bluuebunny/crossref_metadata_2025 huggingface dataset:
Cadherins regulate nuclear topography and function of developing ocular motor circuitry
Authors: Knüfer Athene , Diana Giovanni , Walsh Gregory S. , Clarke Jonathan , Guthrie Sarah
Published: April 2020

In the vertebrate central nervous system, groups of functionally-related neurons, including cranial motor neurons of the brainstem, are frequently organised as nuclei. The molecular mechanisms governing the emergence of nuclear topography and circuit function are poorly understood. Here we investigate the role of cadherin-mediated adhesion in the development of zebrafish ocular motor (sub)nuclei. We find that developing ocular motor (sub)nuclei differentially express classical cadherins. Perturbing cadherin function in these neurons results in distinct defects in neuronal positioning, including scattering of dorsal cells and defective contralateral migration of ventral subnuclei. In addition, we show that cadherin-mediated interactions between adjacent subnuclei are critical for subnucleus position. We also find that disrupting cadherin adhesivity in dorsal oculomotor neurons impairs the larval optokinetic reflex, suggesting that neuronal clustering is important for co-ordinating circuit function. Our findings reveal that cadherins regulate distinct aspects of cranial motor neuron positioning and establish subnuclear topography and motor function.
GABABreceptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals
Authors: Bhandari Pradeep , Vandael David , Fernández-Fernández Diego , Fritzius Thorsten , Kleindienst David , Montanaro Jacqueline , Gassmann Martin , Jonas Peter , Kulik Akos , Bettler Bernhard , Shigemoto Ryuichi , Koppensteiner Peter
Published: April 2020

The connection from medial habenula (MHb) to interpeduncular nucleus is critical for aversion- and addiction-related behaviors. This pathway is unique in selective expression of R-type voltage-gated Ca2+channels (Cav2.3) in its terminals, and robust potentiation of release via presynaptic GABABreceptors (GBRs). To understand the mechanism underlying this peculiar GBR effect, we examined the presynaptic localization and function of Cav2.3, GBR, and its auxiliary subunits, K+-channel tetramerization domain-containing (KCTD) proteins. We found selective co-expression of KCTD12b and Cav2.3 at the presynaptic active zone. GBR-mediated potentiation remained intact in KCTD12b KO mice but lasted significantly shorter. This impairment was associated with increased release and an insertion of KCTD8 into the active zone. In heterologous cells, we found direct binding of KCTD8 and KCTD12b to Cav2.3, and potentiation of Cav2.3 currents by KCTD8. The unexpected interaction of Cav2.3 with KCTDs therefore provides a means to scale synaptic strength independent of GBR activation.
Hypomethylated poplars show higher tolerance to water deficit and highlight a dual role for DNA methylation in shoot meristem: regulation of stress response and genome integrity
Authors: Sow M.D. , Le Gac A-L. , Fichot R. , Lanciano S. , Delaunay A. , Le Jan I. , Lesage-Descauses M-C. , Citerne S. , Caius J. , Brunaud V. , Soubigou-Taconnat L. , Cochard H. , Segura V. , Chaparro C. , Grunau C. , Daviaud C. , Tost J. , Brignolas F. , Strauss S.H. , Mirouze M. , Maury S.
Published: April 2020

As fixed and long living organisms subjected to repeated environmental stresses, trees have developed mechanisms such as phenotypic plasticity that help them to cope with fluctuating environmental conditions. Here, we tested the role DNA methylation as a hub of integration, linking plasticity and physiological response to water deficit in the shoot apical meristem of the model tree poplar (Populus). Using a reverse genetic approach, we compared hypomethylated RNAi-ddm1lines to wild-type trees for drought tolerance. An integrative analysis was realized with phytohormone balance, methylomes, transcriptomes and mobilomes.

Hypomethylated lines were more tolerant when subjected to moderate water deficit and were intrinsically more tolerant to drought-induced cavitation. The alteration of theDDM1machinery induced variation in DNA methylation in a cytosine context dependent manner, both in genes and transposable elements. Hypomethylated lines subjected to water deficit showed altered expression of genes involved in phytohormone pathways, such as salicylic acid and modified hormonal balance. Several transposable elements showed stress- and/or line-specific patterns of reactivation, and we could detect copy number variations for two of them in stressedddm1lines.

Overall, our data highlight two major roles for DNA methylation in the shoot apical meristem: control of stress response and plasticity through transduction of hormone signaling and maintenance of genome integrity through the control of transposable elements.
Estimating COVID-19 outbreak risk through air travel
Authors: Daon Y. , Thompson R.N. , Obolski U.
Published: April 2020

Background

Substantial limitations have been imposed on passenger air travel to reduce transmission of SARS-CoV-2 between regions and countries. However, as case numbers decrease, air travel will gradually resume. We considered a future scenario in which case numbers are low and air travel returns to normal. Under that scenario, there will be a risk of outbreaks in locations worldwide due to imported cases. We estimated the risk of different locations acting as sources of future COVID-19 outbreaks elsewhere.

Methods

We use modelled global air travel data and population density estimates from locations worldwide to analyse the risk that 1364 airports are sources of future COVID-19 outbreaks. We use a probabilistic, branching-process based approach that considers the volume of air travelers between airports and the reproduction number at each location, accounting for local population density.

Results

Under the scenario we model, we identify airports in East Asia as having the highest risk of acting as sources of future outbreaks. Moreover, we investigate the locations most likely to cause outbreaks due to air travel in regions that are large and potentially vulnerable to outbreaks: India, Brazil and Africa. We find that outbreaks in India and Brazil are most likely to be seeded by individuals travelling from within those regions. We find that this is also true for less vulnerable regions, such as the United States, Europe, and China. However, outbreaks in Africa due to imported cases are instead most likely to be initiated by passengers travelling from outside the continent.

Conclusions

Variation in flight volumes and destination population densities create a non-uniform distribution of the risk that different airports pose of acting as the source of an outbreak. Accurate quantification of the spatial distribution of outbreak risk can therefore facilitate optimal allocation of resources for effective targeting of public health interventions.
The focus and timing of COVID-19 pandemic control measures under healthcare resource constraints
Authors: Wei Chen , Wang Zhengyang , Liang Zhichao , Liu Quanying
Published: April 2020

Generalizing COVID-19 control strategies in one community to others is confounded by community’s unique demographic and socioeconomic attributes. Here we propose a tailored dynamic model accounting for community-specific transmission controls and medical resource availability. We trained the model using data from Wuhan and applied it to other countries. We show that isolating suspected cases is most effective in reducing transmission rate if the intervention starts early. Having more hospital beds provides leverage that diminishes with delayed intervention onset. The importance of transmission control in turn increases by 65% with a 7-day delay. Furthermore, prolonging outbreak duration by applying an intermediate, rather than strict, transmission control would not prevent hospital overload regardless of bed capacity, and would likely result in a high ratio (21% ∼ 84%) of the population being infected but not treated. The model could help different countries design control policies and gauge the severity of suppression failure.
Prognostic significance of compound physiology variables in oesophageal cancer
Authors: Powell Arfon G M T , Eley Catherine , Coxon Alexandra H , Chin Carven , Bailey Damian M , Lewis Wyn G ,   South East Wales Oesophagogastric Cancer Collaborative
Published: April 2020

Aims

Objective identification of patient risk profile in Oesophageal Cancer (OC) surgery is critical. This study aimed to evaluate to what extent cardiorespiratory fitness and select metabolic factors predict clinical outcome.

Methods

Consecutive 186 patients were recruited (median age 69 yr. 160 male, 138 neoadjuvant therapy). All underwent pre-operative cardiopulmonary exercise testing to determine peak oxygen uptake , anaerobic threshold (AT), and ventilatory equivalent for carbon dioxide . Cephalic venous blood was assayed for serum C-reactive protein (CRP), albumin, and full blood count. Primary outcome measures were Morbidity Severity Score (MSS), and Overall Survival (OS).

Results

MSS (Clavien-Dindo >2) developed in 33 (17.7%) and was related to elevated CRP (AUC 0.69, p=0.001) and lower V·O2Peak (AUC 0.33, p=0.003). Dichotomisation of CRP (above 10mg/L) and V·O2Peak (below 18.6mL/kg/min) yielded adjusted Odds Ratios (OR) for MSS CD>2, of 4.01 (p=0.002) and 3.74 (p=0.002) respectively. OC recurrence occurred in 36 (19.4%) and 69 (37.1%) patients died. On multivariable analysis; pTNM stage (Hazard Ratio (HR) 2.20, p=0.001), poor differentiation (HR 2.20, p=0.010), resection margin positivity (HR 2.33, p=0.021), and MSS (HR 4.56, p<0.001) were associated with OS.

Conclusions

CRP and V·O2Peak are collective independent risk factors that can account for over half of OC survival variance.
ZBTB18 inhibits SREBP-dependent fatty acid synthesis by counteracting CTBPs and KDM1A/LSD1 activity in glioblastoma
Authors: Ferrarese R. , Izzo A. , Andrieux G. , Lagies S. , Bartmuss J.P. , Masilamani A.P. , Wasilenko A. , Osti D. , Faletti S. , Schulzki R. , Shuai Y. , Kling E. , Ribecco V. , Heiland D.H. , Tholen S.G. , Prinz M. , Pelicci G. , Kammerer B. , Börries M. , Carro M.S.
Published: April 2020

Enhanced fatty acid synthesis is a hallmark of tumors, including glioblastoma. SREBF1/2 regulate the expression of enzymes involved in fatty acid and cholesterol synthesis. Yet, little is known about the precise mechanism regulating SREBP gene expression in glioblastoma. Here, we show that a novel interaction between the co-activator/co-repressor CTBP and the tumor suppressor ZBTB18 regulates the expression of SREBP genes. Our study points at CTBP1/2 and LSD1 as co-activators of SREBP genes whose complex functional activity is altered by ZBTB18. ZBTB18 binding to the SREBP gene promoters is associated with reduced LSD1 demethylase activity of H3 active marks leading to increased di-methylation of lysine 4 (H3K4me2). Concomitantly, we observed increased di-methylation of lysine 9 (H3K9me2), and decrease of the active mark H3K4me3 with consequent repression of the SREBP genes. In line with our findings, lipidomic analysis shows a reduction of several phospholipid species upon ZBTB18 expression. Our results outline a new epigenetic mechanism enrolled by ZBTB18 and its cofactors to regulate fatty acid synthesis that could be targeted to treat glioblastoma patients.
Structural Model of the Proline-rich Domain of Huntingtin exon-1 fibrils
Authors: Falk A. S. , Bravo-Arredondo J. M. , Varkey J. , Pacheco S. , Langen R. , Siemer A. B.
Published: April 2020

Huntington’s disease (HD) is a heritable neurodegenerative disease that is caused by a CAG expansion in the first exon of the huntingtin gene. This expansion results in an elongated polyglutamine (polyQ) domain that increases the propensity of huntingtin exon-1 (HTTex1) to form cross-β fibrils. While the polyQ domain is important for fibril formation, the dynamic, C-terminal proline-rich domain (PRD) of HTTex1 makes up a large fraction of the fibril surface. Because potential fibril toxicity has to be mediated by interactions of the fibril surface with its cellular environment, we wanted to model the conformational space adopted by the PRD. We ran 800 ns long molecular dynamics (MD) simulations of the PRD using an explicit water model optimized for intrinsically disordered proteins. These simulations accurately predicted our previous solid-state NMR data and newly acquired EPR DEER distances, lending confidence in their accuracy. The simulations show that the PRD generally forms an imperfect polyproline II (PPII) helical conformation. The two polyproline (polyP) regions within the PRD stay in a PPII helix for most of the simulation, whereas occasional kinks in the proline rich linker region cause an overall bend in the PRD structure. The dihedral angles of the glycine at the end of the second polyP region are very variable, effectively decoupling the highly dynamic 12 C-terminal residues from the rest of the PRD.

Statement of Significance

HD is caused by a polyQ expansion in the exon-1 of huntingtin, which results in the formation of fibrillar huntingtin aggregates. Although the polyQ domain is the site of the disease-causing mutation, the PRD domain of HTTex1 is important for fibril toxicity and contains many epitopes of fibril-specific HTTex1 antibodies. Here, we present a structural and dynamic model of the highly dynamic PRD domain using a combination of EPR, solid-state NMR, and MD simulations. This model paves the way for studying known HTTex1 fibril specific binders and designing new ones.
Exploring Conformational Transition of 2019 Novel Coronavirus Spike Glycoprotein Between Its Closed and Open States Using Molecular Dynamics Simulations
Authors: Gur Mert , Taka Elhan , Yilmaz Sema Zeynep , Kilinc Ceren , Aktas Umut , Golcuk Mert
Published: April 2020

Since its first recorded appearance in December 2019, a novel coronavirus (SARS-CoV-2) causing the disease COVID-19 has resulted in more than 2,000,000 infections and 128,000 deaths. Currently there is no proven treatment for COVID-19 and there is an urgent need for the development of vaccines and therapeutics. Coronavirus spike glycoproteins play a critical role in coronavirus entry into the host cells, as they provide host cell recognition and membrane fusion between virus and host cell. Thus, they emerged as popular and promising drug targets. Crystal structures of spike protein in its closed and open states were resolved very recently in March 2020. These structures comprise 77% of the sequence and provide almost the complete protein structure. Based on down and up positions of receptor binding domain (RBD), spike protein can be in a receptor inaccessible closed or receptor accessible open state, respectively. Starting from closed and open state crystal structures, and also 16 intermediate conformations, an extensive set of all-atom molecular dynamics (MD) simulations in the presence of explicit water and ions were performed. Simulations show that in its down position, RBD has significantly lower mobility compared to its up position; probably caused by the 6 interdomain salt bridges of RBD in down position compared to 3 in up position. Free energy landscapes based on MD simulations revealed a semi-open state located between closed and open states. Minimum energy pathway between down and up positions comprised a gradual salt bridge switching mechanism. Furthermore, although significantly lower than open state, ACE2 binding surface of RBD contained a partial solvent accessibility in its closed state.
Subcircuits of deep and superficial CA1 place cells support efficient spatial coding across heterogeneous environments
Authors: Sharif Farnaz , Tayebi Behnam , Buzsáki György , Royer Sebastien , Fernandez-Ruiz Antonio
Published: April 2020

The hippocampus is thought to guide navigation by forming a cognitive map of space. However, the behavioral demands for such a map can vary depending on particular features of a given environment. For example, an environment rich in cues may require a finer resolution map than an open space. It is unclear how the hippocampal cognitive map adjusts to meet these distinct behavioral demands. To address this issue, we examined the spatial coding characteristics of hippocampal neurons in mice and rats navigating different environments. We found that CA1 place cells located in the superficial sublayer were more active in cue-poor environments, and preferentially used a firing rate code driven by intra-hippocampal inputs. In contrast, place cells located in the deep sublayer were more active in cue-rich environments and expressed a phase code driven by entorhinal inputs. Switching between these two spatial coding modes was supported by the interaction between excitatory gamma inputs and local inhibition.
It is Never as Good the Second Time Around: Brain Areas Involved in Salience Processing Habituate During Repeated Drug Cue Exposure in Methamphetamine and Opioid Users
Authors: Ekhtiari Hamed , Kuplicki Rayus , Aupperle Robin P , Paulus Martin P.
Published: April 2020

Introduction

The brain response to drug-related cues is an important marker in addiction-medicine, however, the temporal dynamics of this response in repeated exposure to the cues are not well known yet. In an fMRI drug cue-reactivity task, the presence of rapid habituation or sensitization was investigated by modeling time and its interaction with condition (drug>neutral) using an initial discovery-sample. Replication of this temporal response was tested in two other clinical populations.

Methods

Sixty-five male participants (35.8±8.4 years-old) with methamphetamine use disorder (MUD) were recruited as the discovery-sample. A linear mixed effects model was used to identify areas with a time-by-condition interaction in the discovery-sample. Replication of these effects was tested in two other samples (29 female with MUD and 22 male with opioid use disorder). The second replication-sample was re-tested within two weeks.

Results

In the discovery-sample, clusters within the VMPFC, amygdala and ventral striatum showed both significant condition and condition-by-time interaction with a habituation response for the drug-related cues but not neutral cues. The estimates for the main effects and interactions were generally consistent between the discovery and replication-samples across all clusters. The re-test data showed consistent lack of drug>neutral and habituation response within all selected clusters in the second cue-exposure session.

Conclusions

VMPFC, amygdala and ventral striatum show a habituation in response to drug-related cues which is consistent among different clinical populations. Habituation in response in the first session of cue-exposure and lack of reactivity in the second session of exposure provide foundations for development of cue-desensitization interventions.
Identification of molecular specificity between reprogrammed cardiomyocytes and normal cardiomyocytes by bioinformatics
Authors: Liu Mengyao , Zhang yue
Published: April 2020

The adult human heart lacks an effective endogenous repair mechanism and cannot fully restore heart function after injury. We obtained two microarray data sets GSE99814 and GSE22292 from the NCBI GEO database, which include 5 groups of directly reprogrammed cardiomyocyte-like cells (iCMs) and 5 groups of normal mouse cardiomyocytes (CM). And through the GEO2R tool and Venn diagram software to screen the differentially expressed genes (DEG) between iCM and CM. Next, we performed functional enrichment analysis on these DEGs. The protein-protein interaction network (PPI) was constructed by STRING and Cytoscape for module analysis. We have selected a total of 243 DEGs consistently expressed genes in the two data sets, of which 127 up-regulated genes function and pathway enrichment mainly concentrated on biological processes such as innate immune response, inflammatory response, immune system process, positive regulation of apoptosis process and complement and coagulation cascade, while the 116 down-regulated genes are mainly enriched in cell cycle, cell division, cardiac development, myocardial contraction and myocardial cell development and signaling pathways such as cell cycle and adrenergic signaling in cardiomyocytes. Then in the PPI network, we found 27 central genes when analyzing these 243 DEGs by the Molecular Complex Detection (MCODE) plug-in. Finally, we reanalyzed these 27 central genes through DAVID and found that 6 genes (CCNB1, CCNB2, BUB1, TTK, CDC25C, CCNA2) significantly enriched the cell cycle signaling pathway (p<1.20E-07). Therefore, through integrated bioinformatics methods, we found that compary with iCMs and CMs, iCMs were induced by direct reprogramming of neonatal mouse cardiomyocytes, the DEGs were mainly enriched in immune-related processes and myocardial contraction and cell cycle signaling pathways (p< 0.05).
Comprehensive Chromosome End Remodeling During Programmed DNA Elimination
Authors: Wang Jianbin , Veronezi Giovana M.B. , Kang Yuanyuan , Zagoskin Maxim , O’Toole Eileen T. , Davis Richard E.
Published: April 2020

Germline and somatic genomes are typically the same in a multicellular organism. However, in some organisms including the parasitic nematodeAscaris, programmed DNA elimination leads to a reduced somatic genome compared to germline cells. Previous work on the parasitic nematodeAscarisdemonstrated that programmed DNA elimination encompasses high fidelity chromosomal breaks at specific genome locations and loss of specific genome sequences including a major tandem repeat of 120 bp and ~1,000 germline-expressed genes. However, the precise chromosomal locations of the 120 bp repeats, the breaks regions, and the eliminated genes remained unknown. Here, we used PacBio long-read sequencing and chromosome conformation capture (Hi-C) to obtain fully assembled chromosomes ofAscarisgermline and somatic genomes, enabling a complete chromosomal view of DNA elimination. Surprisingly, we found that all 24 germline chromosomes undergo comprehensive chromosome end remodeling with DNA breaks in their subtelomeric regions and loss of distal sequences including the telomeres at both chromosome ends. All newAscarissomatic chromosome ends are recapped byde novotelomere healing. We provide an ultrastructural analysis of DNA elimination and show thatAscariseliminated DNA is incorporated into many double membrane-bound structures, similar to micronuclei, during telophase of a DNA elimination mitosis. These micronuclei undergo dynamic changes including loss of active histone marks and localize to the cytoplasm following daughter nuclei formation and cytokinesis where they form autophagosomes. Comparative analysis of nematode chromosomes suggests that germline chromosome fusions occurred formingAscarissex chromosomes that become independent chromosomes following DNA elimination breaks in somatic cells. These studies provide the first chromosomal view and define novel features and functions of metazoan programmed DNA elimination.
Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients
Authors: Ihling Christian , Tänzler Dirk , Hagemann Sven , Kehlen Astrid , Hüttelmaier Stefan , Sinz Andrea
Published: April 2020

Mass spectrometry (MS) can deliver valuable diagnostic data that complements genomic information and allows us to increase our current knowledge of the COVID-19 disease caused by the SARS-CoV-2 virus. We developed a simple, MS-based method to specifically detect SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. Our protocol consists of an acetone precipitation and tryptic digestion of proteins contained within the gargle solution, followed by a targeted MS analysis. Our methodology identifies unique peptides originating from SARS-CoV-2 nucleoprotein. Building on these promising initial results, faster MS protocols can now be developed as routine diagnostic tools for COVID-19 patients.

Graphical Abstract

Image credit (left): Gerd Altmann, Pixabay License,https://pixabay.com/illustrations/corona-coronavirus-virus-covid-19-4959447
A Timescale for the Radiation of Photosynthetic Eukaryotes
Authors: Evanovich Eliane , de Souza Mendonça-Mattos Patricia Jeanne , Guerreiro João Farias
Published: April 2020

Oxygenic photosynthesis is considered the most important evolutionary innovation in the history of Earth. It depends on two photosystems, responsible for the photolysis of water and the reduction of carbon dioxide. Oxygen and carbohydrates are released at the end of the reaction. Extraordinary, the oxygen released created the stratospheric ozone layer, and transformed the ocean chemistry, whereas the carbohydrates are the primary source of energy for complex cells. Several lines of evidence indicate the photosynthesis arose in the ancestors of cyanobacteria. It was spread over some eukaryotes by the acquisition of a free-living cyanobacterium, which evolved into photosynthetic plastid, the chloroplast. The timing of the chloroplast emergence is still controversy. Estimated ages range from 600 to 2100 million years ago (Mya) in accordance to previous studies. The aim of this study is to clarify several aspects of the origin and diversification of photosynthetic eukaryotes. For this purpose, we utilized a data set based on 27 protein-coding genes from genomes of cyanobacteria and photosynthetic eukaryotes, more genes than other papers that also utilized plastid genes, and performed the Bayesian analysis method to estimate the divergence times of the photosynthetic eukaryotes. Results showed photosynthetic eukaryotes emerged Late Mesoproterozoic about 1342 Mya. The Early Proterozoic oceans did not have adequate conditions for eukaryotes, because chemical elements such as zinc and molybdenum were at reduced concentrations, and they are essential to the formation of eukaryotic proteins.
Neurophysiological indices of audiovisual speech integration are enhanced at the phonetic level for speech in noise
Authors: O’Sullivan Aisling E. , Crosse Michael J. , Di Liberto Giovanni M. , de Cheveigné Alain , Lalor Edmund C.
Published: April 2020

Seeing a speaker’s face benefits speech comprehension, especially in challenging listening conditions. This perceptual benefit is thought to stem from the neural integration of visual and auditory speech at multiple stages of processing, whereby movement of a speaker’s face provides temporal cues to auditory cortex, and articulatory information from the speaker’s mouth can aid recognizing specific linguistic units (e.g., phonemes, syllables). However it remains unclear how the integration of these cues varies as a function of listening conditions. Here we sought to provide insight on these questions by examining EEG responses to natural audiovisual, audio, and visual speech in quiet and in noise. Specifically, we represented our speech stimuli in terms of their spectrograms and their phonetic features, and then quantified the strength of the encoding of those features in the EEG using canonical correlation analysis. The encoding of both spectrotemporal and phonetic features was shown to be more robust in audiovisual speech responses then what would have been expected from the summation of the audio and visual speech responses, consistent with the literature on multisensory integration. Furthermore, the strength of this multisensory enhancement was more pronounced at the level of phonetic processing for speech in noise relative to speech in quiet, indicating that listeners rely more on articulatory details from visual speech in challenging listening conditions. These findings support the notion that the integration of audio and visual speech is a flexible, multistage process that adapts to optimize comprehension based on the current listening conditions.

Significance Statement

During conversation, visual cues impact our perception of speech. Integration of auditory and visual speech is thought to occur at multiple stages of speech processing and vary flexibly depending on the listening conditions. Here we examine audiovisual integration at two stages of speech processing using the speech spectrogram and a phonetic representation, and test how audiovisual integration adapts to degraded listening conditions. We find significant integration at both of these stages regardless of listening conditions, and when the speech is noisy, we find enhanced integration at the phonetic stage of processing. These findings provide support for the multistage integration framework and demonstrate its flexibility in terms of a greater reliance on visual articulatory information in challenging listening conditions.
Concerted interactions between multiple gp41 trimers and the target cell lipidome may be required for HIV-1 entry
Authors: Gorai Biswajit , Sahoo Anil Kumar , Srivastava Anand , Dixit Narendra M. , Maiti Prabal K.
Published: April 2020

The HIV-1 envelope glycoprotein gp41 mediates the fusion between viral and host cell membranes leading to virus entry and target cell infection. Despite years of research, important aspects of this process such as the number of gp41 trimers involved and how they orchestrate the rearrangement of the lipids in the apposed membranes along the fusion pathway remain obscure. To elucidate these molecular underpinnings, we performed coarse-grained molecular dynamics simulations of HIV-1 virions pinned to the CD4 T cell membrane by different numbers of gp41 trimers. We built realistic cell and viral membranes by mimicking their respective lipid compositions. We found that a single gp41 was inadequate for mediating fusion. Lipid mixing between membranes, indicating the onset of fusion, was efficient when 3 or more gp41 trimers pinned the membranes. The gp41 trimers interacted strongly with many different lipids in the host cell membrane, triggering lipid configurational rearrangements, exchange, and mixing. Simpler membranes, comprising fewer lipid types, displayed strong resistance to fusion, revealing the crucial role of the lipidomes in HIV-1 entry. Performing simulations at different temperatures, we estimated the free energy barrier to lipid mixing, and hence membrane stalk formation, with 4 tethering gp41 trimers to be ~6.2 kcal/mol, a >4-fold reduction over estimates without gp41. Together, these findings present molecular-level, quantitative insights into the early stages of gp41-mediated HIV-1 entry. Preventing the requisite gp41 molecules from tethering the membranes or altering membrane lipid compositions may be potential intervention strategies.

SIGNIFICANCE

Interactions between viral envelope proteins and host cell surface receptors leading to HIV-1 entry are well studied, however the role of membrane lipids remains obscure, although entry hinges on lipid mixing and the fusion of viral and cell membranes. We performed detailed simulations of HIV-1 and target cell membranes tethered by viral gp41 trimeric proteins to elucidate the proteo-lipidic contributions to viral entry. We found that the cooperative effects of multiple gp41 trimers and natural lipidomes of the membranes facilitate membrane fusion. The functional domains of gp41 altered local lipid concentrations, reduced membrane repulsions, and facilitated inter-membrane lipid mixing. These molecular-level insights offer a glimpse of the cryptic mechanisms underlying HIV-1 entry and suggest new interventions to combat HIV-1 infection.
Chronic Developmental Lead Exposure increases μ-Opiate Receptor Levels in the Adolescent Rat Brain
Authors: Albores-Garcia Damaris , McGlothan Jennifer L , Bursac Zoran , Guilarte Tomás R.
Published: April 2020

Opioid use and abuse has reached epidemic proportion in the United States resulting in a significant numbers of deaths due to overdose. While environmental factors are implicated in opioid addiction, less is known about the role of exposure to environmental pollutants on the brain opioid system. Human and preclinical studies have suggested an association between childhood lead (Pb2+) intoxication and proclivity to substance abuse and delinquent behavior. Opioid receptors are involved in the biological effects of opioids and other drugs of abuse. In this study, we examine the effect of chronic developmental Pb2+exposure on μ-opioid receptor (MOR) levels in the rat brain using [3H]-D-Ala2-MePhe4-Gly-ol5 enkephalin ([3H]-DAMGO) quantitative receptor autoradiography.

Our results indicate that chronic developmental Pb2+exposure increases the levels of [3H]-DAMGO specific binding to MOR in several limbic regions of the brain in male and female rats during the pre-adolescence (PN14) and early-adolescence (PN28) period. These changes were less pronounced in late-adolescence (PN50) and adult (PN120) animals. Our findings are important because the pre-adolescence and early adolescence period is a time in which there is higher engagement in reward and drug seeking behaviors in humans.

In summary, we show that chronic exposure to Pb2+an ubiquitous and well-known environmental contaminant and neurotoxicant, alters MOR levels in brain regions associated with addiction circuits in the adolescent period with important implications to opioid drug use and abuse.
Rapid ‘multi-directed’ cholinergic transmission at central synapses
Authors: Sethuramanujam Santhosh , Matsumoto Akihiro , McIntosh J. Michael , Jing Miao , Li Yulong , Berson David , Yonehara Keisuke , Awatramani Gautam B.
Published: April 2020

Acetylcholine (ACh) is a key neurotransmitter that plays diverse roles in many parts of the central nervous system, including the retina. However, assessing the precise spatiotemporal dynamics of ACh is technically challenging and whether ACh transmits signals via rapid, point-to-point synaptic mechanisms, or broader-scale ‘non-synaptic’ mechanisms has been difficult to ascertain. Here, we examined the properties of cholinergic transmission at individual contacts made between direction-selective starburst amacrine cells and downstream ganglion cells in the retina. Using a combination of electrophysiology, serial block-face electron microscopy, and two-photon ACh imaging, we demonstrate that ACh signaling bears the hallmarks of both non-synaptic and synaptic forms of transmission. ACh co-activates nicotinic ACh receptors located on the intersecting dendrites of pairs of ganglion cells, with equal efficiency (non-synaptic)— and yet retains the ability to generate rapid ‘miniature’ currents (∼1 ms rise times: synaptic). Fast cholinergic signals do not appear to depend on anatomically well-defined synaptic structures. We estimate that ACh spread is limited to ∼1-2µm from its sites of release, which may help starbursts drive local direction-selective cholinergic responses in ganglion cell dendrites. Together, our results establish the functional architecture for cholinergic signaling at a central synapse and propose a novel motif whereby single presynaptic sites can co-transmit information to multiple neurons on a millisecond timescale.
Quantitative partition of the rhizosphere microbiota assembly processes
Authors: Ling Ning , Xue Chao , Vandenkoornhuyse Philippe , Shen Qirong
Published: April 2020

The soil microbial reservoir and plant recruitment are predominant forces determining microbiota assembly in rhizosphere (i.e. active and passive processes respectively), but to date, no straightforward method to evaluate the respective contribution of forces to the rhizospheric microbiota assembly rules is available. We propose herein a promising way to quantitatively partition the assembling forces of rhizosphere microbiota using ordination metrics. We anticipate that this new method can not only weight the plants individual contributions to microbiota assembly in rhizosphere, but can also indirectly provide a way to quantitatively evaluate soil health by the contribution from plant selection.
Haploinsufficient tumour suppressor PRP4K is negatively regulated during epithelial-to-mesenchymal transition
Authors: Clarke Livia E. , Cook Allyson , Mathavarajah Sabateeshan , Bera Amit , Salsman Jayme , Habib Elias , Van Iderstine Carter , Bydoun Moamen , Lewis Stephen M. , Dellaire Graham
Published: April 2020

The pre-mRNA processing factor 4 kinase (PRP4K, also known as PRPF4B) is an essential gene. However, reduced PRP4K expression is associated with aggressive breast and ovarian cancer phenotypes including taxane therapy resistance, increased cell migration and invasion in vitro and cancer metastasis in mice; results consistent with PRP4K being a haploinsufficient tumour suppressor. Increased cell migration and invasion is associated with epithelial-to-mesenchymal transition (EMT), but how reduced PRP4K levels affect normal epithelial cell migration or EMT has not been studied. Depletion of PRP4K by small hairpin RNA (shRNA) in non-transformed mammary epithelial cell lines (MCF10A, HMLE) reduced or had no effect on 2D migration in the scratch assay but resulted in greater invasive potential in 3D transwell assays. Depletion of PRP4K in mesenchymal triple negative breast cancer cells (MDA-MB-231) resulted in both enhanced 2D migration and 3D invasion, with 3D invasion correlated with higher fibronectin levels in both MDA-MB-231 and MCF10A cells and without changes in E-cadherin. Induction of EMT in MCF10A cells, by treatment with WNT-5a and TGF-β1, or depletion of eukaryotic translation initiation factor 3e (eIF3e) by shRNA, resulted in significantly reduced PRP4K expression. Mechanistically, induction of EMT by WNT-5a/TGF-β1 reduced PRP4K transcript levels, whereas eIF3e depletion led to reduced PRP4K translation. Finally, reduced PRP4K levels after eIF3e depletion correlated with increased YAP activity and nuclear localization, both of which are reversed by overexpression of exogenous PRP4K. Thus, PRP4K is a haploinsufficient tumour suppressor negatively regulated by EMT, that when depleted in normal mammary cells can increase cell invasion without inducing full EMT.
Endosomal spatio-temporal modulation of the cortical RhoA zone conditions epithelial cell organization
Authors: Cécile Gaston , Simon De Beco , Bryant Doss , Meng Pan , Estelle Gauquelin , Joseph D’Alessandro , Teck Lim Chwee , Benoit Ladoux , Delphine Delacour
Published: April 2020

At the basis of cell shape and behavior, actomyosin organization and force-generating property are widely studied, however very little is known about the regulation of the contractile network in space and time. Here we study the role of the epithelial-specific protein EpCAM, a contractility modulator, in cell shape and motility, and we show that it is required for the maturation of stress fibers and frontrear polarity acquisition at the single cell level. There, EpCAM ensures the remodeling of a transient active RhoA zone in the cortex of spreading epithelial cells. GTP-RhoA follows the endosomal pathway mediated by Rab35 and EHD1, where it co-evolves together with EpCAM. In fact, EpCAM balances GTP-RhoA turnover in order to tune actomyosin remodeling for cell shape, polarity and mechanical property acquisition. Impairment of GTP-RhoA endosomal trafficking either by EpCAM silencing or Rab35 / EHD1 mutant expression prevents correct myosin-II activity, stress fiber formation, and ultimately cell polarization. Collectively, this work shows that the coupling of EpCAM/RhoA co-trafficking to actomyosin rearrangement is critical for spreading, and advances our understanding of how biochemical and mechanical properties can be coupled for cell plasticity.
PROX1 transcription factor is a master regulator of myogenic and oncogenic features of rhabdomyosarcoma
Authors: Gizaw Nebeyu Yosef , Kallio Pauliina , Punger Tatjana , Kinnunen Matias , Gucciardo Erika , Lehti Kaisa , Haglund Caj , Böhling Tom , Varjosalo Markku , Sampo Mika , Alitalo Kari , Kivelä Riikka
Published: April 2020

Rhabdomyosarcoma (RMS) is an aggressive pediatric soft tissue cancer in need for novel therapies. Here we show that the PROX1 transcription factor, which is essential for normal myoblast differentiation, is highly expressed in RMS tumors. We demonstrate that PROX1 is needed for RMS cell stemness and growthin vitro, and for RMS tumor formation in mouse xenograft models. In addition, we unveil that PROX1 is an essential for myogenic properties in RMS. PROX1 depletion reprogrammed the RMS transcriptome to resemble benign mesenchymal stem cells and repressed many of the previously identified RMS effector transcripts and myogenic genes. By using proximity labeling and mass spectrometry, we found that PROX1 interacts with the NuRD and CoREST complexes containing class I HDACs. Our studies reveal a major role of PROX1-HDAC interaction in RMS and give insights that inhibiting this interaction could be a promising therapeutic approach.
Parallel RNA and DNA analysis after Deep-sequencing (PRDD-seq) reveals cell type specific lineage patterns in human brain
Authors: Huang August Yue , Li Pengpeng , Rodin Rachel E. , Kim Sonia N. , Dou Yanmei , Kenny Connor J. , Akula Shyam K. , Hodge Rebecca D. , Bakken Trygve E. , Miller Jeremy A. , Lein Ed S. , Park Peter J. , Lee Eunjung Alice , Walsh Christopher A.
Published: April 2020

Elucidating the lineage relationships among different cell types is key to understanding human brain development. Here we developedParallelRNA andDNA analysis afterDeep-sequencing (PRDD-seq), which combines RNA analysis of neuronal cell types with analysis of nested spontaneous DNA somatic mutations as cell lineage markers, identified from joint analysis of single cell and bulk DNA sequencing by single-cell MosaicHunter (scMH). PRDD-seq enables the first-ever simultaneous reconstruction of neuronal cell type, cell lineage, and sequential neuronal formation (“birthdate”) in postmortem human cerebral cortex. Analysis of two human brains showed remarkable quantitative details that relate mutation mosaic frequency to clonal patterns, confirming an early divergence of precursors for excitatory and inhibitory neurons, and an “inside-out” layer formation of excitatory neurons as seen in other species. In addition our analysis allows the first estimate of excitatory neuron-restricted precursors (about 10) that generate the excitatory neurons within a cortical column. Inhibitory neurons showed complex, subtype-specific patterns of neurogenesis, including some patterns of development conserved relative to mouse, but also some aspects of primate cortical interneuron development not seen in mouse. PRDD-seq can be broadly applied to characterize cell identity and lineage from diverse archival samples with single-cell resolution and in potentially any developmental or disease condition.

Significance Statement

Stem cells and progenitors undergo a series of cell divisions to generate the neurons of the brain, and understanding this sequence is critical to studying the mechanisms that control cell division and migration in developing brain. Mutations that occur as cells divide are known as the basis of cancer, but have more recently been shown to occur with normal cell divisions, creating a permanent, forensic map of the clonal patterns that define the brain. Here we develop new technology to analyze both DNA mutations and RNA gene expression patterns in single cells from human postmortem brain, allowing us to define clonal patterns among different types of human brain neurons, gaining the first direct insight into how they form.
Identification of Human Immune Cell Subtypes Most Vulnerable to IL-1β-induced Inflammatory Signaling Using Mass Cytometry
Authors: Kothari Hema , Williams Corey M. , McSkimming Chantel , Vigneshwar Mythili , Zunder Eli R. , McNamara Coleen A.
Published: April 2020

IL-1β has emerged as a key mediator of the cytokine storm linked to high morbidity and mortality from COVID-19 and blockade of the IL-1 receptor (IL-1R) with Anakinra has entered clinical trials in COVID-19 subjects. Yet, knowledge of the specific immune cell subsets targeted by IL-1β and IL-1β-induced signaling pathways in humans is limited. Utilizing mass cytometry (CyTOF) of human peripheral blood mononuclear cells, we identified effector memory CD4 T cells and CD4−CD8low/-CD161+T cells as the circulating immune subtypes with the greatest expression of p-NF-κB in response to IL-1β stimulation. Notably, CCR6 distinctly identified T cells most responsive to IL-1β. Other subsets including CD11c myeloid dendritic cells (mDCs), classical monocytes (CM), two subsets of natural killer cells (CD16−CD56brightCD161−and CD16−CD56dimCD161+) and a population of lineage−(Lin-) cells expressing CD161 and CD25 also showed IL-1β-induced expression of p-NF-kB. The IL-1R antagonist, Anakinra significantly inhibited IL-1β-induced p-NF-kB in the CCR6+T cells and CD11c mDCs with a trending inhibition in CD14 monocytes and Lin−CD161+CD25+cells. IL-1β also induced a rapid but much less robust increase in p-p38 expression as compared to p-NF-kB in the majority of these same immune cell subsets. Prolonged IL-1β stimulation greatly increased p-STAT3 and to a much lesser extent p-STAT1 and p-STAT5 in T cell subsets, monocytes, DCs and the Lin−CD161+CD25+cells suggesting IL-1β-induced production of downstream STAT-activating cytokines, consistent with its role in cytokine storm. Interindividual heterogeneity and inhibition of this activation by Anakinra raises the intriguing possibility that assays to measure IL-1β-induced p-NF-kB in CCR6+T cell subtypes could identify those at higher risk of cytokine storm and those most likely to benefit from Anakinra therapy.
Metabolic and functional impairment of CD8+ T cells from the lungs of influenza-infected obese mice
Authors: Green William D. , Al-Shaer Abrar E. , Shi Qing , MacIver Nancie J , Beck Melinda A. , Shaikh Saame Raza
Published: April 2020

Background

Obesity increases influenza disease risk in millions of adults worldwide. In this study, we investigated the effect of diet-induced obesity on pulmonary CD8+ T cell metabolism and function as a mechanism of impairment.

Methods

Male C57BL/6J mice were fed either control (10% kcal/g) or high-fat (60% kcal/g) diet. Sub-lethal A/PR/8/34 influenza virus infection generated a robust pulmonary immune response. T cell metabolism and function were assessed at day 10 and day 24 post infection.

Results

At day 10 post infection, CD8+ T cells from obese mice had impaired oxidative and glycolytic metabolism, greater fatty acid uptake, and decreased effector populations and cytokine production. At infection resolution, obese mice had lower numbers of naïve and central memory CD8+ T cell populations in the lungs.

Conclusion

Diet-induced obesity increases influenza virus pathogenesis through CD8+ T cell mediated metabolic reprogramming resulting in suppressed effector CD8+ T cell function.

Diet-induced obesity impairs the metabolism of pulmonary CD8+ T cells resulting in reduced effector CD8+ T cells and cytokine production following primary influenza infection.