Prevalence of Human Papillomavirus infection by age and cervical cytology in Thika, Kenya

Human papillomavirus (HPV) infections cause cervical cancer and premalignant dysplasia. Data on HPV and cervical cancer in Kenya are scarce. Type-specific HPV prevalence data provides a basis for assessing the impact of HPV vaccination programs on cervical cytology and how HPV based screening will influence cervical cancer prevention. To investigate HPV infections in a population in Kenya, we obtained cervical cells specimen from 498 women in a population in Thika district. We report HPV type specific prevalence and distribution data for 498 women (age range 18-74 years; mean age 36 years) recruited into the study in relation to age and cervical cytology. The study was conducted between January to May 2010. Pap smears were performed, HR HPV DNA were detected by Digene Hybrid capture 2® (hc2) test and HPV genotyping was performed with Multiplex Luminex HPV genotyping kit (Multimetrix, Progen, Germany). Samples from 106 women (21.3%) tested positive for HPV. Multiple HPV types were detected in 40 (37.7% of HC2-positive samples) and the rest had infection with single HPV type. The most common HR HPV type at all ages was HPV16, 52, 56, 66, and 18. There was a marked decline in the prevalence of HR-HPV with age. The pattern of HR HPV distribution in this population was slightly different from existing literature, which has important consequences for HPV vaccination and prevention programs

Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing

Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established. The error profiles and read length limitations of early versions of next-generation sequencing technologies rendered them ineffective for some sequence variant types, particularly microsatellites and other tandem repeats, and fostered the general misconception that such variants are inherently inaccessible to these platforms. At the same time, tandem repeats have emerged as important sources of functional variation. Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between markers and traits. Sensitive identification of these variants in large-scale next-gen sequencing efforts will enable more comprehensive association studies capable of revealing previously invisible associations. We present a population-scale analysis of microsatellite repeats using whole-genome data from 158 inbred isolates from the Drosophila Genetics Reference Panel, a collection of over 200 extensively phenotypically characterized isolates from a single natural population, to uncover processes underlying repeat mutation and to enable associations with behavioral, morphological, and life-history traits. Analysis of repeat variation from next-generation sequence data will also enhance studies of genome stability and neurodegenerative diseases

Structure and activity of lacustrine sediment bacteria involved in nutrient and iron cycles

Knowledge about the bacterial community structure in sediments is essential to better design restoration strategies for eutrophied lakes. In that regard, the aim of this study was to quantify the abundance and activity of bacteria involved in nutrient and iron cycling in sediments from four Azorean lakes with distinct trophic states (Verde, Azul, Furnas and Fogo). Inferred from quantitative PCR, bacteria performing anaerobic ammonia oxidation, were the most abundant in the eutrophic lakes Verde, Azul and Furnas (4.5 % to 16.6 %), followed by nitrifying bacteria (0.8 % to 13.0 %), denitrifying bacteria (0.5 % to 6.8 %), iron-reducing bacteria (0.2 % to 1.4 %), and phosphorus-accumulating organisms (<0.3 %). In contrast, denitrifying bacteria dominated sediments from the oligo-mesotrophic lake Fogo (8.8 %). Activity assays suggested that bacteria performing ammonia oxidation (aerobic and anaerobic), nitrite oxidation, heterothrophic nitrate reduction, iron reduction and biological phosphorus storage/release were present and active in all Azorean lake sediments. The present work also suggested that the activity of denitrifying bacteria might contribute to the release of phosphorus from sediments.The authors are indebted and grateful to the Regional Department of Water Resources and Land Planning (Azores) for the grant (Contrato Excepcionado no. 4/2008/ DROTRH) and its staff (Dina Pacheco), and to Virgilio Cruz and Paulo Antunes (Geosciences Department, University of Azores) for the useful help in sediments' collection, to the technical staff of the Department of Environmental Engineering - DTU for chemical analysis, to Laurent Philippot (INRA - University of Burgundy) for positive controls for DNB, to Richard Glaven and Derek Lovley (Department of Microbiology, University of Massachusetts) for Geobacter strains, to Paul Bodelier, Marzia Milleto and Marion Meima (Netherlands Institute of Ecology, NIOO-KNAW) for SRB clones and to Yunhong Kong and Per Halkjaer Nielsen (Department of Life Sciences, Section of Environmental Engineering, Aalborg University) for PAO clones. The authors also acknowledge the Grant SFRH/BD/25639/2005 from the Foundation for Science and Technology/M.C.T.(Portugal) awarded to G. M. and a Marie Curie Excellence Award (EC FP6) to B.F.S

Nonsense Mediated Decay Resistant Mutations Are a Source of Expressed Mutant Proteins in Colon Cancer Cell Lines with Microsatellite Instability

BACKGROUND: Frameshift mutations in microsatellite instability high (MSI-High) colorectal cancers are a potential source of targetable neo-antigens. Many nonsense transcripts are subject to rapid degradation due to nonsense-mediated decay (NMD), but nonsense transcripts with a cMS in the last exon or near the last exon-exon junction have intrinsic resistance to nonsense-mediated decay (NMD). NMD-resistant transcripts are therefore a likely source of expressed mutant proteins in MSI-High tumours. METHODS: Using antibodies to the conserved N-termini of predicted mutant proteins, we analysed MSI-High colorectal cancer cell lines for examples of naturally expressed mutant proteins arising from frameshift mutations in coding microsatellites (cMS) by immunoprecipitation and Western Blot experiments. Detected mutant protein bands from NMD-resistant transcripts were further validated by gene-specific short-interfering RNA (siRNA) knockdown. A genome-wide search was performed to identify cMS-containing genes likely to generate NMD-resistant transcripts that could encode for antigenic expressed mutant proteins in MSI-High colon cancers. These genes were screened for cMS mutations in the MSI-High colon cancer cell lines. RESULTS: Mutant protein bands of expected molecular weight were detected in mutated MSI-High cell lines for NMD-resistant transcripts (CREBBP, EP300, TTK), but not NMD-sensitive transcripts (BAX, CASP5, MSH3). Expression of the mutant CREBBP and EP300 proteins was confirmed by siRNA knockdown. Five cMS-bearing genes identified from the genome-wide search and without existing mutation data (SFRS12IP1, MED8, ASXL1, FBXL3 and RGS12) were found to be mutated in at least 5 of 11 (45%) of the MSI-High cell lines tested. CONCLUSION: NMD-resistant transcripts can give rise to expressed mutant proteins in MSI-High colon cancer cells. If commonly expressed in primary MSI-High colon cancers, MSI-derived mutant proteins could be useful as cancer specific immunological targets in a vaccine targeting MSI-High colonic tumours