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Search Results: 1 - 10 of 191798 matches for " D. Barton "
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Scaffolder - software for manual genome scaffolding
Michael D Barton, Hazel A Barton
Source Code for Biology and Medicine , 2012, DOI: 10.1186/1751-0473-7-4
Abstract: The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format which is both human and machine-readable. Command line binaries and extensive documentation are available.This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax. This syntax further allows unknown regions to be specified and additional sequence to be used to fill known gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with large FASTA nucleotide sequences.Scaffolder is easy-to-use genome scaffolding software which promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs webcite.
Genomer — A Swiss Army Knife for Genome Scaffolding
Michael D. Barton, Hazel A. Barton
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0066922
Abstract: The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe “Genomer,” a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs.
Adenoviral Vectors in Veterinary Vaccine Development: Potential for Further Development  [PDF]
Olasumbo L. Ndi, Mary D. Barton, Thiru Vanniasinkam
World Journal of Vaccines (WJV) , 2013, DOI: 10.4236/wjv.2013.33016
Abstract: Vaccines are an integral part of veterinary disease prevention. However there are still a significant number of veterinary diseases for which vaccines do not currently exist or where currently available vaccines do not provide adequate immunity. Adenoviruses have transitioned from tools for gene replacement therapy to bona fide vaccine delivery vehicles because of their ability to elicit potent cell-mediated and humoral responses making them ideal for use against viruses and other intracellular pathogens. Adenoviral vector based vaccines are likely to play a significant role in overcoming these problems in the future. However, this vector is under utilized in veterinary vaccine development at this time. This review focuses on adenoviral vector based vaccines developed to date and explores the potential for veterinary vaccine development based upon this platform: advantages and potential disadvantages of this technology are discussed as well as the potential for developing efficacious commercial veterinary adenoviral vector based vaccines.

The energy costs of biological insulators
John Barton,Eduardo D. Sontag
Quantitative Biology , 2012, DOI: 10.1016/j.bpj.2013.01.056
Abstract: Biochemical signaling pathways can be insulated from impedance and competition effects through enzymatic "futile cycles" which consume energy, typically in the form of ATP. We hypothesize that better insulation necessarily requires higher energy consumption, and provide evidence, through the computational analysis of a simplified physical model, to support this hypothesis.
Advancing Toward HIV-1 Vaccine Efficacy through the Intersections of Immune Correlates
Georgia D. Tomaras,Barton F. Haynes
Vaccines , 2014, DOI: 10.3390/vaccines2010015
Abstract: Interrogating immune correlates of infection risk for efficacious and non-efficacious HIV-1 vaccine clinical trials have provided hypotheses regarding the mechanisms of induction of protective immunity to HIV-1. To date, there have been six HIV-1 vaccine efficacy trials (VAX003, Vaxgen, Inc., San Francisco, CA, USA), VAX004 (Vaxgen, Inc.), HIV-1 Vaccine Trials Network (HVTN) 502 (Step), HVTN 503 (Phambili), RV144 (sponsored by the U.S. Military HIV Research Program, MHRP) and HVTN 505). Cellular, humoral, host genetic and virus sieve analyses of these human clinical trials each can provide information that may point to potentially protective mechanisms for vaccine-induced immunity. Critical to staying on the path toward development of an efficacious vaccine is utilizing information from previous human and non-human primate studies in concert with new discoveries of basic HIV-1 host-virus interactions. One way that past discoveries from correlate analyses can lead to novel inventions or new pathways toward vaccine efficacy is to examine the intersections where different components of the correlate analyses overlap (e.g., virus sieve analysis combined with humoral correlates) that can point to mechanistic hypotheses. Additionally, differences in durability among vaccine-induced T- and B-cell responses indicate that time post-vaccination is an important variable. Thus, understanding the nature of protective responses, the degree to which such responses have, or have not, as yet, been induced by previous vaccine trials and the design of strategies to induce durable T- and B-cell responses are critical to the development of a protective HIV-1 vaccine.
Remarks on the energy costs of insulators in enzymatic cascades
John P. Barton,Eduardo D. Sontag
Quantitative Biology , 2014,
Abstract: The connection between optimal biological function and energy use, measured for example by the rate of metabolite consumption, is a current topic of interest in the systems biology literature which has been explored in several different contexts. In [J. P. Barton and E. D. Sontag, Biophys. J. 104, 6 (2013)], we related the metabolic cost of enzymatic futile cycles with their capacity to act as insulators which facilitate modular interconnections in biochemical networks. There we analyzed a simple model system in which a signal molecule regulates the transcription of one or more target proteins by interacting with their promoters. In this note, we consider the case of a protein with an active and an inactive form, and whose activation is controlled by the signal molecule. As in the original case, higher rates of energy consumption are required for better insulator performance.
Molecular Identification of Yeasts Isolated from Dadih by RFLP-PCR and Assessment on Their Ability in Utilizing Lactate
Microbiology Indonesia , 2012, DOI: 10.5454/mi.6.1.5
Abstract: A wide variety of yeasts have been involved in traditional fermented foods, and potentially contributed to the development of product properties. The existence of indigenous yeasts in dadih, a traditionally fermented form of buffalo milk of West Sumatera, has been reported but an accurate identification is still required to be conducted. This study was aimed to identify yeasts isolated from dadih using a molecular approach, and to evaluate their lactate utilization. A total of 51 isolates were characterized and identified as Pichia jadinii and Candida stellimalicola using PCR amplification of the 5.8S - internal transcribed spacer region combined with restriction fragment length polymorphism (RFLP) analyses and gene sequencing. The former species were the dominant one in this tested product. Their ability to utilize lactate was demonstrated, indicating that they could modify the sensory characteristics of dadih, and hence interact with the indigenous lactic acid bacteria in dadih. The restriction profiles of the dadih yeasts can be used as a data base for rapid identification of yeasts in the future. Further work is still needed to elucidate the dadih yeast ecology.
Effects of healthy aging on human primary visual cortex  [PDF]
Alyssa A. Brewer, Brian Barton
Health (Health) , 2012, DOI: 10.4236/health.2012.429109
Abstract: Aging often results in reduced visual acuity from changes in both the eye and neural circuits [1-4]. In normally aging subjects, primary visual cortex has been shown to have reduced responses to visual stimulation [5]. It is not known, however, to what extent aging affects visual field repre-sentations and population receptive sizes in human primary visual cortex. Here we use func-tional MRI (fMRI) and population receptive field (pRF) modeling [6] to measure angular and ec-centric retinotopic representations and population receptive fields in primary visual cortex in healthy aging subjects ages 57 - 70 and in healthy young volunteers ages 24 - 36 (n = 9). Retinotopic stimuli consisted of black and white, drifting checkerboards comprising moving bars 11 deg in radius. Primary visual cortex (V1) was clearly identifiable along the calcarine sulcus in all hemispheres. There was a significant decrease in the surface area of V1 from 0 to 3 deg eccentricity in the aging subjects with respect to the young subjects (p = 0.039). The coherence of the fMRI% BOLD modulation was significantly decreased in the aging subjects compared to the young subjects in the more peripheral eccentricity band from 7 to 10 deg (p = 0.029). Finally, pRF sizes were significantly increased within the 0 to 3 deg foveal representation of V1 in the aging subjects compared to the young subjects (p = 0.019). Understanding the extent of changes that occur in primary visual cortex during normal aging is essential both for understanding the normal aging process and for comparisons of healthy, aging subjects with aging patients suffering from age-related visual and cortical disorders.
Visual Working Memory in Human Cortex  [PDF]
Brian Barton, Alyssa A. Brewer
Psychology (PSYCH) , 2013, DOI: 10.4236/psych.2013.48093

Visual working memory (VWM) is the ability to maintain visual information in a readily available and easily updated state. Converging evidence has revealed that VWM capacity is limited by the number of maintained objects, which is about 3 - 4 for the average human. Recent work suggests that VWM capacity is also limited by the resolution required to maintain objects, which is tied to the objects’ inherent complexity. Electroencephalogram (EEG) studies using the Contralateral Delay Activity (CDA) paradigm have revealed that cortical representations of VWM are at a minimum loosely organized like the primary visual system, such that the left side of space is represented in the right hemisphere, and vice versa. Recent functional magnetic resonance imaging (fMRI) work shows that the number of objects is maintained by representations in the inferior intraparietal sulcus (IPS) along dorsal parietal cortex, whereas the resolution of these maintained objects is subserved by the superior IPS and the lateral occipital complex (LOC). These areas overlap with recently-discovered, retinotopically-organized visual field maps (VFMs) spanning the IPS (IPS-0/1/2/3/4/5), and potentially maps in lateral occipital cortex, such as LO-1/2, and/or TO-1/2 (hMT+). Other fMRI studies have implicated early VFMs in posterior occipital cortex, suggesting that visual areas V1-hV4 are recruited to represent information in VWM. Insight into whether and how these VFMs subserve VWM may illuminate the nature of VWM. In addition, understanding the nature of these maps may allow a greater investigation into individual differences among subjects and even between hemispheres within subjects.

Se-Bearing Colloidal Particles Produced by Sulfate-Reducing Bacteria and Sulfide-Oxidizing Bacteria: TEM Study  [PDF]
Huifang Xu, Larry L. Barton
Advances in Microbiology (AiM) , 2013, DOI: 10.4236/aim.2013.32031

As determined by transmission electron microscopy (TEM), the reduction of selenate and selenite by Desulfovibrio desulfuricans, a sulfate-reducing bacterium, produces spherical (Se, S) sub-micro particles outside the cell. The particles are crystalline or amorphous, depending on medium composition. Amorphous-like Se-rich spherical particles may also occur inside the bacterial cells. The bacteria are more active in the reduction of selenite than selenate. The Desulfovibrio desulfuricans bacterium is able to extract S in the (S, Se) solid solution particles and transform S-rich particles into Se-rich and Se crystals. Photoautotrophs, such as Chromatium spp., are able to oxidize sulfide (S2-). When the bacteria grow in sulfide- and selenide-bearing environments, they produce amorphous-like (S, Se) globules inside the cells. TEM results show that compositional zonation in the (S, Se) globules occur in Chromatium spp. collected from a top sediment layer of a Se-contaminated pond. S2- may be from the products of sulfate-reducing bacteria. Both the sulfate-reducing bacteria and photosynthetic Chromatium metabolize S preferentially over Se. It is proposed that the S-rich zones are formed during photosynthesis (day) period, and the Se-rich zones are formed during respiration active (night) period. The results indicate that both Desulfovibrio desulfuricans and Chromatium spp. are able to immobilize the oxidized selenium (selenate and/or selenite) in the forms of elemental selenium and (Se, S) solid solutions. The bacteria reduce S in the (Se, S) particles and further enrich Se in the crystalline particles. The reduced S combines with Fe2+ to form amorphous FeS.

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