Shared genetic risk between eating disorder- and substance-use-related phenotypes:Evidence from genome-wide association studies

First published: 16 February 202

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments

Sediments within the Okinawa back-arc basin overlay a subsurface hydrothermal network, creating intense temperature gradients with sediment depth and potential limits for microbial diversity. We investigated taxonomic changes across 45 m of recovered core with a temperature gradient of 3°C/m from the dynamic Iheya North Hydrothermal System. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay at 10 meters below seafloor (mbsf). Here, we present taxonomic results from an analysis of the 16S rRNA gene that support a conceptual model in which common marine subsurface taxa persist into the subsurface, while high temperature adapted archaeal taxa show localized peaks in abundances in the hydrothermal clay horizons. Specifically, the bacterial phylum Chloroflexi accounts for a major proportion of the total microbial community within the upper 10 mbsf, whereas high temperature archaea (Terrestrial Hot Spring Crenarchaeotic Group and methanotrophic archaea) appear in varying local abundances in deeper, hydrothermal clay horizons with higher in situ temperatures (up to 55°C, 15 mbsf). In addition, geochemical evidence suggests that methanotrophy may be occurring in various horizons. There is also relict DNA (i.e., DNA preserved after cell death) that persists in horizons where the conditions suitable for microbial communities have ceased

Novel degenerate PCR method for whole genome amplification applied to Peru Margin (ODP Leg 201) subsurface samples

A degenerate PCR-based method of whole-genome amplification, designed to work fluidly with 454 sequencing technology, was developed and tested for use on deep marine subsurface DNA samples. The method, which we have called Random Amplification Metagenomic PCR (RAMP), involves the use of specific primers from Roche 454 amplicon sequencing, modified by the addition of a degenerate region at the 3’ end. It utilizes a PCR reaction, which resulted in no amplification from blanks, even after 50 cycles of PCR. After efforts to optimize experimental conditions, the method was tested with DNA extracted from cultured E. coli cells, and genome coverage was estimated after sequencing on three different occasions. Coverage did not vary greatly with the different experimental conditions tested, and was around 62% with a sequencing effort equivalent to a theoretical genome coverage of 14.10X. The GC content of the sequenced amplification product was within 2% of the predicted values for this strain of E. coli. The method was also applied to DNA extracted from marine subsurface samples from ODP Leg 201 site 1229 (Peru Margin), and results of a taxonomic analysis revealed microbial communities dominated by Proteobacteria, Chloroflexi, Firmicutes, Euryarchaeota, and Crenarchaeota, among others. These results were similar to those obtained previously for those samples; however, variations in the proportions of taxa show that community analysis can be sensitive to both the amplification technique used and the method of assigning sequences to taxonomic groups. Overall, we find that RAMP represents a valid methodology for amplifying metagenomes from low biomass samples

Integration Sites Obtained from the Three Donors.

Integration Sites Obtained from the Three Donors.</p

Overall stabilities of clones of infected and uninfected T cells.

For each pair of time points for each donor, we determined the differences in the sizes of the each of clones in the dataset. For the comparisons of the differences in the sizes of the clones of infected cells, the 100 largest clones were used and the sizes of the clones were determined as described in the S1 Text. For the uninfected cells, a dataset of clones of a similar size was compiled, and the stability calculations were done using randomly sampled groups of 100 uninfected clones. The uncertainties in the measured sizes of the clones in each of the datasets was determined by doing a within dataset comparisons which are shown in the figure as comparisons for the same time points. The uncertainties within each of the datasets and between the datasets are shown both as a box plot (which shows the standard deviation) and as the 95% confidence limits (marked by horizontal lines separated by a dashed vertical line). The mean is the bar in the middle of the box plots. Any data from the 10,000 runs that falls outside the 95% confidence limits are shown as open circles. The method of calculating the uncertainties is described in the S1 Text. The size differences were combined to obtain a measure of the overall differences in the sizes of the group of clones for the time points being compared. The overall measure of the combined differences in the sizes of the clones, given on the Y axis, provide a good measure of the overall differences in the sizes of the clones, but the numbers on the Y axis do represent a simple metric.</p

Data Analysis.

(DOCX)</p

Stabilities of individual clones of infected and uninfected cells from the three donors.

For each donor, the data for the largest 100 clones of infected T cells are shown for either two or three time points. Stability data are also shown for the same number of clones of uninfected T cells of a similar size, chosen at random from the much larger TCR dataset. Because a significant fraction of the clones of uninfected cells were not detected at all the time points, we also analyzed the stabilities of clones of uninfected T cells for each donor using only data for clones of uninfected cells that were present at all the time points in the analysis. For F-07, there are data for the infected T cells clones from three time points. For the uninfected cells, there are data for only two of those time points. (TIF)</p

Demographics and Clinical Characteristics of Donors with Non-Suppressible Viremia on Antiretroviral Therapy (ART).

Demographics and Clinical Characteristics of Donors with Non-Suppressible Viremia on Antiretroviral Therapy (ART).</p

Integration Sites Recovered and Numbers of Infected Clones.

Integration Sites Recovered and Numbers of Infected Clones.</p

Scatter plots showing the stabilities of clones of infected and uninfected CD4+ T cells.

Each panel shows the sizes of the 20 largest clones of infected T cells (blue triangles) and the sizes of 200 clones of uninfected T cells of a similar size at two different times. The dotted line is the diagonal. Any clone whose size does not change between the time points shown on the axes would fall on this diagonal. Similarly, the change in the sizes of each of the clones can be measured by the distance from the diagonal. Each panel (A-E) shows a comparison for two time points; the donors and the times are noted in each of the panels.</p