Gliotoxin, identified from a screen of fungal metabolites, disrupts 7SK snRNP, releases P-TEFb, and reverses HIV-1 latency

A leading pharmacological strategy toward HIV cure requires "shock" or activation of HIV gene expression in latently infected cells with latency reversal agents (LRAs) followed by their subsequent clearance. In a screen for novel LRAs, we used fungal secondary metabolites as a source of bioactive molecules. Using orthogonal mass spectrometry (MS) coupled to latency reversal bioassays, we identified gliotoxin (GTX) as a novel LRA. GTX significantly induced HIV-1 gene expression in latent ex vivo infected primary cells and in CD4+ T cells from all aviremic HIV-1+ participants. RNA sequencing identified 7SK RNA, the scaffold of the positive transcription elongation factor b (P-TEFb) inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex, to be significantly reduced upon GTX treatment of CD4+ T cells. GTX directly disrupted 7SK snRNP by targeting La-related protein 7 (LARP7), releasing active P-TEFb, which phosphorylated RNA polymerase II (Pol II) C-terminal domain (CTD), inducing HIV transcription

The Calculus of Committee Composition

Modern institutions face the recurring dilemma of designing accurate evaluation procedures in settings as diverse as academic selection committees, social policies, elections, and figure skating competitions. In particular, it is essential to determine both the number of evaluators and the method for combining their judgments. Previous work has focused on the latter issue, uncovering paradoxes that underscore the inherent difficulties. Yet the number of judges is an important consideration that is intimately connected with the methodology and the success of the evaluation. We address the question of the number of judges through a cost analysis that incorporates the accuracy of the evaluation method, the cost per judge, and the cost of an error in decision. We associate the optimal number of judges with the lowest cost and determine the optimal number of judges in several different scenarios. Through analytical and numerical studies, we show how the optimal number depends on the evaluation rule, the accuracy of the judges, the (cost per judge)/(cost per error) ratio. Paradoxically, we find that for a panel of judges of equal accuracy, the optimal panel size may be greater for judges with higher accuracy than for judges with lower accuracy. The development of any evaluation procedure requires knowledge about the accuracy of evaluation methods, the costs of judges, and the costs of errors. By determining the optimal number of judges, we highlight important connections between these quantities and uncover a paradox that we show to be a general feature of evaluation procedures. Ultimately, our work provides policy-makers with a simple and novel method to optimize evaluation procedures

Accuracy of Using Visual Identification of White Sharks to Estimate Residency Patterns

Determining the residency of an aquatic species is important but challenging and it remains unclear what is the best sampling methodology. Photo-identification has been used extensively to estimate patterns of animals' residency and is arguably the most common approach, but it may not be the most effective approach in marine environments. To examine this, in 2005, we deployed acoustic transmitters on 22 white sharks (Carcharodon carcharias) in Mossel Bay, South Africa to quantify the probability of detecting these tagged sharks by photo-identification and different deployment strategies of acoustic telemetry equipment. Using the data collected by the different sampling approaches (detections from an acoustic listening station deployed under a chumming vessel versus those from visual sightings and photo-identification), we quantified the methodologies' probability of detection and determined if the sampling approaches, also including an acoustic telemetry array, produce comparable results for patterns of residency. Photo-identification had the lowest probability of detection and underestimated residency. The underestimation is driven by various factors primarily that acoustic telemetry monitors a large area and this reduces the occurrence of false negatives. Therefore, we propose that researchers need to use acoustic telemetry and also continue to develop new sampling approaches as photo-identification techniques are inadequate to determine residency. Using the methods presented in this paper will allow researchers to further refine sampling approaches that enable them to collect more accurate data that will result in better research and more informed management efforts and policy decisions

Rationality, Irrationality and Escalating Behavior in Lowest Unique Bid Auctions

Information technology has revolutionized the traditional structure of markets. The removal of geographical and time constraints has fostered the growth of online auction markets, which now include millions of economic agents worldwide and annual transaction volumes in the billions of dollars. Here, we analyze bid histories of a little studied type of online auctions – lowest unique bid auctions. Similarly to what has been reported for foraging animals searching for scarce food, we find that agents adopt Lévy flight search strategies in their exploration of “bid space”. The Lévy regime, which is characterized by a power-law decaying probability distribution of step lengths, holds over nearly three orders of magnitude. We develop a quantitative model for lowest unique bid online auctions that reveals that agents use nearly optimal bidding strategies. However, agents participating in these auctions do not optimize their financial gain. Indeed, as long as there are many auction participants, a rational profit optimizing agent would choose not to participate in these auction markets

Concentration Independent Modulation of Local Micromechanics in a Fibrin Gel

Methods for tuning extracellular matrix (ECM) mechanics in 3D cell culture that rely on increasing the concentration of either protein or cross-linking molecules fail to control important parameters such as pore size, ligand density, and molecular diffusivity. Alternatively, ECM stiffness can be modulated independently from protein concentration by mechanically loading the ECM. We have developed a novel device for generating stiffness gradients in naturally derived ECMs, where stiffness is tuned by inducing strain, while local mechanical properties are directly determined by laser tweezers based active microrheology (AMR). Hydrogel substrates polymerized within 35 mm diameter Petri dishes are strained non-uniformly by the precise rotation of an embedded cylindrical post, and exhibit a position-dependent stiffness with little to no modulation of local mesh geometry. Here we present the device in the context of fibrin hydrogels. First AMR is used to directly measure local micromechanics in unstrained hydrogels of increasing fibrin concentration. Changes in stiffness are then mapped within our device, where fibrin concentration is held constant. Fluorescence confocal imaging and orbital particle tracking are used to quantify structural changes in fibrin on the micro and nano levels respectively. The micromechanical strain stiffening measured by microrheology is not accompanied by ECM microstructural changes under our applied loads, as measured by confocal microscopy. However, super-resolution orbital tracking reveals nanostructural straightening, lengthening, and reduced movement of fibrin fibers. Furthermore, we show that aortic smooth muscle cells cultured within our device are morphologically sensitive to the induced mechanical gradient. Our results demonstrate a powerful cell culture tool that can be used in the study of mechanical effects on cellular physiology in naturally derived 3D ECM tissues

Tundra uptake of atmospheric elemental mercury drives Arctic mercury pollution

Anthropogenic activities have led to large-scale mercury (Hg) pollution in the Arctic. It has been suggested that sea-salt-induced chemical cycling of Hg (through 'atmospheric mercury depletion events', or AMDEs) and wet deposition via precipitation are sources of Hg to the Arctic in its oxidized form (Hg(ii)). However, there is little evidence for the occurrence of AMDEs outside of coastal regions, and their importance to net Hg deposition has been questioned. Furthermore, wet-deposition measurements in the Arctic showed some of the lowest levels of Hg deposition via precipitation worldwide, raising questions as to the sources of high Arctic Hg loading. Here we present a comprehensive Hg-deposition mass-balance study, and show that most of the Hg (about 70%) in the interior Arctic tundra is derived from gaseous elemental Hg (Hg(0)) deposition, with only minor contributions from the deposition of Hg(ii) via precipitation or AMDEs. We find that deposition of Hg(0)-the form ubiquitously present in the global atmosphere-occurs throughout the year, and that it is enhanced in summer through the uptake of Hg(0) by vegetation. Tundra uptake of gaseous Hg(0) leads to high soil Hg concentrations, with Hg masses greatly exceeding the levels found in temperate soils. Our concurrent Hg stable isotope measurements in the atmosphere, snowpack, vegetation and soils support our finding that Hg(0) dominates as a source to the tundra. Hg concentration and stable isotope data from an inland-to-coastal transect show high soil Hg concentrations consistently derived from Hg(0), suggesting that the Arctic tundra might be a globally important Hg sink. We suggest that the high tundra soil Hg concentrations might also explain why Arctic rivers annually transport large amounts of Hg to the Arctic Ocean

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field