Characterization of CD41 cells in the lymph node.

Lymph nodes (LNs) are the critical sites of immunity, and the stromal cells of LNs are crucial to their function. Our understanding of the stromal compartment of the LN has deepened recently with the characterization of nontraditional stromal cells. CD41 (integrin αIIb) is known to be expressed by platelets and hematolymphoid cells.

Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.

Background: Multiple sclerosis (MS) is an autoimmune condition of the central nervous system with a well-characterized genetic background. Prior analyses of MS genetics have identified broad enrichments across peripheral immune cells, yet the driver immune subsets are unclear.

Results: We utilize chromatin accessibility data across hematopoietic cells to identify cell type-specific enrichments of MS genetic signals.

DNA methylation profiles unique to Kalahari KhoeSan individuals.

Genomes of KhoeSan individuals of the Kalahari Desert provide the greatest understanding of single nucleotide diversity in the human genome. Compared with individuals in industrialized environments, the KhoeSan have a unique foraging and hunting lifestyle. Given these dramatic environmental differences, and the responsiveness of the methylome to environmental exposures of many types, we hypothesized that DNA methylation patterns would differ between KhoeSan and neighbouring agropastoral and/or industrial Bantu.

MethylToSNP: identifying SNPs in Illumina DNA methylation array data.

Background: Current array-based methods for the measurement of DNA methylation rely on the process of sodium bisulfite conversion to differentiate between methylated and unmethylated cytosine bases in DNA. In the absence of genotype data this process can lead to ambiguity in data interpretation when a sample has polymorphisms at a methylation probe site. A common way to minimize this problem is to exclude such potentially problematic sites, with some methods removing as much as 60% of array probes from consideration before data analysis.

Characterization of Trichodesmium-associated viral communities in the eastern Gulf of Mexico.

Trichodesmium surface aggregations shape the co-occurring microbial community by providing organic carbon and nitrogen and surfaces on which microorganisms can aggregate. Rapid collapse of Trichodesmium aggregations leads to drastic changes in the chemical and physical properties of surrounding waters, eliciting a response from the microbial community and their associated viruses. Three viral metagenomes were constructed from experimentally lysed Trichodesmium collected from two locations in the eastern Gulf of Mexico.

Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes.

Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e.

Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes.

Microbial consortia confer important benefits to animal and plant hosts, and model associations are necessary to examine these types of host/microbe interactions. The accessory nidamental gland (ANG) is a female reproductive organ found among cephalopod mollusks that contains a consortium of bacteria, the exact function of which is unknown. To begin to understand the role of this organ, the bacterial consortium was characterized in the Hawaiian bobtail squid, Euprymna scolopes, a well-studied model organism for symbiosis research.