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(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress. Nature Precedings
Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargoes inside cells.

During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules. Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and...
Tipo: Poster Palavras-chave: Molecular Cell Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/4469/version/3
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Prediction of Evolutionarily important catalytic amino acid of Mycobacterium tuberculosis O-Succinylbenzoate synthase through in silico mutational analysis Nature Precedings
Babajan B; Chaitanya M; Anuradha CM; Suresh Kumar Chitta.
The emergence of tuberculosis resistant to multiple, first- and second-line antibiotics poses challenges to a global control strategy that relies on standard drug treatment regimens. The high drug-resistant strains of Mycobacterium tuberculosis (Mtb) have been implicated in outbreaks and have been found throughout the world; a comprehensive understanding, the magnitude of this threat requires an accurate assessment of the worldwide burden of resistance. In an attempt to design anti-TB drugs, the target chosen is a key enzyme of Mtb, O-Succinylbenzoate synthase (OSBS), which is an attractive target for its role in electron transport chain as OSBS is not available in humans. An attempt has been to built the 3-D structure of Mtb-OSBS using online Swiss model...
Tipo: Poster Palavras-chave: Biotechnology; Microbiology; Pharmacology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3776/version/1
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Genomics and synthetic biology as a viable option to intensify sustainable use of biodiversity Nature Precedings
Elibio L. Rech.
The Amazon basin is an area of mega-biodiversity. Different models have been proposed^1-8^ for the establishment of an effective conservation policy, increasing sustainability and adding value for biodiversity. Currently, a broad spectrum of technologies from genomics to synthetic biology is available, and these permit the collection, manipulation and effective evaluation of countless organisms, metabolic pathways and molecules that exist as potential products of a large, biodiverse ecosystem. The use of Genomics and synthetic biology may constitute an important tool and be a viable option for the prospection, evaluation and manipulation of biodiversity as advocated as well as be useful for developing methods for sustainable use and the production of novel...
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Earth & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/5759/version/1
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Phosphatidylserine polarization is required for proper Cdc42 localization and for development of cell polarity. Nature Precedings
Gregory Fairn; Sergio Grinstein.
We used genetically-encoded fluorescent probes to visualize the distribution of phosphatidylserine (PS) in live S. cerevisiae. The majority of the PS was found to reside in the cytosolic leaflet of the plasma membrane. Remarkably, PS was polarized, accumulating in bud necks, the bud cortex and the tips of mating projections. Polarization required vectorial delivery of PS-enriched secretory and recycling vesicles. Rapid dissipation of the PS gradient is prevented by the slow diffusion of lipids along the plasmalemmal inner leaflet, estimated by photobleaching recovery measurements to be over an order of magnitude slower than in mammalian cells. In mutants lacking PS-synthase the absence of PS was associated with, and likely responsible for impaired...
Tipo: Manuscript Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4232/version/1
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Translating Environmental Science into Policy and Action Nature Precedings
Lee M. Talbot.
Background/Question/Methods: Many ecologists are skilled at identifying environmental problems and defining solutions, but not at achieving concrete action to implement those insights. The question, then, is how to help ecologists translate environmental science into policy and action. Most ecologists' education and training do not prepare them to be effective in the policy arena, much less in ways to achieve action. Ecologists find disincentives in the form of the academic attitude that somehow the application of science is inferior to so-called "pure science." This ivory tower holdover has been largely discredited in the context of environmental issues, and the discipline of conservation biology exists explicitly to foster...
Tipo: Manuscript Palavras-chave: Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/3606/version/1
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Optimising Blue Fluorescent Protein (BFP) for use as a mammalian reporter gene in parallel with Green Fluorescent Protein (GFP). Nature Precedings
Etienne Joly.
To obtain an optimised form of BFP for use as a reporter gene in mammalian cells, the brightest available GFP form, EGFP, was mutated at 5 different positions, yielding 8 different mutagenised forms of BFP. The intensity of the fluorescent signals attained in mammalian cells with all these various versions of BFP was analysed by flow cytometry of transiently transfected COS 7 cells. The best mutant obtained can be detected readily both by flow cytometry and fluorescence microscopy, even when expressed together with GFP. To explore whether cellular localization could enhance the fluorescence signals any further, plasmid constructs were made to target optimised versions of GFP and BFP to the nucleus, the endoplasmic reticulum (ER) and the cell surface....
Tipo: Manuscript Palavras-chave: Biotechnology.
Ano: 2007 URL: http://precedings.nature.com/documents/1259/version/1
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The Teleost Taxonomy Ontology Nature Precedings
Peter E. Midford; James P. Balhoff; Wasila Dahdul; Cartik R. Kothari; Hilmar Lapp; John Lundberg; Paula Mabee; Todd J. Vision; Monte Westerfield.
The Teleost Taxonomy Ontology (TTO) is an ontology of taxonomic groups and associated names for fish (not just teleosts). This ontology has served as a source of names and taxonomic structure within the Phenoscape project since early 2008. Although the TTO is based on Eschmeyer's Catalog of Fishes (CoF) and incorporates all valid species and genus names, it is also extended by the curation needs of the Phenoscape project. Names of fossil taxa not included in the CoF as well as references to specimens identied only to genus (e.g., _Eigenmannia sp._ (Fink and Fink 1981)) are incorporated into the TTO as required by the curation needs of the Phenoscape project. As Phenoscape receives updates to the CoF, a tool called TTOUpdate merges the...
Tipo: Manuscript Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4629/version/1
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Effect of 2-H and 18-O water isotopes in kinesin-1 gliding assay Nature Precedings
Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
We show here the effects of heavy-hydrogen water (^2^H~2~O) and heavy-oxygen water (H~2~^18^O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for biomolecular devices incorporating molecular motors.
Tipo: Manuscript Palavras-chave: Molecular Cell Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7004/version/1
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An uncultured human-associated bacterium model Nature Precedings
Jorge M. Dinis; David E. Barton; Jamsheed Ghadiri; Deepa Surendar; Kavitha Reddy; Fernando Velasquez; Carol M. Chaffee; Wendy Lee; Helen Gavrilova; Hazel Ozuna; Samuel A. Smits; Cleber C. Ouverney.
The Bacteria Domain experienced an explosion of novel lineages identified within the last decade, especially of lineages made entirely of uncultured members. Since numerous cultivable bacteria have been shown to be instrumental in human development, health, and diseases, it is reasonable to speculate that strains from uncultured groups, which comprise nearly 80% of the human gut and 68% of human oral microbial consortia, participate in similar functions. The study of human-associated uncultured bacteria, however, has many practical limitations, such as access to patient samples, unpredictable microbial composition, and low relative abundance, all of which challenge experimental promptness and reproducibility. We propose that uncultured bacteria from...
Tipo: Manuscript Palavras-chave: Microbiology.
Ano: 2011 URL: http://precedings.nature.com/documents/5757/version/1
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Sensitivity Analysis of Self-Identified Race and Ethnicity (SIRE): Screening for Single Nucleotide Polymorphisms. Nature Precedings
Toni P. Miles; Stephen Hanson; LaCreis Kidd; Avonne Connor; Saeed A. Jortani.
Within the realm of medical care, Self-Identified Race and Ethnicity (SIRE) categories are promoted as an inexpensive tool to identify underlying genotypic diversity. Scientific opinion is divided about the adequacy of SIRE to serve this function. If genetic diversity can guide medical decisions, it is important to know the effectiveness of genetic screening via SIRE. Proper development of self-reported measures such as SIRE requires sensitivity and specificity studies. These types of formal evaluation are largely absent for SIRE. To begin this formal process, we estimate the sensitivity of SIRE in screening for variant Single Nucleotide Polymorphism (SNP). Our results indicate that the current use of SIRE is inadequate to screen for selected...
Tipo: Manuscript Palavras-chave: Genetics & Genomics.
Ano: 2008 URL: http://precedings.nature.com/documents/1524/version/1
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The activating receptors 2B4 and NTB-A, but not CRACC are subject to ligand-induced down-regulation on human natural killer cells Nature Precedings
Stephan Meinke; Carolin Böhm; Sibel Durlanik; Carsten Watzl.
Activation of natural killer cells can be mediated by different receptors. Stimulation of the receptors 2B4, NTB-A and CRACC, members of the SLAM-related receptor family, induces cytotoxicity and cytokine production. The surface expression of 2B4 and other activating natural killer cell receptors is down-modulated after receptor engagement, which results in a weaker response to consecutive stimulation. We tested whether this regulatory mechanism applies to all SLAM-related receptors expressed by primary human natural killer cells. After co-culture with target cells expressing the respective ligands different effects on receptor surface expression were observed. While 2B4 ex-pression was strongly reduced, NTB-A showed less prominent down-modulation and the...
Tipo: Manuscript Palavras-chave: Immunology.
Ano: 2010 URL: http://precedings.nature.com/documents/4917/version/1
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The transmission dynamics of syphilis and the CDC’s elimination plan Nature Precedings
Romulus Breban; Virginie Supervie; Justin Okano; Raffaele Vardavas; Sally Blower.
The Centers for Disease Control (CDC) is currently attempting to eliminate syphilis in the United States (US); to ensure that their control strategies will be effective it is important to understand the transmission dynamics of syphilis. Epidemics of certain infectious diseases (e.g., influenza) can rise and fall with a well-defined periodicity; this cycling behavior is important because it can have significant implications for the design and effectiveness of control strategies. Here we discuss the methodology that has been used to identify epidemic cycles in longitudinal data sets, and the endogenous and exogenous mechanisms that generate cycling. We then examine the recently proposed hypothesis that syphilis epidemics cycle. This hypothesis was proposed...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2007 URL: http://precedings.nature.com/documents/1373/version/1
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Reply to “Limusaurus and bird digit identity” Nature Precedings
Xing Xu; James Clark; Jonah Choiniere; David Hone; Corwin Sullivan.
Vargas et al. agree with us that a lateral shift in theropod dinosaur digits occurred prior to the origin of birds, but contend that it occurred as a single “frameshift” with little outward change to the three main digits involved^1^. We consider the digital morphology of Limusaurus, other ceratosaurs, and non-avian tetanurans to provide evidence that the shift was stepwise, and that a stepwise shift better explains theropod manual morphology than a hidden frameshift.
Tipo: Manuscript Palavras-chave: Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6375/version/1
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Body-specific representations of action word meanings in right and left handers Nature Precedings
Daniel Casasanto.
If understanding action words involves mentally simulating our own actions, then the neurocognitive representation of word meanings must differ for people with different kinds of bodies, who perform actions in systematically different ways. In a test of the _Body-Specificity Hypothesis_, right- and left-handers were compared on two motor-meaning congruity tasks. Double dissociations in both action execution and recognition memory results showed that right and left handers form body-specific representations of words for manual actions.
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2007 URL: http://precedings.nature.com/documents/1321/version/1
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Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos Nature Precedings
I. C. Baianu; Tiefeng You; Doina M. Costescu.
Novel methodologies are currently being evaluated for the Chemical Analysis of soybean seeds as well as developing mature soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1μ^2^.
Tipo: Poster Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6591/version/2
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Analysis of plant metabolites – the baseline-threshold principle Nature Precedings
Katja Neubauer; Jenny Bandomir; Anett Grunenberg; Andreas Müller; Udo Kragl; Kerstin Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in contrast to its non-GMP counterpart could refer to a risk and has to be further analysed.

The BioOK company offers the opportunity to analyse very different aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil analysis, we can look into several plant metabolites to identify...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4439/version/2
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Pendent Drops at Elevated P & T Nature Precedings
Apostolos Georgiadis; Geoffrey Maitland; Martin Trusler; Sergei Kazarian; Alexander Bismarck.
Within the scope of producing clean fossil fuels by simultaneously tackling greenhouse gas emissions, the interfacial tension of partially miscible phases containing CO~2~ is being investigated with the pendant drop method. Emphasis is given to measurements at elevated pressures and temperatures, analogous to reservoir conditions. A high pressure apparatus consisting of a view cell and high pressure capillary fittings is used for creating pendent drops at the desired conditions. A computer aided Drop Shape Analysis system is used for capturing images of such drops, which are then analysed for the interfacial tension calculation of the two phases with the KRUSS DSA software. The results acquired from the initial measurements conducted for the H~2~O/CO~2~...
Tipo: Poster Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2636/version/1
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The Neural Control Mechanisms Underlying Memory-Guided Attention Nature Precedings
Ian C. Gould; Mark G. Stokes; Kathryn Atherton; Anna C. Nobre.
The control mechanisms that guide selective attention are typically examined in response to explicit attentional cues. In everyday life, however, the focus of attention is more typically guided according to past experiences than direct instruction. We therefore developed a novel behavioural paradigm to examine the neural substrate of memory-guided attentional orienting. Participants first learn the location of target stimuli hidden within naturalistic scenes. After the target locations have been learned, participants then perform an attention-orienting task. Each experimental trial begins with a cue stimulus, consisting of the memory scene presented without the target stimulus. A test scene is then presented, with a 50% probability of a target stimulus...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/2955/version/1
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NIR Spectroscopy and Microspectroscopy Analysis of Intact Soybean Seeds for Food Applications through Composition Improvements. Version 2.0 Nature Precedings
Tiefeng You; I. C. Baianu.
The soybean-derived products are among the most important agricultural products in the USA and the world. Conventional analytical methods for soybean composition analysis are both time consuming and costly. Faster and less expensive methods are required for most practical applications. To improve the accuracy, reliability and sensitivity of NIR, major advancements in instrumentation, as well as, data analysis / calibration methodology are required. Novel NIR instruments, such as DA-NIR and FT-NIR spectrometers developed in recent years have the potential for improving significantly the quantification of soybean composition at a reasonable cost. We present representative calibrations and data for intact soybean composition analysis obtained at the...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6253/version/1
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The association between having a household member with a cancer-related limitation and human papillomavirus vaccine uptake Nature Precedings
Tabatha N. Offutt-Powell; Rohit P. Ojha; Joseph Tota; Karan P. Singh.
OBJECTIVE: To evaluate the association between having a household member with a cancer-related limitation (physical, mental, or emotional) and human papillomavirus (HPV) vaccine uptake among females aged 9 – 17 years. 
METHODS: We analyzed 2008 National Health Interview Survey for our cross-sectional analysis. All households with females aged 9 – 17 years were eligible for inclusion in our analysis. Our outcomes of interest included HPV vaccine initiation (≥1 dose) and series completion (full 3 doses). A dichotomous variable indicating a cancer-related limitation for a household member was created if at least one adult in the household...
Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4925/version/1
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