentubo,H.D.L..
ABSTRACT Boids are large, constrictor snakes that feed mostly on mammals, reptiles, and birds. These animals are commonly raised as pets, and their improper handling can favor the emergence of fungal infections, which can lead to dermatological diseases that are undiagnosed in nature. Here, we isolate and identify the filamentous fungi that compose the mycobiota of the scales of boid snakes kept in captivity at the Biological Museum of the Butantan Institute. Thirty individuals of four species were evaluated: four Eunectes murinus, twelve Boa constrictor constrictor, seven Corallus hortulanus, and seven Epicrates crassus. Microbiological samples were collected by rubbing small square carpets on the snake scales. We isolated five genera of fungi:...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Microbiology; Filamentous; Fungi; Reptiles.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-09352019000401093
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Data Management Plan for Monogram BioSciences Nature Precedings
Christos J. Petropoulos.
This is the data plan for access to data underlying published reports by Monogram BioSciences.
Tipo: Marker Paper / Data Plan Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Pharmacology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5668/version/1
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Dating the cyanobacterial ancestor of the chloroplast Nature Precedings
Luisa Falcon; Susana Magallon; Amanda Castillo.
Cyanobacteria have played a pivotal role in the history of life on Earth being the first organism to carry out oxygenic photosynthesis, which changed atmospheric chemistry and allowed the evolution of Eukarya. Chloroplasts are the cellular organelles of photoautotrophic eukaryotes in which photosynthesis is conducted. Although the initial suggestion from Mereschkowsky (1905) that cyanobacteria are the ancestors of chloroplasts was greeted with skepticism, the idea is now widely accepted. Here we attempt to resolve and date the cyanobacterial ancestry of the chloroplast using phylogenetic analysis and molecular clocks, because until now, the long-standing question of, from which, among the vast diversity of cyanobacteria, did chloroplasts evolve, has not...
Tipo: Manuscript Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3696/version/1
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Day-length is central to maintaining consistent seasonal diversity in marine bacterioplankton Nature Precedings
Jack A. Gilbert; Paul Somerfield; Ben Temperton; Susan Huse; Ian Joint; Dawn Field.
Marine bacterial diversity is vast, but seasonal variation in diversity is poorly understood. Here we present the longest bacterial diversity time series consisting of monthly (72) samples from the western English Channel over a 6 year period (2003-2008) using 747,494 16SrDNA-V6 amplicon-pyrosequences. Although there were characteristic cycles for each phylum, the overall community cycle was remarkably stable year after year. The majority of taxa were not abundant, although on occasion these rare bacteria could dominate the assemblage. Bacterial diversity peaked at the winter solstice and showed remarkable synchronicity with day-length, which had the best explanatory power compared to a combination of other variables (including temperature and nutrient...
Tipo: Manuscript Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4406/version/1
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Description of variation of genlculate's features of _Phyllodiaptomustunguidus_ shen et Tai and sex-linked inheritance of Calanoida in freshwater Nature Precedings
Sheng-Xing Long; Xiao-Ming Gou; Pin-Hua Xia; Qi-Fei Ren; San Wan; Chuan Chen.
In the present paper, variation of genlculate's features of _Phyllodiaptomustunguidus_ shen et Tai of Calanoida are described.The authors find that the right first antenna of female species has changed into genlculate and first antenna of male species changed into genlculate, which can be explained by X-sex-linked inheritance. This isn't a disease but a genetic characteristic that is better for the living of the species.
Tipo: Manuscript Palavras-chave: Microbiology.
Ano: 2009 URL: http://precedings.nature.com/documents/3003/version/1
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