Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions

The trans-ancestral genomic architecture of glycemic traits

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 x 10(-8)), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution. A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Chronic Effects of Coated Silver Nanoparticles on Marine Invertebrate Larvae: A Proof of Concept Study.

Silver nanoparticles (AgNPs), owing to their unique physical and chemical properties, have become increasingly popular in consumer products. However, data on their potential biological effects on marine organisms, especially invertebrates, remain very limited. This proof of principle study reports the chronic sub-lethal toxicity of two coated AgNPs (oleic acid coated AgNPs and polyvinylpyrrolidone coated AgNPs) on marine benthic invertebrate larvae across three phyla (i.e., the barnacle Balanus Amphitrite, the slipper-limpet Crepidula onyx, and the polychaete Hydroides elegans) in terms of growth, development, and metamorphosis. Bioaccumulation and biodistribution of silver were also investigated. Larvae were also exposed to silver nitrate (AgNO3) in parallel to distinguish the toxic effects derived from nano-silver and the aqueous form of silver. The sub-lethal effect of chronic exposure to coated AgNPs resulted in a significant retardation in growth and development, and reduction of larval settlement rate. The larval settlement rate of H. elegans was significantly lower in the coated AgNP treatment than the AgNO3 treatment, suggesting that the toxicity of coated AgNPs might not be solely evoked by the release of silver ions (Ag+) in the test medium. The three species accumulated silver effectively from coated AgNPs as well as AgNO3, and coated AgNPs were observed in the vacuoles of epithelial cell in the digestive tract of C. onyx. Types of surface coatings did not affect the sub-lethal toxicity of AgNPs. This study demonstrated that coated AgNPs exerted toxic effects in a species-specific manner, and their exposure might allow bioaccumulation of silver, and affect growth, development, and settlement of marine invertebrate larvae. This study also highlighted the possibility that coated AgNPs could be taken up through diet and the toxicity of coated AgNPs might be mediated through toxic Ag+ as well as the novel modalities of coated AgNPs

Particle size distribution by frequency percent of total particle volume and cumulative percentage of size classes.

<p>The individual graphs demonstrate the particles size of OAgNPs (A) and PAgNPs (B) counted using transmission electronic microscope (No. of particle counted = 106).</p

Effect of OAgNPs, PAgNPs and AgNO₃ on the cumulative molts per larva of <i>B</i>. <i>amphitrite</i> on Day 5.

<p>Each bar represents the mean (+ SD) of four replicates. One-way ANOVA was used for the statistics analysis. Different letters above the bar indicate the means that are significantly different as identified by Tukey’s test. Ctrl: FSW control, SN: AgNO₃, O: OAgNP and P: PAgNP.</p

Concentration of silver released from coated AgNPs mixed in filter seawater at 10 and 100 μg L^-1.

<p>OAgNPs at 10 μg L^<b>-1</b> (O10; open triangle) and 100 μg L^<b>-1</b> (O100; filled triangle). PAgNPs at 10 μg L^<b>-1</b> (P10; open circle) and 100 μg L^<b>-1</b> (P100; filled circle). Samples were collected every 24 h followed by ultracentrifugation for silver measurement using inductively coupled plasma-optical emission spectrometer. Each data point represents the mean (± SD) of duplicate.</p

TEM micrographs of coated AgNP localization in <i>C</i>. <i>onyx</i> larva.

<p>Coated AgNPs were found in the intestine region of <i>C</i>. <i>onyx</i> treated with 100 μg L^<b>-1</b> of PAgNPs. Particles are visible in the intestine as black dots indicated by arrow. They are also observed to pass through the plasma membrane and deposit next to the microvilli (A) and in the vacuole (B). Gl: gut lumen; Mv: microvilli; Pm: plasma membrane. Scale bars: 0.5 μm. (C) is the EDS spectrum showing the presence of silver.</p

Total silver uptake (μg g^-1 dw) by <i>C</i>. <i>gracilis</i> (A) and <i>I</i>. <i>galbana</i> (B) after 24 h of exposure.

<p>Each bar represents the mean (+ SD) of triplicates. One-way ANOVA was used for the statistics analysis. Significant different between FSW control and treatments was identified by Tukey’s test; *: <i>p</i> < 0.05; ***: <i>p</i> < 0.001. Ctrl: FSW control, SN: AgNO₃, O: OAgNP and P: PAgNP.</p