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2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/2
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How gut sampling and microbial invasiveness/noninvasiveness provides mucosal immunity with a nonmolecular pattern means to distinguish commensals from pathogens: A review Nature Precedings
John R. Skoyles.
Mucosal immunity distinguishes not only different microbial antigens but also separates those of pathogens from those of commensals. How this is done is unknown. The present view is that the pathogen/commensal determination of antigens depends upon as yet to be discovered molecular patterns. Here I review the biological feasibility that it also involves the detection of the invasive differences in their motility towards the gut wall when they are sampled by differently biased methods. 

By their nature, pathogens and commensals have different motility – invasive and noninvasive – in regard to the epithelium. The immune system is in a position to detect such motility differences. This biological...
Tipo: Manuscript Palavras-chave: Immunology; Microbiology.
Ano: 2008 URL: http://precedings.nature.com/documents/1895/version/1
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HP-23: Co-ordinated Regulation of Gene Expression in H. Pylori in Response to Low pH and Iron Limiting Growth Conditions Nature Precedings
Ananya Gupta; Sergey Ustinov; Kaveh Mashayekhi; Anthony P. Moran.
Establishing a successful infection within the gastric environment and its varied and changing niches requires adaptation achieved through regulation of bacterial gene expression. In the gastric environment in addition to the low pH Helicobacter pylori is required to adapt to conditions of iron limitation. In this study, we used cDNA microarrays to identify genes whose expression was altered when the bacterium was grown under differing conditions of pH (5 versus 7) and iron limitation. cDNA microarray analyses following exposure to different growth conditions were carried out for three H. pylori strains 26695 (gastritis-associated), J99 (ulcer-associated) and AG-1 (atrophic gastritis-associated). Genes were identified whose expression was acid pH-dependent...
Tipo: Poster Palavras-chave: Microbiology.
Ano: 2011 URL: http://precedings.nature.com/documents/5842/version/1
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The Human Virome in Children and its Relationship to Febrile Illness Nature Precedings
Gregory A. Storch; George M. Weinstock; Erica J. Sodergren; Kristine M. Wylie; Max Q. Arens; Richard S. Buller; David M. Jaffe; Jared T. Muenzer.
This study investigates the relationship of viruses to febrile illness in children. Subjects are normal children 2-36 months of age with fever along with normal children of the same age without fever, plus immunocompromised children with fever along with immunocompromised children without fever. Specimens obtained include blood, nasopharyngeal secretions, and feces. Specimens are analyzed using a panel of virus-specific PCR assays and also by high throughput sequencing using 454 and Illumina platforms.
Tipo: Marker Paper / Data Plan Palavras-chave: Biotechnology; Microbiology; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5319/version/1
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Keratinocytes from human skin respond as typical immune cells after the stimulation with _Trichophyton rubrum_ Nature Precedings
Alfonso E. Islas-Rodríguez; Luz A. García-Madrid.
_Trichophyton rubrum_ is the main agent causing dermatophytosis (1). Keratinocytes are
considered to be the first physical barrier of defense against pathogens (2). But not
only a physical barrier. They recognize antigens through Toll like receptors (TLR) (3).
The activation of this TLR, present on the surface of the keratinocytes, induce the
expression of different pro-inflammatory cytokines, co-stimulatory molecules and
antimicrobial peptides such as [beta]-defensins (4).
The main objective of this work is to determine if lipopolysaccharides of G – bacteria
(LPS), lipotheichoic acid from G+ bacteria (LTA), and conidias,...
Tipo: Manuscript Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/930/version/1
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Is the innate bio-protection power against human virus the same between males and females? A conclusion based on blood donor data of HTLV-I infection and case data of infectious diseases Nature Precedings
Nobuoki Eshima; Minoru Tabata; Yasunori Higuchi; Shigeru Karukaya.
Human T-cell leukemia virus type I (HTLV-I) is a retrovirus that causes adult T-cell leukemia. The male-to-female transmission is stronger than the reverse, so the carrier proportion of women is greater than that of men. On the other hand, since the mother-to-child transmission route via the breast-feeding is common for baby boys and girls, it has been thought the HTLV-I proportions of boys and girls are the same until now. A question arises as to whether the ‘innate protection powers against human virus’ are the same between males and females. We utilize HTLV-I infection blood donor data in 1995-1998 and case data of main infectious diseases such as influenza, mumps, herpangina, hand-hoot-and-mouse disease, chicken pox, etc. Blood...
Tipo: Manuscript Palavras-chave: Cancer; Immunology; Microbiology.
Ano: 2008 URL: http://precedings.nature.com/documents/1987/version/2
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DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein Sequences Nature Precedings
Xiaolong Wang; Shuang-yong Xu; Deming Gou.
Alignment of DNA and protein sequences is a basic tool in the study of evolutionary, structural and functional relationship among macromolecules. Present sequence alignment methods are somewhat error-prone, often producing systematic bias. Errors in sequence alignments sometimes lead to subsequent misinterpretation of evolutionary, structural and functional information in genes, proteins and genomes. In traditional sequence alignment algorithms, alignments of DNA and protein sequences are conducted separately. It has been long believed that the phylogenetic signal disappears more rapidly from DNA sequences than from encoded proteins. It is therefore generally preferable to align sequences at the amino acid level. Here we present a new...
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4898/version/1
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Expression profile of genes involved in hydrogen sulphide liberation by _Saccharomyces cerevisiae_ grown under different nitrogen concentrations Nature Precedings
Ana Mendes-Ferreira; Catarina Barbosa; Marcel.lí del Olmo; Arlete Mendes-Faia; Cecília Leão.
The present work aims to elucidate molecular mechanisms underlying hydrogen sulphide production in _S. cerevisiae_ associated to nitrogen deficiency. To assess, at a genome-wide level, how the yeast strain adapted to the progressive nitrogen depletion and to nitrogen re-feeding, gene expression profiles were evaluated during fermentation at different nitrogen concentrations, using the DNA array technology. The results showed that most MET genes displayed higher expression values at the beginning of both control and N-limiting fermentation, just before the time at which the release of sulphide was observed. MET genes were downregulated when yeast stopped growing which could associate MET gene expression levels with cell growth. The over expression of MET...
Tipo: Poster Palavras-chave: Biotechnology; Microbiology.
Ano: 2008 URL: http://precedings.nature.com/documents/2736/version/1
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Ecological, phenological and biochemical significance of bimodal fruiting of Boletus alutaceus morgan Nature Precedings
Nandkumar Kamat.
Boletus alutaceus Morgan an ectomycorrhizal species was extensively studied from an ecologically fragmented microhabitt colonized by its' host plant Ficus benghalensis L. in the Goa University campus, Taleigao, Goa, India. Qualitatively the fruiting cycles were monitored for three years and thereafter detail ecological and morphological investigations were carried out in May and November 2004. A bimodal temporal fruting pattern emerged which may have significant ecological, phenological and biochemical role in EM dynamics.
Tipo: Presentation Palavras-chave: Biotechnology; Developmental Biology; Ecology; Genetics & Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2835/version/1
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Stomatin-like Protein 2 Links Mitochondria to T-Cell Receptor Signalosomes at the Immunological Synapse and Enhances T-Cell Activation Nature Precedings
Mark G. Kirchhof; Luan A. Chau; Caitlin D. Lemke; Santosh Vardhana; Peter J. Darlington; Maria E. Marquez; Roy Taylor; Kamilia Rizkalla; Isaac Blaca; Michael L. Dustin; Joaquin Madrenas.
T cell activation through the antigen receptor (TCR) requires sustained signalling from microclusters in the peripheral region of the immunological synapse (IS). The bioenergetics of such prolonged signaling have been linked to the redistribution of mitochondria to the IS. Here, we report that stomatin-like protein-2 (SLP-2) plays an important role in this process by bridging polarized mitochondria to these signaling TCR microclusters or signalosomes in the IS in a polymerized actin-dependent manner. In this way, SLP-2 helps to sustain TCR-dependent signalling and enhances T cell activation.
Tipo: Manuscript Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1068/version/1
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Identification and Evolution of Transcription Factors in Stramenopiles Nature Precedings
Francisco Buitrago; Silvia Restrepo; Diego Riaño-Pachón.
Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases; in addition to TFs, other transcriptional regulators (TRs) participate in transcriptional modulation. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of TFs and TRs can be identified, described, and compared between species and lineages. The diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they are present in freshwater, marine and terrestrial habitats and embrace many ecologically important algal (e.g. diatoms, brown algae, chrysophytes), and...
Tipo: Poster Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6672/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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Biotransformation of artemisinin mediated through fungal strains for obtaining derivatives with novel activities Nature Precedings
Suchita Srivastava; Suaib Luqman; Atiya Fatima; Mahendra P. Darokar; Arvind S. Negi; J K. Kumar; Karuna Shanker; Chandan S. Chanotiya; Sudeep Tandon; Suman P. S. Khanuja.
Artemisinin, a sesquiterpene lactone, is the active antimalarial constituent of Artemisia annua. Several fungal strains Saccharomyces cerevisiae, Aspergillus flavus, Aspergillus niger and Picchia pastoris were used to biotransform artemisinin. Among these strains, A. flavus was the only microorganism capable of transforming artemisinin to deoxyartemisinin in higher yields than the previous reports. The structure of deoxyartemisinin was elucidated by spectroscopy. Deoxyartemisinin showed antibacterial activity against Staphylococcus aureus, S. epidermidis and S. mutans at a minimum inhibitory concentration (MIC) of 1 mg/mL compared to artemisinin whose MIC was >2 mg/mL.
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/6925/version/1
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Investigations on biological activity of Vetiveria zizanioides L. Nash, a palingenesis of some important findings in miracle grass Nature Precedings
Suaib Luqman.
Vetiveria zizanioides L. Nash synonymously known as Chrysopogon zizanioides L. Roberty (Family: Poaceae/Graminae), widely cultivated in the tropical regions of the world, is a miraculous grass native to India first developed for soil and water conservation by the World Bank during mid 1980s. Popularly known as ‘KHUS’, it is the major source of the well-known oil of vetiver, which is used in medicine, cosmetics and in perfumery making agarbattis, soaps, soft drinks, pan masala. Being a major constituent of ‘Rasayana’ in Ayurveda, different parts of the vetiver plant have traditionally been used by the Indian tribes for treating various ailments, diseases and disorders including boils, burns, epilepsy, fever,...
Tipo: Poster Palavras-chave: Cancer; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/6904/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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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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Small critical RNAs in the scrapie agent Nature Precedings
Steve Simoneau; Marie-Madeleine Ruchoux; Nicolas Vignier; Pierre Lebon; Sophie Freire; Emmanuel Comoy; Jean-Philippe Deslys; Jean-Guy Fournier.
Unconventional infectious agents cause transmissible spongiform encephalopathy (TSE) diseases including scrapie and bovine spongiform encephalopathy (BSE) in animals and Creutzfeldt-Jakob disease in humans. The protein only hypothesis claims that the TSE agent is composed solely of the protein called prion (PrP^sc^)^1^. This protein is the misfolded form of a host-encoded cellular protein, PrP^c^ exerting presumably a vital role at the synapse^2^. Even though now widely accepted, the prion concept fails to provide in certain circumstances^3-6^, a satisfying interpretation of the infectious phenomenon. Using the 263K scrapie-hamster model, we conducted a transmission study to search for a putative prion-associated factor indispensable for infectivity. Here...
Tipo: Manuscript Palavras-chave: Microbiology; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3344/version/1
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Mechanistic mechanisms of competition and biodiversity Nature Precedings
Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The nature of competition and biodiversity are open basic questions since Darwin. To investigate mechanisms of interspecific competition and their contribution in biodiversity as closely as possible we offer a white-box modelling method based on physically interpreted ecological axioms. These models are implemented as deterministic individual-based cellular automata and able to give a direct physico-mechanistic insight into studied phenomena. Competition of two trophically identical but fitness different species, competing for one limiting resource in one stable uniform habitat (which is closed for immigration, emigration, predation, herbivory and parasitism) has been investigated in conditions, which are the most unfavourable for their coexistence. The...
Tipo: Manuscript Palavras-chave: Ecology; Microbiology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7105/version/1
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A Proposal of Genomic Analytical Workflow in a Bacterial Pathogen Outbreak Investigation Nature Precedings
Hoi Shan Kwan; Chun Hang Au; Chi Keung Cheng; Man Kit Cheung; Qianli Huang; Lei Li; Wenyan Nong; Man Chun Wong.
The German Escherichia coli O104:H4 outbreak causing Hemolytic Uremic Syndrome (HUS) started in early May 2011. Conventional typing methods including serotyping, multi-locus sequence typing (MLST) and pulse-field gel electrophoresis (PFGE) seemed to yield only limited information about the causative agent. The advantages of the Genome sequencing approach are apparent compared to conventional methods. Genome sequencing and analyses with an appropriate workflow would be the new paradigm in bacterial outbreak investigation.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology.
Ano: 2011 URL: http://precedings.nature.com/documents/6663/version/1
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X-ray phase contrast imaging of biological specimens with tabletop synchrotron radiation Nature Precedings
Stefan Kneip; Chris McGuffey; Franklin Dollar; Michael S. Bloom; Vladimir Chvykov; Galina Kalintchenko; Karl Krushelnick; Anatoly Maksimchuk; Stuart P. D. Mangles; Takeshi Matsuoka; Zulfikar Najmudin; Charlotte A. J. Palmer; Joerg Schreiber; Will Schumaker; Alexander G. R. Thomas; Victor Yanovsky.
Since their discovery in 1896, x-rays have had a profound impact on science, medicine and technology. Here we show that the x-rays from a novel tabletop source of bright coherent synchrotron radiation can be applied to phase contrast imaging of biological specimens, yielding superior image quality and avoiding the need for scarce or expensive conventional sources.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Microbiology.
Ano: 2011 URL: http://precedings.nature.com/documents/5946/version/1
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