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Discriminatory power of MicroResp^TM^ analyses across variable spatial scales in semiarid ecological zones Nature Precedings
Mohammad E. W. Tahtamouni; Adrian Unc; Mary Lucero; Sa'eb Khresat.
Indirect assessment of enzymatic activity potential via substrate induced respiration is a common tool used to evaluate variability in soil microbial activity induced by environmental or management variables. The MicroResp™ method for total soil sample catabolic profiling has been employed to estimate divergence in microbial activities under contrasting conditions. Here we evaluate the potential for the method to discriminate across samples exposed to similar ecological conditions at distinct geographical locations, and across samples exposed to distinct soil management conditions. Samples used in this report came from four spatially distinct arid or semi arid locations in New Mexico, USA and Jordan. For all scales of comparison, similar...
Tipo: Poster Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/6204/version/1
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Patterns in soil ammonia-oxidizer response to global change Nature Precedings
Kathryn M. Docherty; Brendan Bohannan; Audrey Niboyet; Xavier LeRoux.
Background/Question/Methods
The Domains Archaea and Bacteria contain the vast majority of Earth’s biodiversity and biomass, and their members play critical, often exclusive, roles in many biogeochemical cycles and ecosystem services. Human-induced global change, particularly with respect to increased nitrogen deposition, has the potential to drastically alter how soil nitrifying communities perform their biogeochemical function. Additionally, multi-factor global change can alter how microbial communities interact with each other and with the associated plant communities. This study, performed in the context of the long-term Jasper Ridge Global Change Experiment (JRGCE) in a California grassland ecosystem, examines how...
Tipo: Presentation Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/5508/version/1
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The water clock of Proteus mirabilis paces colony periodic and synchronous swarming Nature Precedings
Elodie Lahaye; Frederic Jamme; Olivier Sire.
For decades, the origin of the concentric ring pattern of bacterial swarming colonies has puzzled microbiologists. Thanks to _in situ_ and real time infrared microspectroscopy and the brilliance of the infrared beam at SOLEIL synchrotron, we demonstrate here that _Proteus mirabilis_ swarming is paced by a periodic variation of the water activity at colony's edge. This periodic variation originates a phase transition within the extracellular matrix water H bond network which switches on and off the exopolysaccharides viscoelasticity and, consequently, the ability of bacterial cells to swarm. A dynamic behaviour emerges from the global properties of the multicellular entity which here relies on the ability of the bacterial cells to tune exoproducts...
Tipo: Manuscript Palavras-chave: Microbiology.
Ano: 2010 URL: http://precedings.nature.com/documents/4455/version/1
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Persisters show heritable phenotype and generate bacterial heterogeneity and noise in protein expression Nature Precedings
Jaison Jacob.
Persisters are a small subpopulation of bacteria that survive a lethal concentration of antibiotic without antibiotic resistance genes. Isolation of persisters from normally dividing population is considered difficult due to their slow growth, low numbers and phenotypic shift i.e. when re-grown in antibiotic free medium, they revert to parent population. Inability to isolate persisters is a major hindrance in this field of research. Here we reject the ‘phenotypic shift’ phenomenon exhibited by persisters. Persisters, on the other hand, exhibit a heritable phenotype and can be easily isolated from a normally dividing population that allows their selective growth. Rather than a single subset, they comprise many distinct subgroups each...
Tipo: Manuscript Palavras-chave: Microbiology.
Ano: 2009 URL: http://precedings.nature.com/documents/1411/version/2
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Is the infection/latency/reactivation cycle of viruses an oncogenic engine? Nature Precedings
Alessandro Ripalti.
Human oncogenic viruses are defined as necessary but not sufficient to initiate cancer. Experimental evidence suggests that the oncogenic potential of a virus is effective only in cells that have already accumulated a number of genetic mutations leading to cell cycle deregulation. Current models for viral driven oncogenesis cannot explain why tumor development in carriers of tumorigenic viruses is a very rare event, occurring decades after virus infection. Considering that viruses are mutagenic agents _per se_ and human oncogenic viruses additionally establish latent and persistent infections, I attempt here to provide a mechanism of tumor initiation both for RNA and DNA viruses, suggesting viruses could be both necessary and sufficient in human...
Tipo: Manuscript Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1285/version/1
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The human genome is composed of viral DNA: Viral homologues of the protein products cause Alzheimer's disease and others via autoimmune mechanisms. Nature Precedings
Christopher J. Carter.
The human genome is composed of millions of fragmented contiguous viral DNA sequences, dating from the dawn of evolution and reflecting retroviral insertions over millions of years of coexistence. Herpes and other viral insertion points correspond to the locations of over 120 Alzheimer's disease susceptibility genes and to linkage hotspots. The greater the number of pathogen matches, the more important the gene. These DNA sequences are translated into short contiguous 5-12 amino acid stretches (vatches), identical in viruses and man, and in other pathogens implicated in Alzheimer's disease (_Borrelia_, _Chlamydia_, _Helicobacter_, _C. Neoformans_ , _P. Gingivalis_). _C. Neoformans_, which has been associated with a rare but curable form...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4765/version/1
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Foregut microbiome in development of esophageal adenocarcinoma Nature Precedings
Liying Yang; William E. Oberdorf; Erika Gerz; Tamasha Parsons; Pinak Shah; Sukhleen Bedi; Carlos W. Nossa; Stuart M. Brown; Yu Chen; Mengling Liu; Michael Poles; Fritz Francois; Morris Traube; Navjeet Singh; Todd Z. DeSantis; Gary L. Andersen; Monika Bihan; Les Foster; Aaron Tenney; Daniel Brami; Mathangi Thiagarajan; Indresh K. Singh; Manolito Torralba; Shibu Yooseph; Yu-Hui Rogers; Eoin L. Brodie; Karen E. Nelson; Zhiheng Pei.
Esophageal adenocarcinoma (EA), the type of cancer linked to heartburn due to gastroesophageal reflux diseases (GERD), has increased six fold in the past 30 years. This cannot currently be explained by the usual environmental or by host genetic factors. EA is the end result of a sequence of GERD-related diseases, preceded by reflux esophagitis (RE) and Barrett’s esophagus (BE). Preliminary studies by Pei and colleagues at NYU on elderly male veterans identified two types of microbiotas in the esophagus. Patients who carry the type II microbiota are >15 fold likely to have esophagitis and BE than those harboring the type I microbiota. In a small scale study, we also found that 3 of 3 cases of EA harbored the type II biota. The findings...
Tipo: Marker Paper / Data Plan Palavras-chave: Cancer; Genetics & Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5026/version/1
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Development and comparison of ECC-rtPCR with in vivo method to determine the viability and infectivity of Giardial cysts Nature Precedings
M. Khalid Ijaz; Absar Alum; Basel Sbai; Hamas Asaad; Joseph Rubino.
Globally, Giardia is one of the major cause of diarrheal illnesses and rapid diagnostic methods differentiating infectious cysts are critical for developing intervention strategies through contaminated surfaces, food and water. This is currently hampered by lack of an in vitro model. We evaluated mRNA expression in trophozoites and their attachment to a CaCo2 (C2bb) cell monolayer and changes in trans-cellular resistance as an indicator of Giardia viability and infectivity. Heat shock mRNA in Giardia cysts and variant specific protein (VSP) mRNA in trophozoites were quantified by RT-PCR. When compared with neonatal mice infectivity, the attachment of trophozoites to cell monolayers, expression of VSP, and changes in the trans-cellular resistance, the...
Tipo: Manuscript Palavras-chave: Biotechnology; Immunology; Microbiology; Earth & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/5501/version/1
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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/2
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Myosin II isoforms with separate but linked functions determine the fate of lamellipodia extension during cell spreading Nature Precedings
Venkaiah Betapudi.
Non-muscle myosin II role has been implicated in the extension of lamellipodia, a critical step in the initiation of directed cell migration, invasion and other cellular processes, but the mechanistic details are limited to driving retrograde actin filaments. The present study reveals distinct localization of myosin IIA and IIB with an unexpected opposite mechanical roles in mediating lamellipodia extension during spreading. Attachment of cells to matrix is impaired in the absence of either isoforms, but differential regulation of focal contacts formation occurs in myosin IIA^-^; and IIB^-^; cells. Spreading cells expressing both isoforms display an organized actin network consisting of retrograde filaments, arcs and central filaments. Loss of actin arcs...
Tipo: Manuscript Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2868/version/1
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Populational analysis of Saccharomyces cerevisiae strains from different appellations of origin and grape varieties by microsatellite analysis. Nature Precedings
Leonor Pereira; Filomena L. Duarte; Paulo T. Ramos; Maria F. Alemão; Paula Gomes; Ana C. Gomes; Susana Sousa; Sofia Machado; Manuel Santos; Margarida Casal; Dorit Schuller.
The objective of the present study was to evaluate populational relationships among Saccharomyces cerevisiae strains isolated from some of the Portuguese most important grapevine varieties in different appellations of origin, using polymorphic microsatellites. 
One hundred ninety two grape samples were collected during the 2006 and 2007 harvest season in the Vinho Verde (grape varieties: Arinto, Alvarinho, Avesso, Loureiro, Touriga Nacional) Bairrada (grape varieties: Arinto, Baga, Castelão Francês, Maria Gomes, Touriga Nacional) Alentejo (grape varieties, Aragonês, Trincadeira, Touriga Nacional), Terras do Sado (grape variety Castelão) Bucelas (grape variety Arinto) and Estremadura (grape varieties:...
Tipo: Poster Palavras-chave: Ecology; Microbiology.
Ano: 2008 URL: http://precedings.nature.com/documents/2290/version/1
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Structural and functional validation of Microsystin synthetases Nature Precedings
Swapnil G. Sanmukh; Waman N. Paunikar.
The structure and function prediction for the Microsystin synthetases from Microsystis aerogenosa (LNSAMB) were carried out for verifying the authenticity of the sequenced genes. The genes for Microsystin synthetases (mcyA, mcyB, mcyD and mcyE,), were predicted by the application of computational methods and Bioinformatics web tools. The probable function prediction for the proteins was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching protein databases for the presence of conserved domains. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural and functional validation of sequenced genes.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/6835/version/1
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Familial and late-onset Alzheimer's disease: Autoimmune disorders triggered by viral, microbial and allergen mimics of beta-amyloid and APP mutants ? Nature Precedings
Christopher Carter.
Beta-amyloid (A[beta]) autoantibodies are common in Alzheimer's disease. Some may be derived from Herpes simplex and 68 other virus proteins matching an immunogenic and fibrillogenic VGGVV A[beta] sequence.Many other viral, microbial and allergenic proteins (particularly from dust mites) align with A[beta] as do proteins from _C.Neoformans_ which has been associated with a rare but curable form of the disorder. Immune-related proteins are present in amyloid plaques and the complement membrane attack complex in neurones in Alzheimer's disease brains. Alzheimer's disease may thus be an autoimmune disorder triggered by pathogenic antigens homologous to A[beta], whose antibodies target and kill A[beta] containing neurones, via immune...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Microbiology.
Ano: 2010 URL: http://precedings.nature.com/documents/4662/version/1
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Inflammation targets specific organs for cancer in carriers of BRCA1/2 pathway mutations Nature Precedings
Bernard Friedenson.
Women who inherit a defective BRCA1 or BRCA2 gene have risks for breast/ovarian cancer that are so high and apparently so selective that many mutation carriers choose to have the most likely targets for cancer surgically removed. Recent research has focused on better methods of treating such seemingly unavoidable hereditary cancers. Prevention has received much less attention so a positive test result for a cancer gene leaves carriers with very limited options. 
In order to prevent BRCA1/2 related cancers, it may be important to understand why they seem to occur only in certain characteristic organs. Results here show that mutations in a pathway depending on BRCA1/2 gene products magnify cancer risks from chronic infection and...
Tipo: Manuscript Palavras-chave: Cancer; Genetics & Genomics; Immunology; Microbiology.
Ano: 2010 URL: http://precedings.nature.com/documents/4225/version/1
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A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains Nature Precedings
Claudiu I. Bandea.
The cellular theory on the nature of life has been one of the first major advancements in biology. Viruses, however, are the most abundant life forms, and their exclusion from mainstream biology and the Tree of Life (TOL) is a major paradox in biology. This article presents a broad, unifying scenario on the origin and evolution of cellular and viral domains that challenges the conventional views about the history of life and supports a TOL that includes viruses. Co-evolution of viruses and their host cells has led to some of the most remarkable developments and transitions in the evolution of life, including the origin of non-coding DNA as a genomic protective device against viral insertion damage. However, one of the major fundamental evolutionary...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3888/version/1
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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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Structural Analysis of Outer Membrane Beta-stranded Porins using Temperature Factor Nature Precedings
Abhishek Kumar.
Computational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors...
Tipo: Manuscript Palavras-chave: Biotechnology; Microbiology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7016/version/1
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Mummification in a Bitch: A case report Nature Precedings
Perumal P; Venkateswaralu B; D.N. Mohanty; Srinibas Das; Ashok Kumar Barik; P.C. Mishra.
A pug aged 5 years was admitted in the Lyka pet clinic with difficulty in parturition. Breeding history of the dog was collected from the owner. X-ray was conducted which confirmed the presence of foetus. The bitch was manually handled to relieve the Dystocia following intravenous drip of N.S.S. and oxytocin. In the vent of unsuccessful attempt the bitch was surgically operated for C.S. and six fetuses of which four normal and two mummified were relieved. Routine post operative care were undertaken and the bitch recovered normally with out any complication. Photographic recording was also made during the recovery of mummified foetus.
Tipo: Presentation Palavras-chave: Microbiology; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/7063/version/1
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The “Minimum Information about an ENvironmental Sequence” (MIENS) specification Nature Precedings
Pelin Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette Johnston; Guy Cochrane; Robert Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn Maguire; Barbara A. Methé; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; Jörg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aymé Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Glöckner.
We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics; Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/5252/version/1
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Bacteria have transient influences on marine corrosion of steel Nature Precedings
Robert E. Melchers; Robert Jeffrey.
The contribution of bacteria to the corrosion mass loss and to pitting of mild steel was observed over 2.5 years using parallel streams of unpolluted natural (biotic) and nominally sterilized (abiotic) Pacific Ocean coastal seawater. As also observed by others, in artificial laboratory exposures, corrosion mass loss within the first few days of exposure was much greater in the biotic stream. However, after only about 10 days the difference in mass losses were gradually reduced and were very similar up to about one year of exposure. Thereafter, the corrosion loss in the biotic stream again became more severe. Pitting corrosion in the biotic stream was more severe from the very first exposure throughout the 2.5 years. Corrosion in both seawater streams...
Tipo: Manuscript Palavras-chave: Chemistry; Microbiology.
Ano: 2011 URL: http://precedings.nature.com/documents/5767/version/1
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