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Search Results: 1 - 10 of 16871 matches for " Barker Gary LA "
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Natural variation in gene expression in the early development of dauer larvae of Caenorhabditis elegans
Simon C Harvey, Gary LA Barker, Alison Shorto, Mark E Viney
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-325
Abstract: There were substantial transcriptional differences between four C. elegans lines under the same environmental conditions. The expression of approximately 2,000 genes differed between genetically different lines, with each line showing a largely line-specific transcriptional profile. The expression of genes that are markers of larval moulting suggested that the lines may be developing at different rates. The expression of a total of 89 genes was putatively affected by dauer larva or non-dauer larva-inducing conditions. Among the upstream regions of these genes there was an over-representation of DAF-16-binding motifs.Under the same environmental conditions genetically different lines of C. elegans had substantial transcriptional differences. This variation may be due to differences in the developmental rates of the lines. Different environmental conditions had a rather smaller effect on transcription. The preponderance of DAF-16-binding motifs upstream of these genes was consistent with these genes playing a key role in the decision between development into dauer or into non-dauer larvae. There was little overlap between the genes whose expression was affected by environmental conditions and previously identified loci involved in the plasticity of dauer larva development.Developmental decisions and processes can be controlled transcriptionally. The free-living nematode Caenorhabditis elegans makes a developmental decision between different larval fates. This decision is based on the 'suitability' of the environment for growth and reproduction. Under 'favourable' conditions, second stage larvae (L2) develop via two larval stages (L3, L4) into reproductive adults [1,2]. However, under 'unfavourable' conditions, L2s form a developmentally arrested L3 stage, the so-called dauer larva. Dauer larvae are environmentally resistant, have a specialised metabolism and are comparatively long-lived [2]. Overall, dauer larvae are transcriptionally repressed compared with actively
A microarray analysis of gene expression in the free-living stages of the parasitic nematode Strongyloides ratti
Fiona J Thompson, Gary LA Barker, Louise Hughes, Clare P Wilkes, Jane Coghill, Mark E Viney
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-157
Abstract: We have constructed an S. ratti cDNA microarray and used it to interrogate changes in gene expression during the free-living phase of the S. ratti life-cycle. We have found very extensive differences in gene expression between first-stage larvae (L1) passed in faeces and infective L3s preparing to infect hosts. In L1 stages there was comparatively greater expression of genes involved in growth. We have also compared gene expression in L2 stages destined to develop directly into infective L3s with those destined to develop indirectly into free-living adults. This revealed relatively small differences in gene expression. We find little evidence for the conservation of transcription profiles between S. ratti and S. stercoralis or C. elegans.This is the first multi-gene study of gene expression in S. ratti. This has shown that robust data can be generated, with consistent measures of expression within computationally determined clusters and contigs. We find inconsistencies between EST representation data and microarray hybridization data in the identification of genes with stage-specific expression and highly expressed genes. Many of the genes whose expression is significantly different between L1 and iL3s stages are unknown beyond alignments to predicted genes. This highlights the forthcoming challenge in actually determining the role of these genes in the life of S. ratti.Parasitic nematodes have complex life-cycles that are affected and controlled by factors both within and outwith their hosts. In the genus Strongyloides, the life-cycle, unusually, includes both an obligate female-only parasitic generation and a facultative dioecious adult free-living generation. In recent years there has been an increasingly detailed understanding of the factors that affect the development of the free-living phase of this life-cycle, particularly for the parasites of rats, S. ratti [1].S. ratti parasitic females lie embedded in the mucosa of the small intestine of their host. These
CerealsDB 2.0: an integrated resource for plant breeders and scientists
Wilkinson Paul A,Winfield Mark O,Barker Gary LA,Allen Alexandra M
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-219
Abstract: Background Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world’s booming population. Wheat is of fundamental importance in this regard being one of the three most important crops for both human consumption and livestock feed; however, increase in crop yields have not kept pace with the demands of a growing world population. In order to address this issue, plant breeders require new molecular tools to help them identify genes for important agronomic traits that can be introduced into elite varieties. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms that may be used by breeders to identify and follow genes when breeding new varieties. The development and application of next-generation sequencing technologies has made the characterisation of SNP markers in wheat relatively cheap and straightforward. There is a growing need for the widespread dissemination of this information to plant breeders. Description CerealsDB is an online resource containing a range of genomic datasets for wheat (Triticum aestivum) that will assist plant breeders and scientists to select the most appropriate markers for marker assisted selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring. Conclusion CerealsDB is an open access website that is rapidly becoming an invaluable resource within the wheat research and plant breeding communities.
Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription
Rebecca L Poole, Gary LA Barker, Kay Werner, Gaia F Biggi, Jane Coghill, J George Gibbings, Simon Berry, Jim M Dunwell, Keith J Edwards
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-475
Abstract: Examination of 71,930 Long SAGE tags generated from six libraries derived from two wheat genotypes grown under two different conditions suggested that SAGE is a reliable and reproducible technique for use in studying the hexaploid wheat transcriptome. However, our results also showed that in poorly annotated and/or poorly sequenced genomes, such as hexaploid wheat, considerably more information can be extracted from SAGE data by carrying out a systematic analysis of both perfect and "fuzzy" (partially matched) tags. This detailed analysis of the SAGE data shows first that while there is evidence of alternative polyadenylation this appears to occur exclusively within the 3' untranslated regions. Secondly, we found no strong evidence for widespread alternative splicing in the developing wheat grain transcriptome. However, analysis of our SAGE data shows that antisense transcripts are probably widespread within the transcriptome and appear to be derived from numerous locations within the genome. Examination of antisense transcripts showing sequence similarity to the Puroindoline a and Puroindoline b genes suggests that such antisense transcripts might have a role in the regulation of gene expression.Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development.With cereals constituting more than 60% of the world's dietary intake, the bread wheat Triticum aestivum is one of the most important crops in world agriculture [1,2]. Despite the high yields achieved in Europe there is still a real need to generate improved cultivars, as yield and flour quality can be dramatically affected by the environment. This need has become even greater in recent years with tight
Ad hoc Cloud Computing: From Concept to Realization
Gary Andrew McGilvary,Adam Barker,Malcolm Atkinson
Computer Science , 2015,
Abstract: This paper presents the first complete, integrated and end-to-end solution for ad hoc cloud computing environments. Ad hoc clouds harvest resources from existing sporadically available, non-exclusive (i.e. primarily used for some other purpose) and unreliable infrastructures. In this paper we discuss the problems ad hoc cloud computing solves and outline our architecture which is based on BOINC.
TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web
Ralph Pethica,Gary Barker,Tim Kovacs,Julian Gough
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008934
Abstract: Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees.
V-BOINC: The Virtualization of BOINC
Gary A. McGilvary,Adam Barker,Ashley Lloyd,Malcolm Atkinson
Computer Science , 2013,
Abstract: The Berkeley Open Infrastructure for Network Computing (BOINC) is an open source client-server middleware system created to allow projects with large computational requirements, usually set in the scientific domain, to utilize a technically unlimited number of volunteer machines distributed over large physical distances. However various problems exist deploying applications over these heterogeneous machines using BOINC: applications must be ported to each machine architecture type, the project server must be trusted to supply authentic applications, applications that do not regularly checkpoint may lose execution progress upon volunteer machine termination and applications that have dependencies may find it difficult to run under BOINC. To solve such problems we introduce virtual BOINC, or V-BOINC, where virtual machines are used to run computations on volunteer machines. Application developers can then compile their applications on a single architecture, checkpointing issues are solved through virtualization API's and many security concerns are addressed via the virtual machine's sandbox environment. In this paper we focus on outlining a unique approach on how virtualization can be introduced into BOINC and demonstrate that V-BOINC offers acceptable computational performance when compared to regular BOINC. Finally we show that applications with dependencies can easily run under V-BOINC in turn increasing the computational potential volunteer computing offers to the general public and project developers.
Finding bridges in packings of colloidal spheres
Matthew C. Jenkins,Mark D. Haw,Gary C. Barker,Wilson C. K. Poon,Stefan U. Egelhaaf
Physics , 2010,
Abstract: We identify putative load-bearing structures (bridges) in experimental colloidal systems studied by confocal microscopy. Bridges are co-operative structures that have been used to explain stability and inhomogeneous force transmission in simulated granular packings with a range of densities. We show that bridges similar to those found in granular simulations are present in real experimental colloidal packings. We describe critically the bridge-finding procedure for real experimental data and propose a new criterion-Lowest Mean Squared Separation (LSQS)-for selecting optimum stabilisations.
C2MS: Dynamic Monitoring and Management of Cloud Infrastructures
Gary A. McGilvary,Josep Rius,í?igo Goiri,Francesc Solsona,Adam Barker,Malcolm Atkinson
Computer Science , 2013,
Abstract: Server clustering is a common design principle employed by many organisations who require high availability, scalability and easier management of their infrastructure. Servers are typically clustered according to the service they provide whether it be the application(s) installed, the role of the server or server accessibility for example. In order to optimize performance, manage load and maintain availability, servers may migrate from one cluster group to another making it difficult for server monitoring tools to continuously monitor these dynamically changing groups. Server monitoring tools are usually statically configured and with any change of group membership requires manual reconfiguration; an unreasonable task to undertake on large-scale cloud infrastructures. In this paper we present the Cloudlet Control and Management System (C2MS); a system for monitoring and controlling dynamic groups of physical or virtual servers within cloud infrastructures. The C2MS extends Ganglia - an open source scalable system performance monitoring tool - by allowing system administrators to define, monitor and modify server groups without the need for server reconfiguration. In turn administrators can easily monitor group and individual server metrics on large-scale dynamic cloud infrastructures where roles of servers may change frequently. Furthermore, we complement group monitoring with a control element allowing administrator-specified actions to be performed over servers within service groups as well as introduce further customized monitoring metrics. This paper outlines the design, implementation and evaluation of the C2MS.
The Effect of Structural Complexity, Prey Density, and “Predator-Free Space” on Prey Survivorship at Created Oyster Reef Mesocosms
Austin T. Humphries, Megan K. La Peyre, Gary A. Decossas
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028339
Abstract: Interactions between predators and their prey are influenced by the habitat they occupy. Using created oyster (Crassostrea virginica) reef mesocosms, we conducted a series of laboratory experiments that created structure and manipulated complexity as well as prey density and “predator-free space” to examine the relationship between structural complexity and prey survivorship. Specifically, volume and spatial arrangement of oysters as well as prey density were manipulated, and the survivorship of prey (grass shrimp, Palaemonetes pugio) in the presence of a predator (wild red drum, Sciaenops ocellatus) was quantified. We found that the presence of structure increased prey survivorship, and that increasing complexity of this structure further increased survivorship, but only to a point. This agrees with the theory that structural complexity may influence predator-prey dynamics, but that a threshold exists with diminishing returns. These results held true even when prey density was scaled to structural complexity, or the amount of “predator-free space” was manipulated within our created reef mesocosms. The presence of structure and its complexity (oyster shell volume) were more important in facilitating prey survivorship than perceived refugia or density-dependent prey effects. A more accurate indicator of refugia might require “predator-free space” measures that also account for the available area within the structure itself (i.e., volume) and not just on the surface of a structure. Creating experiments that better mimic natural conditions and test a wider range of “predator-free space” are suggested to better understand the role of structural complexity in oyster reefs and other complex habitats.
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