A5068462570- Plant Molecular Biology Research
- Photosynthetic Processes and Mechanisms
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Light effects on plants
- Cellular Mechanics and Interactions
- Genomics and Phylogenetic Studies
- Head and Neck Cancer Studies
- RNA Research and Splicing
- Plant Stress Responses and Tolerance
- Protein Structure and Dynamics
- Receptor Mechanisms and Signaling
- Cardiac Fibrosis and Remodeling
- Virus-based gene therapy research
- Plant Micronutrient Interactions and Effects
- Probiotics and Fermented Foods
- Trypanosoma species research and implications
- Animal Disease Management and Epidemiology
- Genetic Neurodegenerative Diseases
- Viral Infections and Immunology Research
- Signaling Pathways in Disease
- Neurobiology and Insect Physiology Research
- Neuroscience and Neuropharmacology Research
- Machine Learning in Bioinformatics
- Plant nutrient uptake and metabolism
University of Glasgow
2015-2024
Glasgow Life
2016-2023
Genomics (United Kingdom)
2004-2009
University of California, Davis
2005
University of York
1992-2001
One of the main objectives in analysis microarray experiments is identification genes that are differentially expressed under two experimental conditions. This task complicated by noisiness data and large number examined simultaneously. Here, we present a novel technique for identifying does not originate from sophisticated statistical model but rather an biological reasoning. The new technique, which based on calculating rank products (RP) replicate experiments, fast simple. At same time,...
UV-B radiation in sunlight has diverse effects on humans, animals, plants, and microorganisms. can cause damage to molecules cells, consequently organisms need protect against repair UV survive sunlight. In low nondamaging levels of stimulate transcription genes involved UV-protective responses. However, remarkably little is known about the underlying mechanisms perception signal transduction. Here we report that Arabidopsis RESISTANCE LOCUS 8 (UVR8) a UV-B-specific signaling component...
Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated reference genome for mexicana and refined the genomes major , infantum braziliensis . This has allowed identification remarkably low number genes or paralog groups (2, 14, 19, 67, respectively) unique one species. These were found be conserved additional isolates same predicted allelic variation find that these isolates, L....
Alternative splicing plays crucial roles by influencing the diversity of transcriptome and proteome regulating protein structure/function gene expression. It is widespread in plants, alteration levels factors leads to a wide variety growth developmental phenotypes. The circadian clock complex piece cellular machinery that can regulate physiology behavior anticipate predictable environmental changes on revolving planet. We have performed system-wide analysis alternative components Arabidopsis...
Abstract Background In arid and semi-arid environments, drought soil salinity usually occur at the beginning end of a plant's life cycle, offering natural opportunity for priming young plants to enhance stress tolerance in mature plants. Chromatin marks, such as histone modifications, provide potential molecular mechanism environmental stresses, but whether transient exposure seedlings hyperosmotic leads chromatin changes that are maintained throughout vegetative growth remains unclear....
Deep sequencing was used to bring high resolution the human cytomegalovirus (HCMV) transcriptome at stage when infectious virion production is under way, and major findings were confirmed by extensive experimentation using conventional techniques. The majority (65.1%) of polyadenylated viral RNA transcription committed producing four noncoding transcripts (RNA2.7, RNA1.2, RNA4.9, RNA5.0) that do not substantially overlap designated protein-coding regions. Additional RNAs are transcribed...
Summary Plant nutrition critically depends on the activity of membrane transporters that translocate minerals from soil into plant and are responsible for their intra‐ intercellular distribution. Most encoded by multigene families whose members often exhibit overlapping expression patterns a high degree sequence homology. Furthermore, many inorganic nutrients transported more than one transporter family. These considerations, coupled with large number so‐far non‐annotated putative genes,...
The circadian oscillator in eukaryotes consists of several interlocking feedback loops through which the expression clock genes is controlled. It generally assumed that all plant cells contain essentially identical and cell-autonomous multiloop clocks. Here, we show roots mature Arabidopsis plants differs markedly from shoots root synchronized by a photosynthesis-related signal shoot. Two are disengaged roots, because two key components, transcription factors CCA1 LHY, able to inhibit gene...
Abstract Background Comprehensive, tissue-specific, microarray analysis is a potent tool for the identification of tightly defined expression patterns that might be missed in whole-organism scans. We applied such an to Drosophila melanogaster Malpighian (renal) tubule, differentiated tissue. Results The transcriptome D. tubule highly reproducible and significantly different from obtained arrays. More than 200 genes are more 10-fold enriched over 1,000 enriched. Of top genes, only 18 have...
The FlyAtlas resource contains data on the expression of genes Drosophila melanogaster in different tissues (currently 25—17 adult and 8 larval) obtained by hybridization messenger RNA to Affymetrix Genome 2 microarrays. microarray probe sets cover 13 250 genes, detecting 12 533 an unambiguous manner. underlying original web application (http://flyatlas.org) have been restructured into a relational database Java servlet written provide new interface, (http://flyatlas.gla.ac.uk/), which...
ABSTRACT The diverse sequences of viral populations within individual hosts are the starting material for selection and subsequent evolution RNA viruses such as foot-and-mouth disease virus (FMDV). Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared two bovine epithelial samples (foot lesions) from single animal with inoculum used to initiate experimental infection. Genomic were determined in duplicate runs, consensus sequence by NGS...
Myelinated axons have a distinct protein architecture essential for action potential propagation, neuronal communication, and maintaining cognitive function. Damage to myelinated axons, associated with cerebral hypoperfusion, contributes age-related decline. We sought determine early alterations in the of mechanisms after hypoperfusion. Using mouse model we assessed changes proteins critical maintenance paranodes, nodes Ranvier, axon–glial integrity, myelin by confocal laser scanning...
Abstract There is a rapidly growing body of literature on the effects topography and critically, nanotopography cell adhesion, apoptosis differentiation. Understanding adhesion morphology consequences shape changes in nucleus, consequently, gene expression offers new approaches to elucidation potential control stem In current study we have used molecular combination with immunohistology transcript analysis understand role mesenchymal phenotype. Results demonstrate large nucleus lamin...
Imatinib and second-generation tyrosine kinase inhibitors (TKIs) nilotinib dasatinib have statistically significantly improved the life expectancy of chronic myeloid leukemia (CML) patients; however, resistance to TKIs remains a major clinical challenge. Although ponatinib, third-generation TKI, improves outcomes for patients with BCR-ABL-dependent mechanisms resistance, including T315I mutation, proportion may or develop BCR-ABL-independent fail ponatinib treatment. By modeling testing...
Salmonid fishes exhibit high levels of phenotypic and ecological variation are thus ideal model systems for studying evolutionary processes adaptive divergence speciation. Furthermore, salmonids major interest in fisheries, aquaculture, conservation research. Improving understanding the genetic mechanisms underlying traits these species would significantly progress research fields. Here we generate quality de novo transcriptomes four salmonid species: Atlantic salmon (Salmo salar), brown...
We have recently introduced a rank-based test statistic, RankProducts (RP), as new non-parametric method for detecting differentially expressed genes in microarray experiments. It has been shown to generate surprisingly good results with biological datasets. The basis this performance and the limits of are, however, little understood. Here we explore such approaches under variety conditions using simulated data, compare it classical Wilcoxon rank sums t-statistics, which form most...
The cAMP-specific phosphodiesterase PDE4D5 can interact with the signalling scaffold proteins RACK (receptors for activated C-kinase) 1 and β-arrestin. Two-hybrid co-immunoprecipitation analyses showed that RACK1 β-arrestin in a mutually exclusive manner. Overlay studies scanning peptide array libraries at overlapping sites within unique N-terminal region of distinct conserved PDE4 catalytic domain. Screening alanine substitution arrays, coupled mutagenesis truncation studies, allowed...
The biological interpretation of even a simple microarray experiment can be challenging and highly complex task. Here we present new method (Iterative Group Analysis) to facilitate, improve, accelerate this process.Our Iterative Analysis approach (iGA) uses elementary statistics identify those functional classes genes that are significantly changed in an at the same time determines which class members most likely differentially expressed. iGA does not require all change is therefore robust...
Metal tolerance proteins (MTPs) are plant members of the cation diffusion facilitator (CDF) transporter family involved in cellular metal homeostasis. Members CDF ubiquitously found all living entities and show principal selectivity for Zn<sup>2+</sup>, Mn<sup>2+</sup>, Fe<sup>2+</sup>. Little is known regarding determinants CDFs. We identified a novel cereal member CDFs barley, termed HvMTP1, that localizes to vacuolar membrane. Unlike its close relative AtMTP1, which highly selective...
A class of anti-virulence compounds, the salicylidene acylhydrazides, has been widely reported to block function type three secretion system several Gram-negative pathogens by a previously unknown mechanism. In this work we provide first identification bacterial proteins that are targeted group compounds. We evidence their mode action is likely result from synergistic effect arising perturbation conserved proteins. also examine contribution selected target pathogenicity Yersinia...
Mycobacterium bovis is the causal agent of bovine tuberculosis, one most important diseases currently facing UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population M. 145 across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can principle expose contributions under-sampled host populations transmission. However, demonstrate our data such signal due molecular type...