Biomedical subjects

Gary L A Barker

Publications and source records attributed to Gary L A Barker.

5 recordsLinked to original sources

PubMed2006

A microarray analysis of gene expression in the free-living stages of the parasitic nematode Strongyloides ratti.

BACKGROUND: The nematode Strongyloides ratti has two adult phases in its lifecycle: one obligate, female and parasitic and one facultative, dioecious and free-living. The molecular control of the development of this free-living generation remains to be elucidated. RESULTS: 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. CONCLUSION: 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.

Animals↗

PubMed2005

An expressed sequence tag analysis of the life-cycle of the parasitic nematode Strongyloides ratti.

14,761 expressed sequence tags (ESTs) were generated, representing five stages during the parasitic and free-living phases of the life-cycle of the parasitic nematode Strongyloides ratti. These ESTs formed 4152 clusters, of which 97% contained 10 or fewer ESTs and 66% were singletons. These 4152 clusters are likely to represent approximately 20% of S. ratti's genes. The clusters' consensus sequences were used to assign each cluster to one of three databases: (i) Caenorhabditis elegans and C. briggsae sequences; (ii) other nematode sequences; (iii) non-nematode sequences. This approach has identified putative nematode-specific genes, that may be targets for developing approaches for parasitic nematode control. Approximately 25% of the clusters have no significant alignments and may therefore represent novel genes. The EST representation between the libraries was used to analyse stage-specific or -biased expression in silico. This showed that 81% of clusters are present in only one library and 12% are present in any two libraries, indicating substantial stage-specificity of gene expression. The 30-most abundantly expressed clusters were analysed in further detail. Many of these have significantly different parasitic- or free-living-specific or -biased expression. Many of the parasitic-specific genes are, as yet, uncharacterised: one of these represents 25% of all ESTs obtained from the parasitic stage.

Animals↗

PubMed2005

Alteration of the embryo transcriptome of hexaploid winter wheat (Triticum aestivum cv. Mercia) during maturation and germination.

Grain dormancy and germination are areas of biology that are of considerable interest to the cereal community. We have used a 9,155-feature wheat unigene cDNA microarray resource to investigate changes in the wheat embryo transcriptome during late grain development and maturation and during the first 48 h of postimbibition germination. In the embryo 392 mRNAs accumulated by twofold or greater over the time course from 21 days postanthesis (dpa) to 40 dpa and on through 1 and 2 days postgermination. These included mRNAs encoding proteins involved in amino acid biosynthesis and metabolism, cell division and subsequent cell development, signal transduction, lipid metabolism, energy production, protein turnover, respiration, initiation of transcription, initiation of translation and ribosomal composition. A number of mRNAs encoding proteins of unknown function also accumulated over the time course. Conversely 163 sequences showed decreases of twofold or greater over the time course. A small number of mRNAs also showed rapid accumulation specifically during the first 48 h of germination. We also examined alterations in the accumulation of transcripts encoding proteins involved in abscisic acid signalling. Thus, we describe changes in the level of transcripts encoding wheat Viviparous 1 (Vp1) and other interacting proteins. Interestingly, the transcript encoding wheat Viviparous-interacting protein 1 showed a pattern of accumulation that correlates inversely with germination. Our data suggests that the majority of the transcripts required for germination accumulate in the embryo prior to germination and we discuss the implications of these findings with regard to manipulation of germination in wheat.

Computational Biology↗

PubMed2004

A transcriptomics resource for wheat functional genomics.

Grain development, germination and plant development under abiotic stresses are areas of biology that are of considerable interest to the cereal community. Within the Investigating Gene Function programme we have produced the resources required to investigate alterations in the transcriptome of hexaploid wheat during these developmental processes. We have single pass sequenced the cDNAs of between 700 and 1300 randomly picked clones from each of 35 cDNA libraries representing highly specific stages of grain and plant development. Annotated sequencing results have been stored in a publicly accessible, online database at http://www.cerealsdb.uk.net. Each of the tissue stages used has also been photographed in detail, resulting in a collection of high-quality micrograph images detailing wheat grain development. These images have been collated and annotated in order to produce a web site focused on wheat development (http://www.wheatbp.net/). We have also produced high-density microarrays of a publicly available wheat unigene set based on the 35 cDNA libraries and have completed a number of microarray experiments which validate their quality.

Journal Article↗

PubMed2000

Allele-specific PCR shows that genetic exchange occurs among genetically diverse Nodularia (cyanobacteria) filaments in the Baltic Sea.

Some cyanobacteria have been shown to exchange genetic information under laboratory conditions, but it has not been clear whether such genetic exchange occurs in the natural environment. To address this, a population genetic study was carried out on the filamentous diazotrophic cyanobacterium Nodularia in the Baltic Sea. Nodularia filaments were collected from 20 widely distributed sampling stations in the Baltic Sea during June and July 1998. Allele-specific PCR (AS-PCR) was used to characterize over 2000 filaments at three loci: a non-coding spacer between adjacent copies of the main structural gas vesicle gene gvpA (gvpA-IGS), the phycocyanin intergenic spacer (PC-IGS) and the rDNA internal transcribed spacer (rDNA-ITS). The three loci were all found to be polymorphic in the 1998 population: two alternative alleles were distinguished at the gvpA-IGS and PC-IGS loci, and three at the rDNA-ITS locus. All 12 possible combinations of alleles were found in the filaments studied, but some were much more common than others. The index of association (I:(A)) for all possible pairwise combinations of isolates was found to differ significantly from zero, which implies that there is some linkage disequilibrium between loci. The I:(A) values for 16 out of 20 individual sampling stations also differed significantly from zero: this shows that the observed linkage disequilibrium is not due to pooling data from genetically distinct subpopulations. Monte-Carlo simulations with random subsets of the data confirmed that some combinations showed significantly more linkage disequilibrium than expected by chance alone. It is concluded that genetic exchange occurs in the natural Nodularia population, but the frequency is not high enough for the loci to be in linkage equilibrium. The distribution of the 12 genotypes across the Baltic Sea was found to be non-random, but did not correlate with temperature, salinity or major nutrient concentrations. A significant relationship was found between the gene diversity among filaments at each station and the distance of the station from the centre of the sampling area: possible reasons for this trend are discussed.

Alleles↗