Intraseasonal Dynamics and Dominant Sequences in H3N2 Influenza

Long-term influenza evolution has been well studied, but the patterns of sequence diversity within seasons are less clear. H3N2 influenza genomes sampled from New York State over ten years indicated intraseasonal changes in evolutionary dynamics. Using the mean Hamming distance of a set of amino acid or nucleotide sequences as an indicator of its diversity, we found that influenza sequence diversity was significantly higher during the early epidemic period than later in the influenza season. Diversity was lowest during the peak of the epidemic, most likely due to the high prevalence of a single dominant amino acid sequence or very few dominant sequences during the peak epidemic period, corresponding with rapid expansion of the viral population. The frequency and duration of dominant sequences varied by influenza protein, but all proteins had an abundance of one distinct sequence during the peak epidemic period. In New York State from 1995 to 2005, high sequence diversity during the early epidemic suggested that seasonal antigenic drift could have occurred primarily in this period, followed by a clonal expansion of typically one clade during the peak of the epidemic, possibly indicating a shift to neutral drift or purifying selection

Thermal counterflow in a periodic channel with solid boundaries

We perform numerical simulations of finite temperature quantum turbulence produced through thermal counterflow in superfluid 4He, using the vortex filament model. We investigate the effects of solid boundaries along one of the Cartesian directions, assuming a laminar normal fluid with a Poiseuille velocity profile, whilst varying the temperature and the normal fluid velocity. We analyze the distribution of the quantized vortices, reconnection rates, and quantized vorticity production as a function of the wall-normal direction. We find that the quantized vortex lines tend to concentrate close to the solid boundaries with their position depending only on temperature and not on the counterflow velocity. We offer an explanation of this phenomenon by considering the balance of two competing effects, namely the rate of turbulent diffusion of an isotropic tangle near the boundaries and the rate of quantized vorticity production at the center. Moreover, this yields the observed scaling of the position of the peak vortex line density with the mutual friction parameter. Finally, we provide evidence that upon the transition from laminar to turbulent normal fluid flow, there is a dramatic increase in the homogeneity of the tangle, which could be used as an indirect measure of the transition to turbulence in the normal fluid component for experiments

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus

Background: The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites. Results: The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules. Conclusions: The draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders

Characterization of organic aerosol across the global remote troposphere: A comparison of ATom measurements and global chemistry models

The spatial distribution and properties of submicron organic aerosol (OA) are among the key sources of uncertainty in our understanding of aerosol effects on climate. Uncertainties are particularly large over remote regions of the free troposphere and Southern Ocean, where very few data have been available and where OA predictions from AeroCom Phase II global models span 2 to 3 orders of magnitude, greatly exceeding the model spread over source regions. The (nearly) pole-to-pole vertical distribution of nonrefractory aerosols was measured with an aerosol mass spectrometer onboard the NASA DC-8 aircraft as part of the Atmospheric Tomography (ATom) mission during the Northern Hemisphere summer (August 2016) and winter (February 2017). This study presents the first extensive characterization of OA mass concentrations and their level of oxidation in the remote atmosphere. OA and sulfate are the major contributors by mass to submicron aerosols in the remote troposphere, together with sea salt in the marine boundary layer. Sulfate was dominant in the lower stratosphere. OA concentrations have a strong seasonal and zonal variability, with the highest levels measured in the lower troposphere in the summer and over the regions influenced by biomass burning from Africa (up to 10 μgsm-3). Lower concentrations (~ 0:1 0.3 μgsm-3) are observed in the northern middle and high latitudes and very low concentrations (< 0:1 μgsm-3) in the southern middle and high latitudes. The ATom dataset is used to evaluate predictions of eight current global chemistry models that implement a variety of commonly used representations of OA sources and chemistry, as well as of the AeroCom-II ensemble. The current model ensemble captures the average vertical and spatial distribution of measured OA concentrations, and the spread of the individual models remains within a factor of 5. These results are significantly improved over the AeroCom-II model ensemble, which shows large overestimations over these regions. However, some of the improved agreement with observations occurs for the wrong reasons, as models have the tendency to greatly overestimate the primary OA fraction and underestimate the sec-ondary fraction. Measured OA in the remote free troposphere is highly oxygenated, with organic aerosol to organic carbon (OA= OC) ratios of ~ 2.2 2.8, and is 30 % 60% more oxygenated than in current models, which can lead to significant errors in OA concentrations. The model measurement comparisons presented here support the concept of a more dynamic OA system as proposed by Hodzic et al. (2016), with enhanced removal of primary OA and a stronger production of secondary OA in global models needed to provide better agreement with observations. © 2020 IEEE Computer Society. All rights reserved

Ambient aerosol properties in the remote atmosphere from global-scale in-situ measurements

In situ measurements of aerosol microphysical, chemical, and optical properties were made during global-scale flights from 2016–2018 as part of the Atmospheric Tomography Mission (ATom). The NASA DC-8 aircraft flew from ∼ 84∘ N to ∼ 86∘ S latitude over the Pacific, Atlantic, Arctic, and Southern oceans while profiling nearly continuously between altitudes of ∼ 160 m and ∼ 12 km. These global circuits were made once each season. Particle size distributions measured in the aircraft cabin at dry conditions and with an underwing probe at ambient conditions were combined with bulk and single-particle composition observations and measurements of water vapor, pressure, and temperature to estimate aerosol hygroscopicity and hygroscopic growth factors and calculate size distributions at ambient relative humidity. These reconstructed, composition-resolved ambient size distributions were used to estimate intensive and extensive aerosol properties, including single-scatter albedo, the asymmetry parameter, extinction, absorption, Ångström exponents, and aerosol optical depth (AOD) at several wavelengths, as well as cloud condensation nuclei (CCN) concentrations at fixed supersaturations and lognormal fits to four modes. Dry extinction and absorption were compared with direct in situ measurements, and AOD derived from the extinction profiles was compared with remotely sensed AOD measurements from the ground-based Aerosol Robotic Network (AERONET); this comparison showed no substantial bias. The purpose of this work is to describe the methodology by which ambient aerosol properties are estimated from the in situ measurements, provide statistical descriptions of the aerosol characteristics of different remote air mass types, examine the contributions to AOD from different aerosol types in different air masses, and provide an entry point to the ATom aerosol database. The contributions of different aerosol types (dust, sea salt, biomass burning, etc.) to AOD generally align with expectations based on location of the profiles relative to continental sources of aerosols, with sea salt and aerosol water dominating the column extinction in most remote environments and dust and biomass burning (BB) particles contributing substantially to AOD, especially downwind of the African continent. Contributions of dust and BB aerosols to AOD were also significant in the free troposphere over the North Pacific. Comparisons of lognormally fitted size distribution parameters to values in the Optical Properties of Aerosols and Clouds (OPAC) database commonly used in global models show significant differences in the mean diameters and standard deviations for accumulation-mode particles and coarse-mode dust. In contrast, comparisons of lognormal parameters derived from the ATom data with previously published shipborne measurements in the remote marine boundary layer show general agreement. The dataset resulting from this work can be used to improve global-scale representation of climate-relevant aerosol properties in remote air masses through comparison with output from global models and assumptions used in retrievals of aerosol properties from both ground-based and satellite remote sensing

The Fate of miRNA* Strand through Evolutionary Analysis: Implication for Degradation As Merely Carrier Strand or Potential Regulatory Molecule?

BACKGROUND: During typical microRNA (miRNA) biogenesis, one strand of a approximately 22 nt RNA duplex is preferentially selected for entry into a silencing complex, whereas the other strand, known as the passenger strand or miRNA* strand, is degraded. Recently, some miRNA* sequences were reported as guide miRNAs with abundant expression. Here, we intended to discover evolutionary implication of the fate of miRNA* strand by analyzing miRNA/miRNA* sequences across vertebrates. PRINCIPAL FINDINGS: Mature miRNAs based on gene families were well conserved especially for their seed sequences across vertebrates, while their passenger strands always showed various divergence patterns. The divergence mainly resulted from divergence of different animal species, homologous miRNA genes and multicopy miRNA hairpin precursors. Some miRNA* sequences were phylogenetically conserved in seed and anchor sequences similar to mature miRNAs, while others revealed high levels of nucleotide divergence despite some of their partners were highly conserved. Most of those miRNA precursors that could generate abundant miRNAs from both strands always were well conserved in sequences of miR-#-5p and miR-#-3p, especially for their seed sequences. CONCLUSIONS: The final fate of miRNA* strand, either degraded as merely carrier strand or expressed abundantly as potential functional guide miRNA, may be destined across evolution. Well-conserved miRNA* strands, particularly conservation in seed sequences, maybe afford potential opportunities for contributing to regulation network. The study will broaden our understanding of potential functional miRNA* species

Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins

DEF-like and GLO-like class B floral homeotic genes encode closely related MADS-domain transcription factors that act as developmental switches involved in specifying the identity of petals and stamens during flower development. Class B gene function requires transcriptional upregulation by an autoregulatory loop that depends on obligate heterodimerization of DEF-like and GLO-like proteins. Because switch-like behavior of gene expression can be displayed by single genes already, the functional relevance of this complex circuitry has remained enigmatic. On the basis of a stochastic in silico model of class B gene and protein interactions, we suggest that obligate heterodimerization of class B floral homeotic proteins is not simply the result of neutral drift but enhanced the robustness of cell-fate organ identity decisions in the presence of stochastic noise. This finding strongly corroborates the view that the appearance of this regulatory mechanism during angiosperm phylogeny led to a canalization of flower development and evolution

Mycobacterium marinum antagonistically induces an autophagic response while repressing the autophagic flux in a TORC1- and ESX-1-dependent manner.

Autophagy is a eukaryotic catabolic process also participating in cell-autonomous defence. Infected host cells generate double-membrane autophagosomes that mature in autolysosomes to engulf, kill and digest cytoplasmic pathogens. However, several bacteria subvert autophagy and benefit from its machinery and functions. Monitoring infection stages by genetics, pharmacology and microscopy, we demonstrate that the ESX-1 secretion system of Mycobacterium marinum, a close relative to M. tuberculosis, upregulates the transcription of autophagy genes, and stimulates autophagosome formation and recruitment to the mycobacteria-containing vacuole (MCV) in the host model organism Dictyostelium. Antagonistically, ESX-1 is also essential to block the autophagic flux and deplete the MCV of proteolytic activity. Activators of the TORC1 complex localize to the MCV in an ESX-1-dependent manner, suggesting an important role in the manipulation of autophagy by mycobacteria. Our findings suggest that the infection by M. marinum activates an autophagic response that is simultaneously repressed and exploited by the bacterium to support its survival inside the MCV

TOI-3235 b: a transiting giant planet around an M4 dwarf star

We present the discovery of TOI-3235 b, a short-period Jupiter orbiting an M-dwarf with a stellar mass close to the critical mass at which stars transition from partially to fully convective. TOI-3235 b was first identified as a candidate from TESS photometry, and confirmed with radial velocities from ESPRESSO, and ground-based photometry from HATSouth, MEarth-South, TRAPPIST-South, LCOGT, and ExTrA. We find that the planet has a mass of $\mathrm{0.665\pm0.025\,M_J}$ and a radius of $\mathrm{1.017\pm0.044\,R_J}$. It orbits close to its host star, with an orbital period of $\mathrm{2.5926\,d}$, but has an equilibrium temperature of $\mathrm{\approx 604 \, K}$, well below the expected threshold for radius inflation of hot Jupiters. The host star has a mass of $\mathrm{0.3939\pm0.0030\,M_\odot}$, a radius of $\mathrm{0.3697\pm0.0018\,R_\odot}$, an effective temperature of $\mathrm{3389 \, K}$, and a J-band magnitude of $\mathrm{11.706\pm0.025}$. Current planet formation models do not predict the existence of gas giants such as TOI-3235 b around such low-mass stars. With a high transmission spectroscopy metric, TOI-3235 b is one of the best-suited giants orbiting M-dwarfs for atmospheric characterization.Comment: 15 pages, 4 figures. Accepted for publication in APJ

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy