Deciphering the Code for Retroviral Integration Target Site Selection

Upon cell invasion, retroviruses generate a DNA copy of their RNA genome and integrate retroviral cDNA within host chromosomal DNA. Integration occurs throughout the host cell genome, but target site selection is not random. Each subgroup of retrovirus is distinguished from the others by attraction to particular features on chromosomes. Despite extensive efforts to identify host factors that interact with retrovirion components or chromosome features predictive of integration, little is known about how integration sites are selected. We attempted to identify markers predictive of retroviral integration by exploiting Precision-Recall methods for extracting information from highly skewed datasets to derive robust and discriminating measures of association. ChIPSeq datasets for more than 60 factors were compared with 14 retroviral integration datasets. When compared with MLV, PERV or XMRV integration sites, strong association was observed with STAT1, acetylation of H3 and H4 at several positions, and methylation of H2AZ, H3K4, and K9. By combining peaks from ChIPSeq datasets, a supermarker was identified that localized within 2 kB of 75% of MLV proviruses and detected differences in integration preferences among different cell types. The supermarker predicted the likelihood of integration within specific chromosomal regions in a cell-type specific manner, yielding probabilities for integration into proto-oncogene LMO2 identical to experimentally determined values. The supermarker thus identifies chromosomal features highly favored for retroviral integration, provides clues to the mechanism by which retrovirus integration sites are selected, and offers a tool for predicting cell-type specific proto-oncogene activation by retroviruses

'I believe that the staff have reduced their closeness to patients': an exploratory study on the impact of HIV/AIDS on staff in four rural hospitals in Uganda

<p>Abstract</p> <p>Background</p> <p>Staff shortages could harm the provision and quality of health care in Uganda, so staff retention and motivation are crucial. Understanding the impact of HIV/AIDS on staff contributes to designing appropriate retention and motivation strategies. This research aimed 'to identify the influence of HIV/AIDS on staff working in general hospitals at district level in rural areas and to explore support required and offered to deal with HIV/AIDS in the workplace'. Its results were to inform strategies to mitigate the impact of HIV/AIDS on hospital staff.</p> <p>Methods</p> <p>A cross-sectional study with qualitative and quantitative components was implemented during two weeks in September 2005. Data were collected in two government and two faith-based private not-for-profit hospitals purposively selected in rural districts in Uganda's Central Region. Researchers interviewed 237 people using a structured questionnaire and held four focus group discussions and 44 in-depth interviews.</p> <p>Results</p> <p>HIV/AIDS places both physical and, to some extent, emotional demands on health workers. Eighty-six per cent of respondents reported an increased workload, with 48 per cent regularly working overtime, while 83 per cent feared infection at work, and 36 per cent reported suffering an injury in the previous year. HIV-positive staff remained in hiding, and most staff did not want to get tested as they feared stigmatization. Organizational responses were implemented haphazardly and were limited to providing protective materials and the HIV/AIDS-related services offered to patients. Although most staff felt motivated to work, not being motivated was associated with a lack of daily supervision, a lack of awareness on the availability of HIV/AIDS counselling, using antiretrovirals and working overtime. The specific hospital context influenced staff perceptions and experiences.</p> <p>Conclusion</p> <p>HIV/AIDS is a crucially important contextual factor, impacting on working conditions in various ways. Therefore, organizational responses should be integrated into responses to other problematic working conditions and adapted to the local context. Opportunities already exist, such as better use of supervision, educational sessions and staff meetings. However, exchanges on interventions to improve staff motivation and address HIV/AIDS in the health sector are urgently required, including information on results and details of the context and implementation process.</p

Oligonucleotide Sequence Motifs as Nucleosome Positioning Signals

To gain a better understanding of the sequence patterns that characterize positioned nucleosomes, we first performed an analysis of the periodicities of the 256 tetranucleotides in a yeast genome-wide library of nucleosomal DNA sequences that was prepared by in vitro reconstitution. The approach entailed the identification and analysis of 24 unique tetranucleotides that were defined by 8 consensus sequences. These consensus sequences were shown to be responsible for most if not all of the tetranucleotide and dinucleotide periodicities displayed by the entire library, demonstrating that the periodicities of dinucleotides that characterize the yeast genome are, in actuality, due primarily to the 8 consensus sequences. A novel combination of experimental and bioinformatic approaches was then used to show that these tetranucleotides are important for preferred formation of nucleosomes at specific sites along DNA in vitro. These results were then compared to tetranucleotide patterns in genome-wide in vivo libraries from yeast and C. elegans in order to assess the contributions of DNA sequence in the control of nucleosome residency in the cell. These comparisons revealed striking similarities in the tetranucleotide occurrence profiles that are likely to be involved in nucleosome positioning in both in vitro and in vivo libraries, suggesting that DNA sequence is an important factor in the control of nucleosome placement in vivo. However, the strengths of the tetranucleotide periodicities were 3–4 fold higher in the in vitro as compared to the in vivo libraries, which implies that DNA sequence plays less of a role in dictating nucleosome positions in vivo. The results of this study have important implications for models of sequence-dependent positioning since they suggest that a defined subset of tetranucleotides is involved in preferred nucleosome occupancy and that these tetranucleotides are the major source of the dinucleotide periodicities that are characteristic of positioned nucleosomes

Low Dosage of Histone H4 Leads to Growth Defects and Morphological Changes in Candida albicans

Chromatin function depends on adequate histone stoichiometry. Alterations in histone dosage affect transcription and chromosome segregation, leading to growth defects and aneuploidies. In the fungal pathogen Candida albicans, aneuploidy formation is associated with antifungal resistance and pathogenesis. Histone modifying enzymes and chromatin remodeling proteins are also required for pathogenesis. However, little is known about the mechanisms that generate aneuploidies or about the epigenetic mechanisms that shape the response of C. albicans to the host environment. Here, we determined the impact of histone H4 deficit in the growth and colony morphology of C. albicans. We found that C. albicans requires at least two of the four alleles that code for histone H4 (HHF1 and HHF22) to grow normally. Strains with only one histone H4 allele show a severe growth defect and unstable colony morphology, and produce faster-growing, morphologically stable suppressors. Segmental or whole chromosomal trisomies that increased wild-type histone H4 copy number were the preferred mechanism of suppression. This is the first study of a core nucleosomal histone in C. albicans, and constitutes the prelude to future, more detailed research on the function of histone H4 in this important fungal pathogen

Phosphatized early Cambrian archaeocyaths and small shelly fossils (SSFs) of southwestern Mongolia

Archaeocyaths are an enigmatic group of calcifying sponges prevalent in early Cambrian (Terreneuvian to Series 2) successions around the world and preserved predominantly in reefal buildups, but also in adjacent reworked deposits. Here we report exceptionally preserved phosphatized archaeocyaths and small shelly fossils from phosphatized reef flank deposits at the top of the Salaagol Formation of southwestern Mongolia. Recent chemostratigraphic age models suggest that these archaeocyaths are among the earliest reported in the Terreneuvian Stage 2 (Tommotian). These fossils provide a window into the mechanisms of archaeocyath phosphatization, a generally rare mode of archaeocyath preservation. To assess the composition and nature of phosphatization, fossil assemblages were examined in insoluble residue and thin section. These archaeocyaths are preserved as phosphatic internal molds in residue, and both phosphatized and unphosphatized archaeocyaths are present in thin section. The occurrence of internal molds and complementary mineralogical data suggest that the decay of organic material within the archaeocyaths created the necessary redox conditions for apatite nucleation. We propose that, shortly after death, this assemblage was transported to a deeper water environment, and that the presence of organic matter in a low oxygen setting led to abundant phosphatization of archaeocyaths

Phosphatized early Cambrian archaeocyaths and small shelly fossils (SSFs) of southwestern Mongolia

Archaeocyaths are an enigmatic group of calcifying sponges prevalent in early Cambrian (Terreneuvian to Series 2) successions around the world and preserved predominantly in reefal buildups, but also in adjacent reworked deposits. Here we report exceptionally preserved phosphatized archaeocyaths and small shelly fossils from phosphatized reef flank deposits at the top of the Salaagol Formation of southwestern Mongolia. Recent chemostratigraphic age models suggest that these archaeocyaths are among the earliest reported in the Terreneuvian Stage 2 (Tommotian). These fossils provide a window into the mechanisms of archaeocyath phosphatization, a generally rare mode of archaeocyath preservation. To assess the composition and nature of phosphatization, fossil assemblages were examined in insoluble residue and thin section. These archaeocyaths are preserved as phosphatic internal molds in residue, and both phosphatized and unphosphatized archaeocyaths are present in thin section. The occurrence of internal molds and complementary mineralogical data suggest that the decay of organic material within the archaeocyaths created the necessary redox conditions for apatite nucleation. We propose that, shortly after death, this assemblage was transported to a deeper water environment, and that the presence of organic matter in a low oxygen setting led to abundant phosphatization of archaeocyaths