Biogenesis of JC Polyomavirus Associated Extracellular Vesicles

JC polyomavirus (JCPyV) is a small, non-enveloped virus that persists in the kidney in about half the adult population. In severely immune-compromised individuals JCPyV causes the neurodegenerative disease progressive multifocal leukoencephalopathy (PML) in the brain. JCPyV has been shown to infect cells by both direct and indirect mechanisms, the latter involving extracellular vesicle (EV) mediated infection. While direct mechanisms of infection are well studied indirect EV mediated mechanisms are poorly understood. Using a combination of chemical and genetic approaches we show that several overlapping intracellular pathways are responsible for the biogenesis of virus containing EV. Here we show that targeting neutral sphingomyelinase 2 (nSMase2) with the drug cambinol decreased the spread of JCPyV over several viral life cycles. Genetic depletion of nSMase2 by either shRNA or CRISPR/Cas9 reduced EV-mediated infection. Individual knockdown of seven ESCRT-related proteins including HGS, ALIX, TSG101, VPS25, VPS20, CHMP4A, and VPS4A did not significantly reduce JCPyV associated EV (JCPyV(+) EV) infectivity, whereas knockdown of the tetraspanins CD9 and CD81 or trafficking and/or secretory autophagy-related proteins RAB8A, RAB27A, and GRASP65 all significantly reduced the spread of JCPyV and decreased EV-mediated infection. These findings point to a role for exosomes and secretory autophagosomes in the biogenesis of JCPyV associated EVs with specific roles for nSMase2, CD9, CD81, RAB8A, RAB27A, and GRASP65 proteins

Release of mineral-bound water prior to subduction tied to shallow seismogenic slip off Sumatra

Plate-boundary fault rupture during the 2004 Sumatra-Andaman subduction earthquake extended closer to the trench than expected, increasing earthquake and tsunami size. International Ocean Discovery Program Expedition 362 sampled incoming sediments offshore northern Sumatra, revealing recent release of fresh water within the deep sediments. Thermal modeling links this freshening to amorphous silica dehydration driven by rapid burial-induced temperature increases in the past 9 million years. Complete dehydration of silicates is expected before plate subduction, contrasting with prevailing models for subduction seismogenesis calling for fluid production during subduction. Shallow slip offshore Sumatra appears driven by diagenetic strengthening of deeply buried fault-forming sediments, contrasting with weakening proposed for the shallow Tohoku-Oki 2011 rupture, but our results are applicable to other thickly sedimented subduction zones including those with limited earthquake records

Slow slip source characterized by lithological and geometric heterogeneity

Slow slip events (SSEs) accommodate a significant proportion of tectonic plate motion at subduction zones, yet little is known about the faults that actually host them. The shallow depth (<2 km) of well-documented SSEs at the Hikurangi subduction zone offshore New Zealand offers a unique opportunity to link geophysical imaging of the subduction zone with direct access to incoming material that represents the megathrust fault rocks hosting slow slip. Two recent International Ocean Discovery Program Expeditions sampled this incoming material before it is entrained immediately down-dip along the shallow plate interface. Drilling results, tied to regional seismic reflection images, reveal heterogeneous lithologies with highly variable physical properties entering the SSE source region. These observations suggest that SSEs and associated slow earthquake phenomena are promoted by lithological, mechanical, and frictional heterogeneity within the fault zone, enhanced by geometric complexity associated with subduction of rough crust

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)

Biochar-Induced Changes in Soil Hydraulic Conductivity and Dissolved Nutrient Fluxes Constrained by Laboratory Experiments

<div><p>The addition of charcoal (or biochar) to soil has significant carbon sequestration and agronomic potential, making it important to determine how this potentially large anthropogenic carbon influx will alter ecosystem functions. We used column experiments to quantify how hydrologic and nutrient-retention characteristics of three soil materials differed with biochar amendment. We compared three homogeneous soil materials (sand, organic-rich topsoil, and clay-rich Hapludert) to provide a basic understanding of biochar-soil-water interactions. On average, biochar amendment decreased saturated hydraulic conductivity (<i>K</i>) by 92% in sand and 67% in organic soil, but increased <i>K</i> by 328% in clay-rich soil. The change in <i>K</i> for sand was not predicted by the accompanying physical changes to the soil mixture; the sand-biochar mixture was less dense and more porous than sand without biochar. We propose two hydrologic pathways that are potential drivers for this behavior: one through the interstitial biochar-sand space and a second through pores within the biochar grains themselves. This second pathway adds to the porosity of the soil mixture; however, it likely does not add to the effective soil <i>K</i> due to its tortuosity and smaller pore size. Therefore, the addition of biochar can increase or decrease soil drainage, and suggests that any potential improvement of water delivery to plants is dependent on soil type, biochar amendment rate, and biochar properties. Changes in dissolved carbon (C) and nitrogen (N) fluxes also differed; with biochar increasing the C flux from organic-poor sand, decreasing it from organic-rich soils, and retaining small amounts of soil-derived N. The aromaticity of C lost from sand and clay increased, suggesting lost C was biochar-derived; though the loss accounts for only 0.05% of added biochar-C. Thus, the direction and magnitude of hydraulic, C, and N changes associated with biochar amendments are soil type (composition and particle size) dependent.</p></div

The mean (and standard deviation) of physical, hydraulic, and nutrient properties of the three replicates of each soil and soil+biochar treatment.

<p>Two-tailed t-tests were conducted to determine statistical differences between control and +biochar treatments; p-values are shown in italics below mean and standard deviation values for each treatment.</p><p>The mean (and standard deviation) of physical, hydraulic, and nutrient properties of the three replicates of each soil and soil+biochar treatment.</p

Impact of biochar amendment on saturated soil hydraulic conductivity.

<p>The saturated hydraulic conductivity (<i>K</i>), as measured using falling head experiments, for six soil treatments over subsequent flushing events: (a) sand and sand+biochar, (b) organic and organic+biochar, and (c) clay and clay+biochar. Note: the different soil treatment flushing events varied in duration with the clay (c) taking up to 10× longer to drain than the sand (a) or organic soil (b). Saturated hydraulic conductivity data and flushing duration for each flushing experiment available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108340#pone.0108340.s001" target="_blank">Table S1</a>.</p

A comparison of studies that examined the impact of biochar amendments on soil saturated hydraulic conductivity (<i>K</i>) and bulk density (ρ_d).

a<p> Biochar application rate reported in paper.</p>b<p> Biochar application rate converted using bulk density of soils or column materials provided in the paper and assuming tillage depth of 10 cm.</p><p>NR: not reported.</p><p>NA: not applicable.</p><p>Biochar amendment rates are provided two ways: the units provided by the study and in tons biochar ha⁻¹. The conversion assumed a tillage depth of 10 cm and the bulk density of the soil or column materials provided in the paper. Studies are organized by soil type, top to bottom: organic-rich soils, clay- and silt-rich soils, and sandy soils. Results from this study are in italics.</p><p>A comparison of studies that examined the impact of biochar amendments on soil saturated hydraulic conductivity (<i>K</i>) and bulk density (ρ_d).</p