bluuebunny/crossref_metadata_2025 huggingface dataset:
Diastolic Dysfunction Accompanies Alterations in Myocardial Structure, Cellular Composition and Macrophage Polarization in Survivors of Ionizing Radiation Exposure
Authors: Michalson Kristofer T. , Dugan Gregory O. , Caudell David L. , Cline J. Mark , Kitzman Dalane W. , Register Thomas C.
Published: February 2020

Rationale

Radiation induced heart disease (RIHD) is a significant delayed/late effect of ionizing radiation exposure.

Objective

To determine the cardiac effects of total body irradiation (TBI) in male rhesus macaques, a translational non-human primate (NHP) model.

Methods and Results

Echocardiography was performed on survivors of a single dose (6.4-8.5 Gy) of TBI (n=34) and non-irradiated controls (n=26) divided into longer (LT IRR) and shorter term (ST IRR) survivors and controls to assess the effects of time since TBI on phenotypes. LT IRR had increased Doppler transmitral early filling velocities (E), decreased early mitral annular descent velocities (e’), and higher E/e’ ratio compared to LT CTL (all p≤0.05), indicating left ventricular (LV) diastolic dysfunction. Echocardiographic stroke volume, cardiac output, and end-diastolic and systolic volumes were also lower in LT IRR than controls (all p ≤ 0.05). ST IRR had similar alterations in LV diastolic function but not in cardiac volumetric measures. Analyses of LV, interventricular septum (IVS), and right ventricle (RV) myocardium from deceased irradiated animals (n=17) exposed to a single dose (6.9-8.05 Gy) TBI and non-irradiated controls (n=12) showed that IRR animals had decreased LV and IVS capillary density, and increased LV fibrosis, pan-cardiac fibroblast and macrophage staining, LV and IVS M2 macrophages, and pan-cardiac M1 macrophages (all p<0.05). While M2 predominated over M1 macrophages in both groups, M1 showed greater increases than M2 in IRR.

Conclusions

LV diastolic dysfunction due to radiation exposure may be due to a combination of capillary rarefication, activation and expansion of fibroblasts, and increased accumulation of both pro-fibrotic and pro-inflammatory macrophages, all of which lead to increased myocardial stiffness due to fibrosis. Collectively, these findings provide insights into the delayed effects of acute ionizing radiation exposure and suggest that therapies targeting macrophage regulation of fibrosis may mitigate radiation induced heart disease.
Dynamic expressions of confidence within an evidence accumulation framework
Authors: Desender Kobe , Donner Tobias H. , Verguts Tom
Published: February 2020

Human observers can reliably report their confidence in the choices they make. An influential framework conceptualizes decision confidence as the probability of a decision being correct, given the choice made and the evidence on which it was based. This framework accounts for three diagnostic signatures of human confidence reports, including an opposite dependence of confidence on evidence strength for correct and error trials. However, the framework does not account for the temporal evolution of these signatures, because it only describes the transformation of a static representation of evidence into choice and the associated confidence. Here, we combine this framework with another influential framework: dynamic accumulation of evidence over time, and build on the notion that confidence reflects the probability of being correct, given the choice and accumulated evidenceup until that point. Critically, we show that such a dynamic model predicts that the diagnostic signatures of confidence depend on time; most critically, it predicts a stronger opposite dependence of confidence on evidence strength and choice correctness as a function of time. We tested, and confirmed, these predictions in human behaviour during random dot motion discrimination, in which confidence judgments were queried at different points in time. We conclude that human confidence reports reflect the dynamics of the probability of being correct given the accumulated evidence and choice.
Differential Expression and Interaction network construction of Noncoding RNA and mRNA in Heart Tissue associated with Tetralogy of Fallot
Authors: Wang Hongdan , Cui Cunying , Li Yanan , Liu Yuanyuan , Fan Taibing , Peng Bangtian , Liu Lin
Published: February 2020

Tetralogy of Fallot (TOF) is still the most common and complicated cyanotic congenital heart defect of all congenital heart diseases with a 10% incidence. Surgery repair is often necessary in infancy. The etiology of TOF is complex and genetic and epigenetic mechanisms such as chromosomal abnormalities, gene mutations, nucleic acid modifications, non-coding RNA, and circular RNA(circRNA) play an important role in its occurrence. RNA not only plays an auxiliary role of genetic information carrier, but also plays a more important role in various regulatory functions. There are few studies on the action mechanism of non-coding RNA. Aim to gain more in-depth knowledge of TOF, we collected tissue samples of the right ventricular outflow tract of 5 TOF children with no other intracardiac and extracardiac malformations and 5 normal fetuses. We systematically analyzed the specific long non-coding RNA (lncRNA), microRNA(miRNA), circRNA and messenger RNA(mRNA) profiles of TOF. To our knowledge, there are no reports of genome-wide study of transcriptome in TOF and we first obtained meaningful differentially expressed lncRNAs, miRNAs, circle RNA and mRNAs.
The genomic landscape of divergence across the speciation continuum in island-colonising silvereyes (Zosterops lateralis)
Authors: Sendell-Price Ashley T. , Ruegg Kristen C. , Anderson Eric C. , Quilodrán Claudio S. , Van Doren Benjamin M. , Underwood Vinh Le , Coulson Tim , Clegg Sonya. M.
Published: February 2020

A goal of the genomic era is to infer the evolutionary dynamics at play during the process of speciation by analysing the genomic landscape of divergence. However, empirical assessments of genomic landscapes under varying evolutionary scenarios are few, limiting the ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape in the silvereye (Zosterops lateralis). Using comparisons matched for divergence timeframe and gene flow context, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. Furthermore, we modelled the transition from localised to genome-wide levels of divergence using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.

DATA ACCESSION NUMBERS

Resequencing data from this study have been submitted to the National Center for Biotechnology Information (NCBI;https://www.ncbi.nlm.nih.gov) under accession number PRJNA489169.
Emergent properties of HNF4α-PPARγ network may drive consequent phenotypic plasticity in NAFLD
Authors: Sahoo Sarthak , Singh Divyoj , Chakraborty Priyanka , Jolly Mohit Kumar
Published: February 2020

Non-Alcoholic Fatty Liver Disease (NAFLD) is the most common form of chronic liver disease in adults and children. It is characterized by excessive accumulation of lipids in the hepatocytes of patients without any excess alcohol intake. With a global presence of 24% and limited therapeutic options, the disease burden of NAFLD is increasing. Thus, it becomes imperative to attempt to understand the dynamics of disease progression at a systems-level. Here, we decode the emergent dynamics of underlying gene regulatory networks that have been identified to drive the initiation and progression of NAFLD. We have developed a mathematical model to elucidate the dynamics of the HNF4α-PPARγ gene regulatory network. Our simulations reveal that this network can enable multiple co-existing phenotypes under certain biological conditions: an adipocyte, a hepatocyte, and a “hybrid” adipocyte-like state of the hepatocyte. These phenotypes may also switch among each other, thus enabling phenotypic plasticity and consequently leading to simultaneous deregulation of the levels of molecules that maintain a hepatic identity and/or facilitate a partial or complete acquisition of adipocytic traits. These predicted trends are supported by the analysis of clinical data, further substantiating the putative role of phenotypic plasticity in driving NAFLD. Our results unravel how the emergent dynamics of underlying regulatory networks can promote phenotypic plasticity, thereby propelling the clinically observed changes in gene expression often associated with NAFLD.
Sampling bias and model choice in continuous phylogeography: getting lost on a random walk
Authors: Kalkauskas Antanas , Perron Umberto , Sun Yuxuan , Goldman Nick , Baele Guy , Guindon Stephane , De Maio Nicola
Published: February 2020

Phylogeographic inference allows reconstruction of past geographical spread of pathogens or living organisms by integrating genetic and geographic data. A popular model in continuous phylogeography — with location data provided in the form of latitude and longitude coordinates — describes spread as a Brownian motion (Brownian Motion Phylogeography, BMP) in continuous space and time, akin to similar models of continuous trait evolution. Here, we show that reconstructions using this model can be strongly affected by sampling biases, such as the lack of sampling from certain areas. As an attempt to reduce the effects of sampling bias on BMP, we consider the addition of sequence-free samples from under-sampled areas. While this approach alleviates the effects of sampling bias, in most scenarios this will not be a viable option due to the need for prior knowledge of an outbreak’s spatial distribution. We therefore consider an alternative model, the spatial Λ-Fleming-Viot process (ΛFV), which has recently gained popularity in population genetics. Despite the ΛFV’s robustness to sampling biases, we find that the different assumptions of the ΛFV and BMP models result in different applicabilities, with the ΛFV being more appropriate for scenarios of endemic spread, and BMP being more appropriate for recent outbreaks or colonizations.
Comparative Genome Analysis ofScutellaria baicalensisandScutellaria barbataReveals the Evolution of Active Flavonoid Biosynthesis
Authors: Xu Zhichao , Gao Ranran , Pu Xiangdong , Xu Rong , Wang Jiyong , Zheng Sihao , Zeng Yan , Chen Jun , He Chunnian , Song Jingyuan
Published: February 2020

Scutellaria baicalensisandScutellaria barbata, common medicinal plants of the Lamiaceae family, produce specific flavonoid compounds with antioxidant and antitumor activities, including baicalein, scutellarein, norwogonin, wogonin, and their glycosides. Here, we reported two chromosome-level genome assemblies ofS. baicalensisandS. barbatawith significant quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence ofS. baicalensisandS. barbataoccurred far earlier than previously reported, and a whole-genome duplication event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. The comparative genome analysis of congeneric species elucidated the species-specific evolution of chrysin and apigenin biosynthetic genes, such as theS. baicalensis-specific tandem duplication of the phenylalanine ammonia lyase (PAL) and chalcone synthase (CHS) genes, and theS. barbata-specific duplication of 4-CoA ligase (4CL) genes. In addition, the paralogous duplication, collinearity, and expression diversity of CYP82D subfamily members revealed the functional divergence of flavone hydroxylase genes betweenS. baicalensisandS. barbata. TheseScutellariagenomes highlight the common and species-specific evolution of flavone biosynthetic genes, promoting the development of molecular breeding and the study of the biosynthesis and regulation of bioactive compounds.
Comparison of three glycoproteomic methods for the analysis of CHO cells treated with 1,3,4-O-Bu3ManNAc
Authors: Mertz Joseph L. , Sun Shisheng , Yin Bojiao , Betenbaugh Michael J. , Yarema Kevin J. , Zhang Hui
Published: February 2020

Comprehensive analysis of the glycoproteome is critical due to the widespread importance of this post-translational modification to protein function, and difficult because of the tremendous complexity it exhibits. Here we compared three glycoproteomic analysis methods, a recently described chemoenzymatic glycoproteome analysis methods, N-linked glycans and glycosite containing peptides (NGAG), Solid-phase extraction of N-linked glycoproteins (SPEG), and hydrophilic interaction liquid chromatography (HILIC), for the analysis of N-linked glycosites of Chinese hamster ovarian (CHO) cells treated with 1,3,4-O-Bu3ManNAc. The NGAG protocol resulted in substantially increased glycosite identifications over both SPEG and HILIC. Interestingly, while the glycosites identified by SPEG and HILIC overlapped strongly, NGAG identified many glycosites not observed in either of the other two methods. Further, utilizing the enhanced intact glycopeptide identification afforded by the NGAG workflow, we also found that of the sugar analog 1,3,4-O-Bu3ManNAc increases sialylation of proteins secreted by CHO cells, including an ectopically expressed human proteins.
A lipocalin mediates unidirectional haem biomineralization in malaria parasites
Authors: Matz Joachim M. , Drepper Benjamin , Blum Thorsten B. , van Genderen Eric , Burrell Alana , Martin Peer , Stach Thomas , Collinson Lucy , Abrahams Jan Pieter , Matuschewski Kai , Blackman Michael J.
Published: February 2020

During blood stage development, malaria parasites are challenged with the detoxification of enormous amounts of haem released during the proteolytic catabolism of erythrocytic haemoglobin. They tackle this problem by sequestering haem into bioinert crystals known as haemozoin. The mechanisms underlying this biomineralization process remain enigmatic. Here, we demonstrate that both rodent and human malaria parasite species secrete and internalize a lipocalin-like protein, PV5, to control haem crystallization. Transcriptional deregulation ofPV5in the rodent parasitePlasmodium bergheiresults in inordinate elongation of haemozoin crystals, while conditionalPV5inactivation in the human malaria agentPlasmodium falciparumcauses excessive multi-directional crystal branching. Although haemoglobin processing remains unaffected, PV5-deficient parasites generate less haemozoin. Electron diffraction analysis indicates that despite the distinct changes in crystal morphology neither the crystalline order nor unit cell of haemozoin are affected by impaired PV5 function. Deregulation ofPV5expression rendersP. bergheihypersensitive to the antimalarial drugs artesunate, chloroquine, and atovaquone, resulting in accelerated parasite clearance following drug treatmentin vivo. Together, our findings demonstrate thePlasmodium-tailored role of a lipocalin family member in haemozoin formation and underscore the haem biomineralization pathway as an attractive target for therapeutic exploitation.

SIGNIFICANCE

During blood stage development, the malaria parasite replicates inside erythrocytes of the vertebrate host, where it engulfs and digests most of the available haemoglobin. This results in release of the oxygen-binding prosthetic group haem, which is highly toxic in its unbound form. The parasite crystallizes the haem into an insoluble pigment called haemozoin, a process that is vital for parasite survival and which is exploited in antimalarial therapy. We demonstrate that the parasite uses a protein called PV5 in haemozoin formation and that interfering with PV5 expression can increase the parasite’s sensitivity to antimalarial drugs during blood infection. An improved understanding of the mechanisms underlying haem sequestration will provide valuable insights for future drug development efforts.
Subjective value and decision entropy are jointly encoded by aligned gradients across the human brain
Authors: Bobadilla-Suarez Sebastian , Guest Olivia , Love Bradley C.
Published: February 2020

Abstract

Recent work has considered the relationship between value and confidence in both behavior and neural representation. Here we evaluated whether the brain organizes value and confidence signals in a systematic fashion that reflects the overall desirability of options. If so, regions that respond to either increases or decreases in both value and confidence should be widespread. We strongly confirmed these predictions through a model-based fMRI analysis of a mixed gambles task that assessed subjective value (SV) and inverse decision entropy (iDE), which is related to confidence. Purported value areas more strongly signalled iDE than SV, underscoring how intertwined value and confidence are. A gradient tied to the desirability of actions transitioned from positive SV and iDE in ventromedial prefrontal cortex to negative SV and iDE in dorsal medial prefrontal cortex. This alignment of SV and iDE signals could support retrospective evaluation to guide learning and subsequent decisions.
Fine-tuning of the PAX-SIX-EYA-DACH network by multiple microRNAs controls embryo myogenesis
Authors: Viaut Camille , Münsterberg Andrea
Published: February 2020

MicroRNAs (miRNAs), short non-coding RNAs, which act post-transcriptionally to regulate gene expression, are of widespread significance during development and disease, including muscle disease. Advances in sequencing technology and bioinformatics led to the identification of a large number of miRNAs in vertebrates and other species, however, for many of these miRNAs specific roles have not yet been determined. LNAin situhybridisation has revealed expression patterns of somite-enriched miRNAs, here we focus on characterising the functions of miR-128. We show that antagomir-mediated knock-down (KD) of miR-128 in developing chick somites has a negative impact on skeletal myogenesis. Computational analysis identified the transcription factorEYA4as a candidate target consistent with the observation that miR-128 andEYA4display similar expression profiles. Luciferase assays confirmed that miR-128 interacts with theEYA43’UTR. Furthermore,in vivoexperiments suggest thatEYA4is regulated by miR-128, asEYA4expression is derepressed after antagomir-mediated inhibition of miR-128. EYA4 is a member of the PAX-SIX-EYA-DACH (PSED) network of transcription factors. Therefore, we identified additional candidate miRNA binding sites in the 3’UTR ofSIX1/4, EYA1/2/3andDACH1. Using the miRanda algorithm, we found sites for miR-128, as well as for other myogenic miRNAs, miR-1a, miR-206 and miR-133a, some of these were experimentally confirmed as functional miRNA-target sites. Our results reveal that miR-128 is involved in regulating skeletal myogenesis by targetingEYA4transcripts and moreover that the PSED network of transcription factors is co-regulated by multiple muscle-enriched microRNAs.
An Envelope Protein of a Prokaryotic Organelle Function towards Conserving Catalytic Activity of the Native Enzyme at Higher Temperatures
Authors: Kumar Gaurav , Bari Naimat K. , Hazra Jagadish P. , Sinha Sharmistha
Published: February 2020

A classic example of an all-protein natural nano-bioreactor, the bacterial microcompartments are a special kind of prokaryotic organelles that confine enzymes within a small volume enveloped by an outer layer of shell proteins. This arrangement provides conditional metabolic aid to the bacteria. The outer shell allows selective diffusion of small molecules and sequesters toxic metabolites. In this work we use 1,2-propanediol utilization microcompartment as a model to study the effect of molecular confinement on the stability and catalytic activity of native enzymes in microcompartment. We observe a 50% decrease in the activity of free enzyme PduCDE at 45°C, while PduMCP retains its optimum activity till 50°C followed by more than 40% reduced activity at 55°C. PduBB’, the major component of the outer shell contributes to the increased catalytic activity of PduCDE. PduBB’ also prevents the unfolding and aggregation of PduCDE under thermal stress. Using a combination of experimental and theoretical studies we probe the interactions of the shell proteins PduBB’, N-terminal truncated PduB and single mutant PduB’M38L with PduCDE. We observe that all the three variants of PduB* shell proteins interact with the enzyme in vitro, but only PduBB’ influences its activity and stability, underscoring the significance of the unique combination of PduB and PduB’ in PduMCP assembly.
ASH1L REGULATES THE STRUCTURAL DEVELOPMENT OF NEURONAL CIRCUITRY BY MODULATING BDNF/TrkB SIGNALING IN HUMAN NEURONS
Authors: Cheon Seon Hye , Culver Allison M. , Bagnell Anna M. , Ritchie Foster D. , Clytus Janay M. , McCord Mikayla , Papendorp Carin M. , Chukwurah Evelyn , Smith Austin J. , Cowen Mara H. , Ghate Pankaj S. , Davis Shannon W. , Liu Judy S. , Lizarraga Sofia B.
Published: February 2020

Autism spectrum disorders (ASD) are associated with defects in neuronal connectivity and are highly heritable. Genetic findings suggest that there is an overrepresentation of chromatin regulatory genes among the genes associated with ASD. ASH1 like histone lysine methyltransferase (ASH1L) was identified as a major risk factor for autism. ASH1L methylates Histone H3 on Lysine 36, which is proposed to result primarily in transcriptional activation. However, how mutations in ASH1L lead to deficits in neuronal connectivity associated with autism pathogenesis is not known. We report that ASH1L regulates neuronal morphogenesis by counteracting the catalytic activity of Polycomb Repressive complex 2 group (PRC2) in stem cell-derived human neurons. Depletion of ASH1L decreases neurite outgrowth and decreases expression of the gene encoding the neurotrophin receptor TrkB whose signaling pathway is linked to neuronal morphogenesis. This is overcome by inhibition of PRC2 activity, indicating a balance between the Trithorax group protein ASH1L and PRC2 activity determines neuronal morphology and connectivity. Thus, ASH1L epigenetically regulates neuronal connectivity by modulating the BDNF-TrkB signaling pathway, which likely contributes to the neurodevelopmental pathogenesis associated with ASD in patients with ASH1L mutations.

eTOC BLURB

Cheon et al. report a novel epigenetic mechanism that implicates the counteracting activities of the evolutionarily conserved Trithorax (ASH1L) and Polycomb (PRC2) chromatin regulators, in the modulation of human neuronal connectivity by regulating the developmentally important TrkB-BDNF signaling pathway.

HIGHLIGHTS

ASH1L regulates neuronal morphogenesis by modulating neurotrophin signaling

Counteracting activities of Trithorax (ASH1L) and Polycomb (PRC2) affect neuronal arborization

Loss of ASH1L modulates growth cone size in human neurons
Discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiome using nanopore sequencing
Authors: Tourancheau Alan , Mead Edward A. , Zhang Xue-Song , Fang Gang
Published: February 2020

Nanopore sequencing provides a great opportunity for direct detection of chemical DNA modification. However, existing computational methods were either trained for detecting a specific form of DNA modification from one, or a few, specific sequence contexts (e.g.5-methylcytosine from CpG dinucleotides) or for allowingde novodetection without effectively differentiating between different forms of DNA modifications. As a result, none of these methods supportsde novo, systematic study of unknown bacterial methylomes. In this work, by examining three types of DNA methylation in a large diversity of sequence contexts, we observed that nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To capture this complexity and enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a novel method that couples the identification and fine mapping of the three forms of DNA methylation into a multi-label classification design. We evaluated the method and then applied it to individual bacteria and mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated in the microbiome analysis the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes, and for the first time, identifying misassembled metagenomic contigs. This novel method has broad utility for discovering different forms of DNA methylation from bacteria, assisting functional studies of epigenetic regulation in bacteria, and exploiting bacterial epigenomes for more effective metagenomic analyses.
Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress
Authors: Sharma Anupama , Wood Kevin B.
Published: February 2020

Antibiotic resistance in microbial communities reflects a combination of processes operating at different scales. The molecular mechanisms underlying antibiotic resistance are increasingly understood, but less is known about how these molecular events give rise to spatiotemporal behavior on longer length scales. In this work, we investigate the population dynamics of bacterial colonies comprised of drug-resistant and drug-sensitive cells undergoing range expansion under antibiotic stress. Using the opportunistic pathogenE. faecaliswith plasmid-encoded (β-lactamase) resistance as a model system, we track colony expansion dynamics and visualize spatial pattern formation in fluorescently labeled populations exposed to ampicillin, a commonly-usedβ-lactam antibiotic. We find that the radial expansion rate of mixed communities is approximately constant over a wide range of drug concentrations and initial population compositions. Fluorescence imaging of the final populations shows that resistance to ampicillin is cooperative, with sensitive cells surviving in the presence of resistant cells even at drug concentrations lethal to sensitive-only communities. Furthermore, despite the relative invariance of expansion rate across conditions, the populations exhibit a diverse range of spatial segregation patterns, with both the spatial structure and the population composition depending on drug concentration, initial composition, and initial population size. Agent based models indicate that the observed dynamics are consistent with long-range cooperation, despite the fact thatβ-lactamase remains cell-associated inE. faecalis, and experiments confirm that resistant colonies provide a protective effect to sensitive cells on length scales multiple times the size of a single colony. Furthermore, in the limit of small inoculum sizes, we experimentally show that populations seeded with (on average) no more than a single resistant cell can produce mixed communities in the presence of drug. While biophysical models of diffusion-limited drug degradation suggest that individual resistant cells offer only short-range protection to neighboring sensitive cells, we show that long-range protection may arise from synergistic effects of multiple resistant cells, even when they represent only a small fraction of a colony’s surface area. Our results suggest thatβ-lactam resistance can be cooperative even in spatially extended systems where genetic segregation typically disfavors exploitation of locally produced public goods.
Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls
Authors: Fujito Naoko T. , Hanna Zachary R. , Levy-Sakin Michal , Bowie Rauri C. K. , Kwok Pui-Yan , Dumbacher John P. , Wall Jeffrey D.
Published: February 2020

Spotted owls (SO,Strix occidentalis) are a keystone species inhabiting old-growth forests in Western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO,Strix varia). The northern spotted owl (subspeciesS. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here we present a comprehensive look at genetic variation to elucidate the population histories of SO and invading western BO. Specifically, we present an improved SO genome assembly, based on 10x and Bionano Genomics data, along with 51 high-coverage whole-genome sequences including 11 SO from two subspecies (caurinaandoccidentalis), 25 BO, 2 confirmed and 13 potential hybrids. We identified potential hybrids based on intermediate morphology and found them to be a mixture of pure BO, F1 hybrids, and F1 x BO backcrosses. Unlike previous studies reporting asymmetries in the species-specific genders of the parents of F1 hybrids, we did not observe any significant asymmetry. Within species, we found that Western BO genetic variation is not simply a subset of the genetic variation in Eastern BO, suggesting that the two groups have been genetically isolated for longer (thousands of years) than previously suspected (80-130 years). Similarly, we found evidence of substantial genetic differentiation between the two SO subspecies. Finally, our analyses suggest that Northern SO experienced a moderate population bottleneck around the end of the last glaciation, while BO population sizes have always been large.
Thioesterase Superfamily Member 1 Undergoes Stimulus-coupled Reorganization to Regulate Metabolism
Authors: Li Yue , Imai Norihiro , Goyal Samaksh , Nicholls Hayley T. , Krisko Tibor I. , Baqai Mahnoor , Ang Lay-Hong , Tillman Matthew C. , Ortlund Eric A. , Cohen David E. , Hagen Susan J.
Published: February 2020

In brown adipose tissue, cold exposure promotes thermogenesis, in large part by increasing mitochondrial β-oxidation of lipid droplet-derived fatty acids. This process is suppressed by thioesterase superfamily member 1 (Them1), a long chain fatty acyl-CoA thioesterase that is highly upregulated by cold ambient temperatures. Them1 reduces fatty acid availability for β-oxidation in mitochondria and limits thermogenesis by cellular mechanisms that are not well defined. We show that Them1 regulates metabolism by undergoing marked intracellular conformational changes that occur in response to β-adrenergic stimulation. Mechanistically, Them1 formed puncta that were localized near LD and mitochondria in an immortalized brown adipose cell line. In response to stimulation by norepinephrine, Them1 was phosphorylated by PKCβ at S15, which specifically inhibited puncta formation and resulted in a diffuse intracellular localization. This change in Them1 localization also occurred after stimulation in vivo. Puncta formation activated Them1 metabolic activity in vitro, as evidenced by suppression of oxygen consumption following β-adrenergic stimulation. We show by correlative light and electron microscopy that puncta are biomolecular condensates (also known as membraneless organelles) that typically form by phase separation. Them1 contains one intrinsically disordered region at the N-terminus with multiple interacting motifs that is frequently observed in phase-separating proteins. Phosphorylation, which is known to disrupt phase separation and aggregation, results in a diffuse Them1 localization. Our data thus establish that Them1 forms intracellular biomolecular condensates that limit fatty acid oxidation and suppress thermogenesis. During a period of energy demand, the condensates are disrupted by phosphorylation to allow for maximal thermogenesis. The stimulus-coupled reorganization of Them1 thus provides fine-tuning of thermogenesis and energy expenditure.
The Gene Expression Profile of UropathogenicEscherichia coliin Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
Authors: Frick-Cheng Arwen E. , Sintsova Anna , Smith Sara N. , Krauthammer Michael , Eaton Kathryn A. , Mobley Harry L. T.
Published: February 2020

UropathogenicEscherichia coli(UPEC) is the primary causative agent of uncomplicated urinary tract infections (UTIs). UPEC fitness and virulence determinants have been evaluated in a variety of laboratory settings that include a well-established mouse model of UTI. However, the extent to which bacterial physiology differs between experimental models and human infections remains largely understudied. To address this important question, we compared the transcriptomes of three different UPEC isolates in human infection and a variety of laboratory conditions including LB culture, filter-sterilized urine culture, and the UTI mouse model. We observed high correlation in gene expression between the mouse model and human infection in all three strains examined (Pearson correlation coefficient of 0.86-0.87). Only 175 of 3,266 (5.4%) genes shared by all three strains had significantly different expression levels, with the majority of them (145 genes) down-regulated in patients. Importantly, gene expression of both canonical virulence factors and metabolic machinery were highly similar between the mouse model and human infection, while thein vitroconditions displayed more substantial differences. Interestingly, comparison of gene expression between the mouse model and human infection hint at differences in bladder oxygenation as well as nutrient composition. In summary, our work strongly validates the continued use of this mouse model for the study of the pathogenesis of human UTI.

Importance

Different experimental models have been used to study UPEC pathogenesis includingin vitrocultures in different media, tissue culture, as well as mouse models of infection. The latter is especially important since it allows evaluation of mechanisms of pathogenesis and potential therapeutic strategies against UPEC. Bacterial physiology is greatly shaped by environment and it is therefore critical to understand how closely bacterial physiology in any experimental model relates to human infection. In this study, we found a very strong correlation in bacterial gene expression between the mouse model and human UTI using identical strains, suggesting that the mouse model accurately mimics human infection, definitively supporting its continued use in UTI research.
Anethole dithiolethione improves liver fatty acid metabolism in hamster fed high-fat diets
Authors: Zhao Chengcheng , Yu Nannan , Li Wenqun , Cai Hualin , Liu Mouze , Hu Yanjie , Liu Yiping , Tang Mimi
Published: February 2020

“Lipotoxicity” induced by excessive accumulation of free fatty acids (FFAs) in the liver, especially saturated FAs and their toxic metabolites, is closely related to metabolic diseases such as nonalcoholic fatty liver disease (NAFLD). Hydrogen sulfide (H2S), a novel gaseous signaling molecule, has been reported to have lipid-lowering effects, but its effect on FAs metabolism remains unclear. The purpose of this study was to investigate the effect and mechanisms of anethole dithiolethione (ADT, a sustained-release H2S donor) on hepatic FAs metabolism. ADT was administered daily for 4 weeks in male Syrian golden hamsters fed a high fat diet (HFD), and FAs profiles of liver tissues were analyzed using GC-MS. The results showed that in HFD-fed hamsters, ADT treatment significantly reduced the accumulation of saturated and monounsaturated fatty acids (C16:0, C18:0, C16:1, and C18:1n9), while increased the content of n-6 and n-3 series polyunsaturated fatty acids (C20:3n6, C20:4n6, and C22:6n3). Mechanistically, ADT obviously inhibited the overexpression of ACC1, FAS and SCD1, and up-regulated the levels of FATPs, L-FABP, CPT1α, FADS1 and FADS2. Notably, ADT evidently induced Mitofusin1 to facilitate mitochondrial fusion and optimize β-oxidation. These findings suggest that ADT plays a beneficial role by regulating the synthesis, desaturation, β-oxidation, uptake, binding/isolation, and transport of FAs. In conclusion, ADT is effective in improving liver FAs metabolic disorders and liver injuries caused by HFD.
Plant-soil nitrogen, carbon and phosphorus content after the addition of biochar, bacterial inoculums and N fertilizer
Authors: Mikajlo Irina , Pourrut Bertrand , Louvel Brice , Hynšt Jaroslav , Záhora Jaroslav
Published: February 2020

The use of biochar in combination with mineral or biological amendments in order to improve its influence on soil-plant properties has received growing attention. The changes of N, C and P content inLactuca sativa var. capitataaboveground plant biomass and soil after the addition of beech wood biochar combined with the addition of bacterial inoculums (Bacofil and Novarefm) and N fertilizer have been studied using spectrophotometry methods. Pots were filled with the arable soil from the plots in protection zone of water sources (Březová nad Svitavou, South Moravia, Czech Republic). Biochar with inoculums decreased plant growth in the first yield of Novaferm treatment and in both yields of Bactofil treatment. Increased plant biomass growth was observed with Novaferm addition in the second yield. Total N increase has been obtained in the plant aboveground biomass and soil of the treatments amended with inoculums and nitrogen fertilizer. The decrease of P content has been observed in plant aboveground biomass in the biochar amended samples.
Adolescent Social Isolation Reprograms the Medial Amygdala: Transcriptome and Sex Differences in Reward
Authors: Walker Deena M. , Zhou Xianxiao , Ramakrishnan Aarthi , Cates Hannah M. , Cunningham Ashley M. , Peña Catherine J. , Bagot Rosemary C. , Issler Orna , Van der Zee Yentl , Lipschultz Andrew P. , Godino Arthur , Browne Caleb J. , Hodes Georgia E. , Parise Eric M. , Torres-Berrio Angélica , Kennedy Pamela J. , Shen Li , Zhang Bin , Nestler Eric J.
Published: February 2020

Adolescence is a sensitive window for reward- and stress-associated behavior. Although stress during this period causes long-term changes in behavior in males, how females respond is relatively unknown. Here we show that social isolation stress in adolescence, but not adulthood, induces persistent but opposite effects on anxiety- and cocaine-related behaviors in male vs. female mice, and that these effects are reflected in transcriptional profiles within the adult medial amygdala (meA). By integrating differential gene expression with co-expression network analyses, we identified crystallin mu (Crym), a thyroid-binding protein, as a key driver of these transcriptional profiles. Manipulation ofCrymspecifically withinadultmeA neurons recapitulates the behavioral and transcriptional effects of social isolation and re-opens a window of plasticity that is otherwise closed. Our results establish that meA is essential for sex-specific responses to stressful and rewarding stimuli through transcriptional programming that occurs during adolescence.
Urine as a high-quality source of host genomic DNA from wild populations
Authors: Ozga Andrew T. , Webster Timothy H. , Gilby Ian C. , Wilson Melissa A. , Nockerts Rebecca S. , Wilson Michael L. , Pusey Anne E. , Li Yingying , Hahn Beatrice H. , Stone Anne C.
Published: February 2020

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as feces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.
Multiple timescales of neural dynamics and integration of task-relevant signals across cortex
Authors: Spitmaan Mehran , Seo Hyojung , Lee Daeyeol , Soltani Alireza
Published: February 2020

Recent studies have proposed the orderly progression in the time constants of neural dynamics as an organizational principle of cortical computations. However, relationships between these timescales and their dependence on response properties of individual neurons are unknown. We developed a comprehensive method to simultaneously estimate multiple timescales in neuronal dynamics and integration of task-relevant signals along with selectivity to those signals. We found that most neurons exhibited multiple timescales in their response, which consistently increased from parietal to prefrontal to cingulate cortex. While predicting rates of behavioral adjustments, these timescales were not correlated across individual neurons in any cortical area, resulting in independent parallel hierarchies of timescales. Additionally, none of these timescales depended on selectivity to task-relevant signals. Our results not only suggest multiple canonical mechanisms for increasing timescales of neural dynamics across cortex but also point to additional mechanisms that allow decorrelation of these timescales to enable more flexibility.
Molecular origins of transcriptional heterogeneity in diazotrophicK. oxytoca
Authors: Bashir Tufail , Brackston Rowan D , Waite Christopher J , Kotta-Loizou Ioly , Engl Christoph , Buck Martin , Schumacher Jörg
Published: February 2020

Phenotypic heterogeneity in clonal bacterial batch cultures is an important adaptive strategy to changing environments, including in diazotrophs with the unique capacity to convert di-nitrogen into bio-available ammonium. In diazotrophicKlebsiella oxytocawe simultaneously measured mRNA levels of key regulatory (glnK-amtB, nifLA) and structural (nifHDK) operons required for establishing nitrogen fixation, using dual molecule, single cell RNA-FISH. Through stochastic transcription models and mutual information analysis we revealed likely molecular origins for heterogeneity in nitrogenase expression. In wildtype and regulatory variant strains we inferred contributions from intrinsic and extrinsic noise, finding thatnifHDKtranscription is inherently bursty, but that noise propagation through signalling is also significant. The regulatory geneglnKhad the highest discernible effect onnifHDKvariance, while noise from factors outside of the regulatory pathway were negligible. Results provide evidence that heterogeneity is a fundamental property of this regulatory system, indicating potential constraints for engineering homogeneous nitrogenase expression.
Mutations inTAC1B: a novel genetic determinant of clinical fluconazole resistance inC. auris
Authors: Rybak Jeffrey M. , Muñoz José F. , Barker Katherine S. , Parker Josie E. , Esquivel Brooke D. , Berkow Elizabeth L. , Lockhart Shawn R. , Gade Lalitha , Palmer Glen E. , White Theodore C. , Kelly Steve L. , Cuomo Christina A. , Rogers P. David
Published: February 2020

Candida aurishas emerged as a multidrug-resistant pathogen of great clinical concern. Approximately 90% of clinicalC. aurisisolates are resistant to fluconazole, the most commonly prescribed antifungal agent, yet it remains unknown what mechanisms underpin this fluconazole resistance. To identify novel mechanisms contributing to fluconazole resistance inC. auris, the fluconazole-susceptibleC. aurisclinical isolate AR0387 was passaged in media supplemented with fluconazole to generate derivative strains which had acquired increased fluconazole resistancein vitro. Comparative analysis of comprehensive sterol profiles, [3H]-fluconazole uptake, sequencing ofC. aurisgenes homologous to genes known to contribute to fluconazole resistance in other species ofCandida, and the relative expression ofC. auris ERG11, CDR1, andMDR1were performed. All fluconazole-evolved derivative strains were found to have acquired mutations in the zinc-cluster transcription factor-encoding gene,TAC1B, and a corresponding increase inCDR1expression relative to the parental clinical isolate, AR0387. Mutations inTAC1Bwere also identified in a set of 304 globally distributedC. aurisclinical isolates representing each of the four major clades. Introduction of the most common mutation found among fluconazole-resistant clinical isolates ofC. aurisinto the fluconazole-susceptible isolate AR0387, was confirmed to increase fluconazole resistance by 8-fold, and the correction of the same mutation in a fluconazole-resistant isolate, AR0390, decreased fluconazole MIC by 16-fold. Taken together, these data demonstrate thatC. auriscan rapidly acquire resistance to fluconazolein-vitro, and that mutations inTAC1Bsignificantly contribute to clinical fluconazole resistance.

IMPORTANCE

Candida aurisis an emerging multidrug-resistant pathogen of global concern, known to be responsible for outbreaks on six continents and commonly resistant to antifungals. While the vast majority of clinicalC. aurisisolates are highly resistant to fluconazole, an essential part of the available antifungal arsenal, very little is known about the mechanisms contributing to resistance. In this work, we show that mutations in the transcription factorTAC1Bsignificantly contribute to clinical fluconazole resistance. These studies demonstrate that mutations inTAC1Bcan arise rapidly in vitro upon exposure to fluconazole, and that a multitude of resistance-associatedTAC1Bmutations are present among the majority of fluconazole-resistantC. aurisisolates from a global collection and appear specific to a subset of lineages or clades. Thus, identification of this novel genetic determinant of resistance significantly adds to the understanding of clinical antifungal resistance inC. auris.