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The purpose of the current project is to investigate whether we can detect treatment preference of different depression treatments from psychological and demographic features.

Hainan wildlife community questionnaire

Additional file 1. Heatmap depicting fold-changes of individual or combinatorial histone PTMs during sequential stages of spermatogenesis, i.e., meiotic to rounds spermatids (M-RS), round spermatids to elongating spermatids (RS-ES), and elongating spermatids to mature sperm (ES-Sp). Histone PTMs are ranked and ordered based on greatest fold increase in the ES to Sp transition by histone.

Additional file 5. Western blot validation of histone PTM analyzed by LC-MS/MS. Left: Acid extracted protein from male mouse germ cells exhibit similar levels of H3K27me3 and H4ac. Right Top: Western blot and coomassie stained protein gel of acid extracted histones from human sperm depicting variation in H3K9me3 between individuals, but not H4K20me2. Right Bottom: Western validation of H4K16ac in human sperm.

Additional file 4. DAPI staining of mouse testis germ cell fractions. Representative images of final pooled STAPUT fraction from WT male mice. Left: meiotic fraction, Center: round spermatid fraction, Right: Elongating and condensing fraction. Bottom: Pyrosequencing analysis of DNA methylation in mouse sperm. Average percent of CpGs methylated in paternally imprinted H19 and maternally imprinted Snrpn (ÂąSD).

Additional file 3. Variation in PTM abundance between individuals. Coefficient of variation for histone modifications on H3 and H4 with a total abundance >10 %.

Additional file 2. Relative abundance of additional histone PTMs on H3 in human sperm. Dotplot demonstrating relative abundance of individual and combinatorial PTMs on H3 in different individual sperm samples.

Global multiple regression linear mixed-effects kinship models incorporating all significant predictors ( P

Ranking of candidate models (representing all possible combinations of the five predictors in each global model) by AICc, along with relative log-likelihood (RLL), ΔAICc, and model Akaike weights ( w i ) for: a) home range and b) group size. (DOCX 25 kb)

Sources of gibbon comparative data for three response variables (home range, group size, mating system) by species and site (gibbon population). (DOCX 50Â kb)

During spermiogenesis, the post-meiotic phase of mammalian spermatogenesis, transcription is progressively repressed as nuclei of haploid spermatids are compacted through a dramatic chromatin reorganization involving hyper-acetylation and replacement of most histones with protamines. Although BRDT functions in transcription and histone removal in spermatids, it is unknown whether other BET family proteins play a role. Immunofluorescence of spermatogenic cells revealed BRD4 in a ring around the nuclei of spermatids containing hyper-acetylated histones. The ring lies directly adjacent to the acroplaxome, the cytoskeletal base of the acrosome, previously linked to chromatin reorganization. The BRD4 ring does not form in acrosomal mutant mice. ChIP sequencing in spermatids revealed enrichment of BRD4 and acetylated histones at the promoters of active genes. BRD4 and BRDT show distinct and synergistic binding patterns, with a pronounced enrichment of BRD4 at spermatogenesis-specific genes. Direct association of BRD4 with acetylated H4 decreases in late spermatids as acetylated histones are removed from the condensing nucleus in a wave following the progressing acrosome. These data provide evidence for a prominent transcriptional role of BRD4 and suggest a possible removal mechanism for chromatin components from the genome via the progressing acrosome as transcription is repressed in response to chromatin condensation during spermiogenesis.

Assessment of effect of phylogenetic uncertainty in the form of alternative tree topologies on phylogenetic signals within the Hylobatidae. (PDF 770Â kb)

Background: The maintenance, regulation, and dynamics of heterochromatin in the human malaria parasite, Plasmodium falciparum, has drawn increasing attention due to its regulatory role in mutually exclusive virulence gene expression and the silencing of key developmental regulators. The advent of genome-wide analyses such as chromatin-immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental in understanding chromatin composition; however, even in model organisms, ChIP-seq experiments are susceptible to intrinsic experimental biases arising from underlying chromatin structure. Methods: We performed a control ChIP-seq experiment, re-analyzed previously published ChIP-seq datasets and compared different analysis approaches to characterize biases of genome-wide analyses in P. falciparum. Results: We found that heterochromatic regions in input control samples used for ChIP-seq normalization are systematically underrepresented in regard to sequencing coverage across the P. falciparum genome. This underrepresentation, in combination with a non-specific or inefficient immunoprecipitation, can lead to the identification of false enrichment and peaks across these regions. We observed that such biases can also be seen at background levels in specific and efficient ChIP-seq experiments. We further report on how different read mapping approaches can also skew sequencing coverage within highly similar subtelomeric regions and virulence gene families. To ameliorate these issues, we discuss orthogonal methods that can be used to characterize bona fide chromatin-associated proteins. Conclusions: Our results highlight the impact of chromatin structure on genome-wide analyses in the parasite and the need for caution when characterizing chromatin-associated proteins and features.

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces., Gordon and Betty Moore Foundation (Grant 492.01), Gordon and Betty Moore Foundation (Grant 3777), United States. Environmental Protection Agency (STAR Fellowship)