Halocercus lagenorhynchi infection in a stranded striped dolphin Stenella coeruleoalba (Meyen, 1833) on the Southwest coastline of India.

Necropsy on a striped dolphin Stenella coeruleoalba (Meyen, 1833) entangled in ghost fishing net and dead while rescuing yielded some helminth parasites, later identified as Halocercus lagenorhynchi. DNA barcoding of the host and parasite and the phylogenetic analysis of the parasite was conducted. This study provides valuable information towards establishing basal data of marine mammal parasite diversity and distribution in the Indian waters. We believe this is the first report of the occurrence of Halocercus lagenorhynchi in marine mammals in India.

H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity.

The H3K4 demethylase KDM5B is overexpressed in multiple cancer types, and elevated expression levels of KDM5B is associated with decreased survival. However, the underlying mechanistic contribution of dysregulated expression of KDM5B and H3K4 demethylation in cancer is poorly understood. Our results show that loss of KDM5B in multiple types of cancer cells leads to increased proliferation and elevated expression of cancer stem cell markers. In addition, we observed enhanced tumor formation following KDM5B depletion in a subset of representative cancer cell lines. Our findings also support a role for KDM5B in regulating epigenetic plasticity, where loss of KDM5B in cancer cells with elevated KDM5B expression leads to alterations in activity of chromatin states, which facilitate activation or repression of alternative transcriptional programs. In addition, we define KDM5B-centric epigenetic and transcriptional patterns that support cancer cell plasticity, where KDM5B depleted cancer cells exhibit altered epigenetic and transcriptional profiles resembling a more primitive cellular state. This study also provides a resource for evaluating associations between alterations in epigenetic patterning upon depletion of KDM5B and gene expression in a diverse set of cancer cells.

Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains.

Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.

CAMP: Collection of sequences and structures of antimicrobial peptides.

Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists databases of AMPs, information on structures of AMPs is limited in these databases. CAMP is manually curated and currently holds 6756 sequences and 682 3D structures of AMPs. Sequence and structure analysis tools have been incorporated to enhance the usefulness of the database.