Ancient Ancestry of KFDV and AHFV Revealed by Complete Genome Analyses of Viruses Isolated from Ticks and Mammalian Hosts

Alkhurma hemorrhagic fever (AHF) and Kyasanur Forest disease (KFD) viruses both cause serious and sometimes fatal human disease in their respective ranges, Saudi Arabia and India. AHFV was first identified in the mid-1990s and due to its strong genetic similarity to KFDV it has since been considered the result of a recent introduction of KFDV into Saudi Arabia. To gain a better understanding of the evolutionary history of AHFV and KFDV, we sequenced the full-length genomes of 3 KFDV and 16 AHFV. Sequence analyses show a greater genetic diversity within AHFV than previously thought, particularly within the tick population. The phylogeny constructed with these 19 full-length sequences and two AHFV sequences from GenBank indicates AHFV diverged from KFDV almost 700 years ago. Given the presence of competent tick vectors in the regions between and surrounding Saudi Arabia and India and the recent identification of AHFV in Egypt, these results suggest a broader geographic range of AHFV and KFDV, and raise the possibility of other AHFV/KFDV–like viruses circulating in these regions

Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

Background: Prostate cancer cells in primary tumors have been typed CD10(-)/CD13(-)/CD24(hi)/CD26(+)/CD38(lo)/CD44(-)/CD104(-). This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. Methods: CD26(+) cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. Results: The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Conclusions: Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types.National Institutes of Health (NIH)[CA111244]National Institutes of Health (NIH)[CA98699]National Institutes of Health (NIH)[CA85859]National Institutes of Health (NIH)[DK63630][P50-GMO-76547

Differential expression of anterior gradient gene AGR2 in prostate cancer

<p>Abstract</p> <p>Background</p> <p>The protein AGR2 is a putative member of the protein disulfide isomerase family and was first identified as a homolog of the <it>Xenopus laevis </it>gene XAG-2. AGR2 has been implicated in a number of human cancers. In particular, AGR2 has previously been found to be one of several genes that encode secreted proteins showing increased expression in prostate cancer cells compared to normal prostatic epithelium.</p> <p>Methods</p> <p>Gene expression levels of AGR2 were examined in prostate cancer cells by microarray analysis. We further examined the relationship of AGR2 protein expression to histopathology and prostate cancer outcome on a population basis using tissue microarray technology.</p> <p>Results</p> <p>At the RNA and protein level, there was an increase in AGR2 expression in adenocarcinoma of the prostate compared to morphologically normal prostatic glandular epithelium. Using a tissue microarray, this enhanced AGR2 expression was seen as early as premalignant PIN lesions. Interestingly, within adenocarcinoma samples, there was a slight trend toward lower levels of AGR2 with increasing Gleason score. Consistent with this, relatively lower levels of AGR2 were highly predictive of disease recurrence in patients who had originally presented with high-stage primary prostate cancer (P = 0.009).</p> <p>Conclusions</p> <p>We have shown for the first time that despite an increase in AGR2 expression in prostate cancer compared to non-malignant cells, relatively lower levels of AGR2 are highly predictive of disease recurrence following radical prostatectomy.</p

Genome of Diuraphis noxia, a global aphid pest of small grains

Background: The Russian wheat aphid, Diuraphis noxia Kurdjumov, is one of the most important pests of small grains throughout the temperate regions of the world. This phytotoxic aphid causes severe systemic damage symptoms in wheat, barley, and other small grains as a direct result of the salivary proteins it injects into the plant while feeding.Results: We sequenced and de novo assembled the genome of D. noxia Biotype 2, the strain most virulent to resistance genes in wheat. The assembled genomic scaffolds span 393 MB, equivalent to 93% of its 421 MB genome, and contains 19,097 genes. D. noxia has the most AT-rich insect genome sequenced to date (70.9%), with a bimodal CpG(O/E) distribution and a complete set of methylation related genes. The D. noxia genome displays a widespread, extensive reduction in the number of genes per ortholog group, including defensive, detoxification, chemosensory, and sugar transporter groups in comparison to the Acyrthosiphon pisum genome, including a 65% reduction in chemoreceptor genes. Thirty of 34 known D. noxia salivary genes were found in this assembly. These genes exhibited less homology with those salivary genes commonly expressed in insect saliva, such as glucose dehydrogenase and trehalase, yet greater conservation among genes that are expressed in D. noxia saliva but not detected in the saliva of other insects. Genes involved in insecticide activity and endosymbiont-derived genes were also found, as well as genes involved in virus transmission, although D. noxia is not a viral vector.Conclusions: This genome is the second sequenced aphid genome, and the first of a phytotoxic insect. D. noxia's reduced gene content of may reflect the influence of phytotoxic feeding in shaping the D. noxia genome, and in turn in broadening its host range. The presence of methylation-related genes, including cytosine methylation, is consistent with other parthenogenetic and polyphenic insects. The D. noxia genome will provide an important contrast to the A. pisum genome and advance functional and comparative genomics of insects and other organisms.Peer reviewedBiochemistry and Molecular Biolog

Plankton communities of the South Atlantic anticyclonic gyre

Data collected during cruises of the Former Soviet Union (in 1963-1989) and the British Atlantic meridional transect program (in 1995-1999) were used to analyse macroscale patterns in phyto- and zooplankton biomass, size structure, species diversity, chlorophyll a, and plankton bioluminescence in the macroscale anticyclonic gyre of the South Atlantic Ocean. The spatial pattern of bioluminescence intensity was in good agreement with that of remotely sensed (CZCS) chlorophyll a, phosphate, salinity, and copepod species diversity index distributions especially in terms of geographic inclinations of the isolines, both associated with the north-westward pattern off the South equatorial current. Among the 416 copepod species recorded in samples, 51 species were noted throughout the whole gyre. On the other hand, there were a number of species found only in one of the currents. The mesozooplankton biomass size spectra (calculated in carbon units), exhibited a fairly stable slope of the curve from the eastern periphery of the gyre to its centre. The British Atlantic meridional transect program meridional transect through the western part of the gyre showed mesozooplankton size spectra in greater detail between the equator and 50degrees S. Although the spectra change slowly along the transect as far as 36degrees S, there is a general trend toward increasing slopes from the equatorial region to the oligotrophic central gyre. The calculated phyto-to-zooplankton ratio indicated that for the tropical anticyclonic gyres, the mesozooplankton carbon biomass could be represented as the exponential function of the phytoplankton carbon.Les données collectées durant les campagnes de l’ex-URSS (1963 à 1989) et la section britannique dans l'Atlantique Sud (1995–1999) permettent d’analyser la distribution macro-échelle du phytoplancton et du zooplancton, la structure de taille, la diversité spécifique, la teneur en chlorophylle a, et la bioluminescence du plancton dans le tourbillon phytoplanctonique de l’Atlantique Sud. La répartition de la bioluminescence est en bon accord avec celle de la chlorophylle mesurée par télédétection (CZCS), les phosphates, la salinité et l’indice de diversité des copépodes. Cette répartition suit l’inclinaison des isolignes liée à la distribution générale du nord vers l’ouest au large du courant sud-équatorial. Parmi les 416 espèces de copépodes, 51 se rencontrent dans tout le tourbillon; à l’inverse, nombre d’espèces sont spécifiques à l’un des courants. La distribution en taille de la biomasse du mésoplancton, calculée en termes de carbone, suit une courbe à pente constante de la périphérie est au centre du tourbillon. Les sections réalisées par les anglais au travers de la partie ouest du tourbillon permettent de détailler cette répartition en taille du mézooplancton entre l’équateur et 50° S. Bien que le spectre se modifie lentement jusque vers 36° S, la tendance générale est bien à une élévation des pentes de la zone équatoriale au centre oligotrophe du tourbillon. Le taux calculé entre phytoplancton et zooplancton souligne que, pour les tourbillons anticycloniques tropicaux, la biomasse carbonée du mésozooplancton peut être représentée par une fonction exponentielle du carbone phytoplanctonique