Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa.

Microbial diversity in saliva of oral squamous cell carcinoma.

In the oral cavity, chronic inflammation has been observed at various stages of oral squamous cell carcinomas (OSCC). Such inflammation could result from persistent mucosal or epithelial cell colonization by microorganisms. There is increasing evidence of the involvement of oral bacteria in inflammation, warranting further studies on the association of bacteria with the progression of OSCC.

The genome of woodland strawberry (Fragaria vesca).

The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F.

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types.

Background: Cucumber, Cucumis sativus L., is an economically and nutritionally important crop of the Cucurbitaceae family and has long served as a primary model system for sex determination studies. Recently, the sequencing of its whole genome has been completed.

Rapid and reliable single nucleotide polymorphism-based differentiation of Brucella live vaccine strains from field strains.

The reliable differentiation of live Brucella vaccine strains from field isolates is an important element in brucellosis control programs. We describe the design, validation, and implementation of a novel single nucleotide polymorphism (SNP)-based typing platform that offers a rapid, reliable, and robust tool to achieve this with improved diagnostic accuracy compared to existing molecular tests. Furthermore, the assays described are designed such that they supplement, and can be run as an intrinsic part of, a previously described assay identifying Brucella isolates to the species level (K.

Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis.

Entamoeba histolytica contains a large and novel family of transmembrane kinases (TMKs). The expression patterns of the E. histolytica TMKs in individual trophozoites and the roles of the TMKs for sensing and responding to extracellular cues were incompletely characterised.

Modulation of hepatic PPAR expression during Ft LVS LPS-induced protection from Francisella tularensis LVS infection.

Background: It has been shown previously that administration of Francisella tularensis (Ft) Live Vaccine Strain (LVS) lipopolysaccharide (LPS) protects mice against subsequent challenge with Ft LVS and blunts the pro-inflammatory cytokine response.

Methods: To further investigate the molecular mechanisms that underlie Ft LVS LPS-mediated protection, we profiled global hepatic gene expression following Ft LVS LPS or saline pre-treatment and subsequent Ft LVS challenge using Affymetrix arrays.

Results: A large number of genes (> 3,000) were differentially expressed at 48 hours post-infection.

Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.

Background: Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC) reference RNA samples using Roche's 454 Genome Sequencer FLX.

Results: We generated more that 3.

Gene expression in primate liver during viral hemorrhagic fever.

Background: Rhesus macaques infected with lymphocytic choriomeningitis virus (LCMV) provide a model for human Lassa fever. Disease begins with flu-like symptoms and progresses rapidly with fatal consequences. Previously, we profiled the blood transcriptome of LCMV-infected monkeys (M.

An essential role for the antiviral endoribonuclease, RNase-L, in antibacterial immunity.

Type I IFNs were discovered as the primary antiviral cytokines and are now known to serve critical functions in host defense against bacterial pathogens. Accordingly, established mediators of IFN antiviral activity may mediate previously unrecognized antibacterial functions. RNase-L is the terminal component of an RNA decay pathway that is an important mediator of IFN-induced antiviral activity.

Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.

The Brucella abortus strain S19, a spontaneously attenuated strain, has been used as a vaccine strain in vaccination of cattle against brucellosis for six decades. Despite many studies, the physiological and molecular mechanisms causing the attenuation are not known. We have applied pyrosequencing technology together with conventional sequencing to rapidly and comprehensively determine the complete genome sequence of the attenuated Brucella abortus vaccine strain S19.

Early blood profiles of virus infection in a monkey model for Lassa fever.

Acute arenavirus disease in primates, like Lassa hemorrhagic fever in humans, begins with flu-like symptoms and leads to death approximately 2 weeks after infection. Our goal was to identify molecular changes in blood that are related to disease progression. Rhesus macaques (Macaca mulatta) infected intravenously with a lethal dose of lymphocytic choriomeningitis virus (LCMV) provide a model for Lassa virus infection of humans.

Open architecture expression profiling of plant transcriptomes and gene discovery using GeneCalling technology.

The recent rapid developments in genomics tools, technologies, and bioinformatics have revolutionized gene expression analysis. It is now routine to measure gene expression modulation at the genomic level. GeneCalling technology is an open architecture system capable of assaying more than 95% of genes expressed in a tissue.

Comprehensive transcript profiling of Pto- and Prf-mediated host defense responses to infection by Pseudomonas syringae pv. tomato.

The disease resistance gene Pto encodes a serine/threonine protein kinase that confers resistance in tomato to Pseudomonas syringae pv. tomato strains that express the effector protein AvrPto. Pto-mediated resistance to bacterial speck disease also requires Prf, a protein with leucine-rich repeats and a putative nucleotide-binding site, although the role of Prf in the defense pathway is not known.