bluuebunny/crossref_metadata_2025 huggingface dataset:
SARS-CoV-2 Envelope (E) Protein Interacts with PDZ-Domain-2 of Host Tight Junction Protein ZO1
Authors: Shepley-McTaggart Ariel , Sagum Cari A. , Oliva Isabela , Rybakovsky Elizabeth , DiGuilio Katie , Liang Jingjing , Bedford Mark T. , Cassel Joel , Sudol Marius , Mullin James M. , Harty Ronald N.
Published: December 2020

Newly emerged SARS-CoV-2 is the cause of an ongoing global pandemic leading to severe respiratory disease in humans. SARS-CoV-2 targets epithelial cells in the respiratory tract and lungs, which can lead to amplified chloride secretion and increased leak across epithelial barriers, contributing to severe pneumonia and consolidation of the lungs as seen in many COVID-19 patients. There is an urgent need for a better understanding of the molecular aspects that contribute to SARS-CoV-2-induced pathogenesis and for the development of approaches to mitigate these damaging pathologies. The multifunctional SARS-CoV-2 Envelope (E) protein contributes to virus assembly/egress, and as a membrane protein, also possesses viroporin channel properties that may contribute to epithelial barrier damage, pathogenesis, and disease severity. The extreme C-terminal (ECT) sequence of E also contains a putative PDZ-domain binding motif (PBM), similar to that identified in the E protein of SARS-CoV-1. Here, we screened an array of GST-PDZ domain fusion proteins using either a biotin-labeled WT or mutant ECT peptide from the SARS-CoV-2 E protein. Notably, we identified a singular specific interaction between the WT E peptide and the second PDZ domain of human Zona Occludens-1 (ZO1), one of the key regulators of TJ formation/integrity in all epithelial tissues. We used homogenous time resolve fluorescence (HTRF) as a second complementary approach to further validate this novel modular E-ZO1 interaction. We postulate that SARS-CoV-2 E interacts with ZO1 in infected epithelial cells, and this interaction may contribute, in part, to tight junction damage and epithelial barrier compromise in these cell layers leading to enhanced virus spread and severe respiratory dysfunction that leads to morbidity. Prophylactic/therapeutic intervention targeting this virus-host interaction may effectively reduce airway barrier damage and mitigate virus spread.
Elucidating the antiviral mechanism of different MARCH factors
Authors: Umthong Supawadee , Lynch Brian , Timilsina Uddhav , Waxman Brandon , Ivey Emily B. , Stavrou Spyridon
Published: December 2020

The Membrane Associated RING-CH (MARCH) proteins belong to a family of E3 ubiquitin ligases, whose main function is to remove transmembrane proteins from the plasma membrane. Recent work has shown that the human MARCH1, 2 and 8 are antiretroviral factors that target the Human Immunodeficiency virus-1 (HIV-1) envelope glycoproteins by reducing their incorporation in the budding virions. Nevertheless, the dearth of information regarding the antiviral mechanism of this family of proteins necessitates further examination. In this study, using both the human MARCH proteins and their mouse homologues, we provide a comprehensive analysis of the antiretroviral mechanism of this family of proteins. Moreover, we show that human MARCH proteins restrict to varying degrees the envelope glycoproteins of a diverse number of viruses. This report sheds light on the important antiviral function of MARCH proteins and their significance in cell intrinsic immunity.
Long-read assemblies reveal structural diversity in genomes of organelles - an example withAcacia pycnantha
Authors: Syme Anna E. , McLay Todd G.B. , Udovicic Frank , Cantrill David J. , Murphy Daniel J.
Published: December 2020

Although organelle genomes are typically represented as single, static, circular molecules, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle,Acacia pycnantha,using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using ade novoassembly approach agnostic to previous hypotheses about structure, we found different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths.
RoDiCE: Robust differential protein co-expression analysis for cancer complexome
Authors: Matsui Yusuke , Abe Yuichi , Uno Kohei , Miyano Satoru
Published: December 2020

Motivation

The full spectrum of abnormalities in cancer-associated protein complexes remains largely unknown. Comparing the co-expression structure of each protein complex between tumor and healthy cells may provide insights regarding cancer-specific protein dysfunction. However, the technical limitations of mass spectrometry-based proteomics, including contamination with biological protein variants, causes noise that leads to non-negligible over- (or under-) estimating co-expression.

Results

We propose a robust algorithm for identifying protein complex aberrations in cancer based on differential protein co-expression testing. Our method based on a copula is sufficient for improving identification accuracy with noisy data compared to conventional linear correlation-based approaches. As an application, we use large-scale proteomic data from renal cancer to show that important protein complexes, regulatory signaling pathways, and drug targets can be identified. The proposed approach surpasses traditional linear correlations to provide insights into higher order differential co-expression structures.

Availability and Implementation

https://github.com/ymatts/RoDiCE.
Fam72acontrols the balance between error-prone and error-free DNA repair during antibody diversification
Authors: Rogier Mélanie , Moritz Jacques , Robert Isabelle , Lescale Chloé , Heyer Vincent , Thomas-Claudepierre Anne-Sophie , Abello Arthur , Deriano Ludovic , Reina-San-Martin Bernardo
Published: December 2020

Efficient humoral responses rely on DNA damage, mutagenesis and error-prone DNA repair. B cell receptor diversification through somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by cytidine deamination in DNA mediated by activation induced cytidine deaminase (AID)1and by the subsequent excision of the resulting uracils by Uracil DNA glycosylase (UNG) and by mismatch repair (MMR) proteins2–4. Although uracils arising in DNA are faithfully repaired2–7, it is not known how these pathways are co-opted to generate mutations and double stranded DNA breaks (DSBs) in the context of SHM and CSR2,4,8. Here we have performed a genome-wide CRISPR/Cas9 knockout screen for genes involved in CSR. The screen identified FAM72A, a protein that interacts with the nuclear isoform of UNG (UNG2)9and that is overexpressed in several cancers9. We show that the FAM72A-UNG2 interaction controls the protein levels of UNG2 and that CSR is defective inFam72a−/−B cells due to the specific upregulation of UNG2. Moreover, we show that inFam72a−/−B cells SHM is reduced by 5-fold and that upregulation of UNG2 results in a skewed mutation pattern. Our results are consistent with a model in which FAM72A interacts with UNG2 to control its physiological level by triggering its degradation. Consequently, deficiency inFam72aleads to supraphysiological levels of UNG2 and enhanced uracil excision, shifting the balance from error-prone to error-free DNA repair. Our findings have potential implications for tumorigenesis, asFam72aoverexpression would lead to reduced UNG2 levels, shifting the balance toward mutagenic DNA repair and rendering cells more prone to acquire mutations.
Distinct VIP interneurons in the cingulate cortex encode anxiogenic and social stimuli
Authors: Johnson Connor , Kretsge Lisa N. , Yen William W. , Sriram Balaji , Jimenez Jessica C. , Jinadasa Tushare J. , O’Connor Alexandra , Sky Liu Ruichen , Nguyen Thanh P. H. , Cho Eun Seon , Fuchs Erelle , Spevack Eli D. , Velasco Berta Escude , Hausmann Frances S. , Cruz-Martín Alberto
Published: December 2020

A hallmark of higher-order cortical regions is their functional heterogeneity, but it is not well understood how these areas encode such diverse information. The anterior cingulate cortex (ACC), for example, is important in both emotional regulation and social cognition. Previous work shows activation of the ACC to anxiety-related and social stimuli, but it is unknown how subpopulations or microcircuits within the ACC simultaneously encode these distinct stimuli. One type of inhibitory interneuron, which is positive for vasoactive intestinal peptide (VIP), is known to alter the activity of many cells in local cortical microcircuits, but it is unknown whether the activity of VIP cells in the ACC (VIPACC) encodes anxiety-related or social information. Using in vivo calcium imaging and miniscopes in freely behaving mice to monitor VIPACCactivity, we identified distinct, non-overlapping subpopulations of VIPACCthat preferentially activated to either anxiogenic, anxiolytic, social, or non-social stimuli. We determined that stimulus-selective cells encode the animal’s behavioral states and VIP interneuron clusters may co-activate, improving this encoding. Finally, we used trans-synaptic tracing to show that VIPACCreceive widespread inputs from regions implicated in emotional regulation and social cognition. These findings demonstrate not only that the ACC is not homogeneous in its function, but also that there is marked functional heterogeneity even within disinhibitory interneuron populations. This work contributes to our understanding of how the cortex encodes information across diverse contexts and provides insight into the complexity of neural processes involved in anxiety and social behavior.
Population genetics of recent colonization suggests the importance of recurrent immigration on remote islands
Authors: Aoki Daisuke , Matsui Shin , Esashi Mari , Nishiumi Isao , Nagata Junco , Takagi Masaoki
Published: December 2020

Aim

Founder effects and recurrent immigration are two major factors that potentially contribute to genetic differentiation and population persistence in the early-stage of remote island colonization. However, their relative importance remains controversial. By conducting population genetics analyses of multiple remote island populations of the bull-headed shrike established naturally within several decades, we examined the relative contributions of founder effects and recurrent immigration on these island populations.

Location

Japan

Taxon

Lanius bucephalus

Methods

We used 15 microsatellite loci to analyze the population genetics of four newly established island populations and five Japanese mainland populations. Allelic richness, heterozygosity, genetic differentiation, and the strength of the genetic bottleneck were compared among the islands. Two analyses, STRUCTURE and the DAPC, were conducted to assess the relative influence of founder effects and recurrent immigration on genetic differentiation. Temporal samples collected over eight years on Minami-Daito Island were used to detect any change in genetic structure due to recurrent immigration.

Results

The founder effect strongly influenced genetic differentiation on the most remote oceanic island, Chichi-jima Island. However, this population became extinct 20 years after colonization, possibly owing to a lack of recurrent immigration. The founder effect moderately influenced a land-bridge island, Kikai-jima Island, indicating the presence of a relatively large founder population without recurrent immigration. Surprisingly, another distant oceanic island, Minami-Daito Island, was likely subject to multiple recurrent immigration events from the mainland, which obscured any genetic differentiation previously established by the founder effect.

Main conclusion

Underlying the island-specific population dynamics of colonization, founder effects contributed to the genetic differentiation among the three studied island populations. Importantly, however, recurrent immigration strongly affected the population persistence and subsequent evolutionary processes of remote island populations, potentially overwhelming the founder effect. We argue the importance of recurrent immigration in highly remote island colonization, which has been previously overlooked.
Risk factors for community transmission of SARS-CoV-2. A cross-sectional study in 116,678 people
Authors: Kjetland Eyrun F. , Kalleberg Karl Trygve , Søraas Camilla Lund , Hammarström Bato , Myklebust Tor Åge , Jenum Synne , Axelsen Eyvind , Lind Andreas , Bævre-Jensen Roar , Jørgensen Silje Bakken , Pettersen Frank Olav , Solberg Lene B. , Hadley Cathrine Lund , Istre Mette S. , Liestøl Knut , Dahl John Arne , Ursin Giske , Søraas Arne
Published: December 2020

Background

The risk factors for SARS-CoV-2 transmission are not well characterised in Western populations. We sought to identify potential risk factors for transmission and actionable information to prevent for SARS-CoV-2.

Methods

Individuals tested for SARS-CoV-2 at four major laboratories were invited. In addition, participants were sampled by convenience after a media campaign. Self-reported test results were compared with laboratory results, demographic data and behavioural facts were collected using a digital platform. In a cross-sectional design positive cases were compared with negative and untested control groups.

Findings

Approximately 14 days after a countrywide lockdown in Norway, 116,678 participants were included. Median age was 46 years, 44% had children in preschool or in school; 18% were practicing health professionals. International flights, contact with infected, and gatherings of more than 50 people, were associated with high risk. Health professionals who used public transport were at higher risk of testing positive than those who did not. Having undergone light infections, the last six months was strongly associated with lower odds ratio of SARS-CoV-2 positivity. Contact with children, use of hand sanitiser and use of protective gloves in private were also associated with lower odds ratio of testing positive for SARS-CoV-2.

Interpretation

Further research is needed to explore if being a parent or looking after children is associated with lower risk of SARS-CoV-2 positivity in the next phases of the pandemic. Immunological research should be done to determine the effects of prior trivial infections on SARS-CoV-2 infection. We confirm that large gatherings during the pandemic should be avoided and those who are infected, or under suspicion thereof, posed very high risks to others this population.
Risk Assessment and Mitigation of Airborne Disease Transmission in Orchestral Wind Instrument Performance
Authors: Abraham Aliza , He Ruichen , Shao Siyao , Kumar S. Santosh , Wang Changchang , Guo Buyu , Trifonov Maximilian , Placucci Rafael Grazzini , Willis Mele , Hong Jiarong
Published: December 2020

There has been growing concern about high risk of airborne infection during wind instrument performance as the COVID-19 pandemic evolves. In collaboration with 16 musicians from the Minnesota Orchestra, we employ multiple experimental and numerical techniques to quantify the airflow and aerosol concentration emitted from ten wind instruments under realistic performance conditions. For all instruments, the extent of the flow and aerosol influence zones are limited to 30 cm. Further away, the thermal plume generated by the human body is the dominant source of flow. Flow and aerosol concentration vary in response to changes in music amplitude, pitch, and note duration, depending on playing technique and instrument geometry. Covering the trumpet bell with speaker cloth and placing filters above the instrument outlet can substantially reduce the aerosol concentration. Our findings indicate that with appropriate risk mitigation strategies, musical instrument performance can be conducted with low risk of airborne disease transmission.
Spotlight on the dark figure: Exhibiting dynamics in the case detection ratio of COVID-19 infections in Germany
Authors: Schneble Marc , De Nicola Giacomo , Kauermann Göran , Berger Ursula
Published: December 2020

The case detection ratio of COVID-19 infections varies over time due to changing testing capacities, modified testing strategies and also, apparently, due to the dynamics in the number of infected itself. In this paper we investigate these dynamics by jointly looking at the reported number of detected COVID-19 infections with non-fatal and fatal outcomes in different age groups in Germany. We propose a statistical approach that allows us to spotlight the case detection ratio and quantify its changes over time. With this we can adjust the case counts reported at different time points so that they become comparable. Moreover we can explore the temporal development of the real number of infections, shedding light on the dark number. The results show that the case detection ratio has increased and, depending on the age group, is four to six times higher at the beginning of the second wave compared to what it was at the peak of the first wave. The true number of infection in Germany in October was considerably lower as during the peak of the first wave, where only a small fraction of COVID-19 infections were detected. Our modelling approach also allows quantifying the effects of different testing strategies on the case detection ratio. The analysis of the dynamics in the case detection rate and in the true infection figures enables a clearer picture of the course of the COVID-19 pandemic.
Improving the heterologous production of fungal peroxygenases through an episomalPichia pastorispromoter and signal peptide shuffling system
Authors: Püllmann Pascal , Weissenborn Martin J.
Published: December 2020

Fungal Peroxygenases (UPOs) have emerged as oxyfunctionalization catalysts of tremendous interest in recent years. However, their widespread use in the field of biocatalysis is still hampered by their challenging heterologous production, substantially limiting the panel of accessible enzymes for investigation and enzyme engineering. Building upon previous work on UPO production in yeast, we have developed a combined promoter and -signal peptide shuffling system for episomal high throughput UPO production in the industrially relevant, methylotrophic yeastPichia pastoris. 11 endogenous and orthologous promoters were shuffled with a diverse set of 17 signal peptides. Three previously described UPOs were selected as first test set, leading to the identification of beneficial promoter/signal peptide combinations for protein production. We applied the system then successfully to produce two novel UPOs:MfeUPO fromMyceliophthora fergusiiandMhiUPO fromMyceliophthora hinnulea.To demonstrate the feasibility of the developed system to other enzyme classes, it was applied for the industrially relevant lipase CalB and the laccase Mrl2. In total, approximately 3200 transformants of eight diverse enzymes were screened and the best promoter/signal peptide combinations studied at various co-feeding, derepression and induction conditions. High volumetric production titers were achieved by subsequent creation of stable integration lines and harnessing orthologous promoters fromHansenula polymorpha. In most cases promising yields were also achieved without the addition of methanol under derepressed conditions. To foster the use of the episomal high throughput promoter/signal peptidePichia pastorissystem, we made all plasmids available through Addgene.
MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis
Authors: Carroll Patrick A. , Cheng Pei Feng , Freie Brian W , Kasinathan Sivakanthan , Gu Haiwei , Hedrich Theresa , Dowdle James A. , Venkataramani Vivek , Ramani Vijay , Raftery Daniel , Shendure Jay , Ayer Donald E. , Muller Charles H. , Eisenman Robert N.
Published: December 2020

Male germ cell production is a metabolically-driven and apoptosis-prone process. Here we show that the glucose-sensing transcription factor MLX, and its binding partner MondoA, are both required for male fertility in the mouse, as well as survival of human tumor cells derived from the male germ line. Loss ofMlxresults in altered metabolism as well as activation of multiple stress pathways and germ cell apoptosis in the testes. This is concomitant with dysregulation of the expression of male-specific germ cell transcripts and proteins, manifesting as oligoasthenoteratozoospermia (OAT). Our genomic and functional analyses identify loci directly bound by MLX involved in these processes, including metabolic targets, apoptotic effectors and obligate components of male-specific germ cell development. Thesein vivoandin vitrostudies implicate MLX and other members of the proximal MYC network, such as MNT, in regulation of metabolism and differentiation, as well as in suppression of intrinsic and extrinsic death signaling pathways in both spermatogenesis and male germ cell tumors.

Highlights

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The MAX-like bHLHLZ protein MLX is required for male fertility, but not embryonic development.

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MLX and its heterodimeric partner MondoA are each required for both male fertility and survival of male germ cell tumors.

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Genomic analysis identifies direct MLX targets associated with metabolism, stress and male germ cell development.

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Loss of MLX alters MYC network genome occupancy and transcriptional output.
Fucoidan but not 2’-Fucosyllactose could inhibit human norovirus replication in zebrafish larvae
Authors: Tan Malcolm Turk Hsern , Li Yan , Gorji Mohamad Eshaghi , Gong Zhiyuan , Li Dan
Published: December 2020

Human noroviruses (hNoVs) cause heavy disease burden worldwide and there is no clinically approved vaccination or antivirals hitherto. In this study, with the use of a zebrafish larvaein vivoplatform, we investigated the anti-hNoV potentials of fucoidan and 2’-Fucosyllactose (2’-FL). As a result, although both fucoidan and 2-’FL were able to block hNoV GII.4 virus-like particle (VLPs) from binding to type A saliva as expected, only fucoidan but not 2-’FL was able to inhibit the replication of hNoV GII.P16-GII.4 in zebrafish larvae, indicating the possible needs of higher molecular weights for fucosylated carbohydrates to exert anti-hNoV effect.
QKI 6 ameliorates CIRI through promoting synthesis of triglyceride in neuron and inhibiting neuronal apoptosis associated with SIRT1-PPARγ-PGC-1α axis
Authors: Liu Rui , Li Hongzeng , Deng Jingyuan , Wu Qunqiang , Liao Chunhua , Xiao Qun , Chang Qi
Published: December 2020

The stroke induced by ischemia of brain remains high incidence and death rate. The study wanted to confirm the effects of QKI 6 on the protection role in neurons of rat model of cerebral ischemia/reperfusion injury (CIRI). The rat model with CIRI induced by MCAO (middle cerebral artery occlusion) was well established and rat neurons were isolated to characterize the effects of QKI 6 mediated by SIRT1 on synthesis of triglyceride in neuron and neuronal apoptosis via activation of SIRT1-PPARγ-PGC-1α signaling pathway. The expression levels of SIRT1 or QKI 6, and acetylation level of QKI 6 was decreased in neurons of rat model with CIRI. QKI 6 deacetylated and mediated by SIRT1 that contributed to suppressing the progression of neuronal apoptosis in rat through promoting synthesis of triglyceridein vivoandin vitrovia SIRT1-PPARγ-PGC-1α signaling pathway, then inhibiting CIRI. In conclusion, our results demonstrated SIRT1 deacetylates QKI 6, the RNA-binding protein, that affects significantly the synthesis of triglyceride in neurons of CIRI rat model. Moreover, it activated transcription factor PGC-1α through post-transcriptional regulation of the expression of PPARγ, and further enhanced synthesis of triglyceride, thereby restrained the progression of neural apoptosis and CIRI.
Analysis of the intrinsic chromatin binding property of HIV-1 integrase and its regulation by LEDGF/p75 using human chromosomes spreads
Authors: Lapaillerie D. , Mauro E. , Lelandais B. , Ferran G. , Kuschner N. , Calmels C. , Métifiot M. , Rooryck C. , Ruff M. , Zimmer C. , Lesbats P. , Toutain J. , Parissi V.
Published: December 2020

Retroviral integration requires the stable insertion of the viral genome into the host chromosomes. During this process, the functional integration complex must associate with cellular chromatinviathe interaction between retroviral integrase and nucleosomes. The final association between the HIV-1 integration complex and the nucleosomal target DNA remains unclear and may involve the chromatin-binding properties of both the retroviral integrase and its cellular cofactor LEDGF/p75. To date, there is no experimental system allowing the direct monitoring of this protein association with chromatin to depict the molecular mechanism of this process fully. To investigate this and understand the LEDGF/p75-mediated chromatin tethering of HIV-1 integrase further, we used both biochemical approaches and an unedited chromosome-binding assays. Our study revealed that retroviral IN has an intrinsic ability to bind and recognize specific chromatin regions even in the absence of its cofactor. We also showed that this integrase chromatin-binding property was modulated by the interaction with its cofactor LEDGF/p75, which redirected the enzyme to alternative chromatin regions. Using these approaches, we also better determined the chronology of efficient LEDGF/p75-mediated targeting of HIV-1 integrase to chromatin. In addition to supporting a chromatin-binding function of the integrase protein acting in concert with LEDGF/p75 for the optimal association with the nucleosomal substrate, our work precisely elucidates the mechanism of action of LEDGF/p75 in this crucial integration step.
Docosahexaenoic fatty acid-containing phospholipids affect plasma membrane susceptibility to disruption by bacterial toxin-induced macroapertures
Authors: Tsai Meng-Chen , Fleuriot Lucile , Janel Sébastien , Gonzalez-Rodriguez David , Morel Camille , Mettouchi Amel , Debayle Delphine , Dallongeville Stéphane , Olivo-Marin Jean-Christophe , Antonny Bruno , Lafont Frank , Lemichez Emmanuel , Barelli Hélène
Published: December 2020

Metabolic studies and animal knockout models point to the critical role of polyunsaturated docosahexaenoic acid (22:6, DHA)-containing phospholipids (PLs) in physiology. Here, we study the impact of DHA-PLs on the dynamics of transendothelial cell macroapertures (TEMs) tunnels triggered by the RhoA GTPase inhibitory exotoxin C3 fromClostridium botulinum. Through lipidomic analyses, we show that primary human umbilical vein endothelial cells (HUVECs) subjected to DHA-diet undergo a 6-fold DHA-PLs enrichment in plasma membrane at the expense of monounsaturated OA-PLs. In contrast, OA-diet had almost no effect on PLs composition. Consequently, DHA treatment increases the nucleation rate of TEMs by 2-fold that we ascribe to a reduction of cell thickness. We reveal that the global transcellular area of cells remains conserved through a reduction of the width and lifetime of TEMs. Altogether, we reveal a homeostasis between plasma membrane DHA-PLs content and large-scale membrane dynamics.
Are specialised ABC transporters responsible for the circularisation of type I circular bacteriocins?
Authors: Vezina Ben , Rehm Bernd H. A. , Smith Andrew T.
Published: December 2020

Disclaimer

The authors have withdrawn their manuscript whilst they perform further analysis to verify some interpretations and conclusions. Therefore, the authors do not wish this work to be cited as a reference. If you have any questions, please contact the corresponding author.
Short-term audiovisual spatial training enhances electrophysiological correlates of auditory selective spatial attention
Authors: Hanenberg Christina , Schlüter Michael-Christian , Getzmann Stephan , Lewald Jörg
Published: December 2020

Audiovisual cross-modal training has been proposed as a tool to improve human spatial hearing. Here, we investigated training-induced modulations of auditory-evoked event-related potential (ERP) components that have been associated with processes of auditory selective spatial attention when a speaker of interest has to be localized in a multiple speaker (“cocktail-party”) scenario. Forty-five healthy subjects were tested, including younger (19-29 yrs;n= 21) and older (66-76 yrs;n= 24) age groups. Three conditions of short-term training (duration 15 minutes) were compared, requiring localization of non-speech targets under “cocktail-party” conditions with either (1) synchronous presentation of co-localized auditory-target and visual stimuli (audiovisual-congruency training) or (2) immediate visual feedback on correct or incorrect localization responses (visual-feedback training), or (3) presentation of spatially incongruent auditory-target and visual stimuli presented at random positions with synchronous onset (control condition). Prior to and after training, subjects were tested in an auditory spatial attention task (15 minutes), requiring localization of a predefined spoken word out of three distractor words, which were presented with synchronous stimulus onset from different positions. Peaks of ERP components were analyzed with a specific focus on the N2, which is known to be a correlate of auditory selective spatial attention. N2 amplitudes were significantly larger after audiovisual-congruency training compared with the remaining training conditions for younger, but not older, subjects. Also, at the time of the N2, electrical imaging revealed an enhancement of electrical activity induced by audiovisual-congruency training in dorsolateral prefrontal cortex (Brodmann area 9) for the younger group. These findings suggest that cross-modal processes induced by audiovisual-congruency training under “cocktail-party” conditions at a short time scale resulted in an enhancement of correlates of auditory selective spatial attention.
Isolation and characterization ofPseudomonas chlororaphisstrain ST9 and its potential as a bioinoculant for agriculture
Authors: Bertani Iris , Zampieri Elisa , Bez Cristina , Volante Andrea , Venturi Vittorio , Monaco Stefano
Published: December 2020

The development of biotechnologies based on beneficial microorganisms for improving soil fertility and crop yields could help addressing many current agriculture challenges, such as food security, climate change, pests control, soil depletion while decreasing the use of chemical fertilizers and pesticides. Plant Growth Promoting (PGP) microbes can be used as probiotics in order to increase plant tolerance/resistance to abiotic/biotic stresses and in this context strains belonging to thePseudomonas chlororaphisgroup have shown to have potential as PGP candidates. In this work a newP. chlororaphisisolate is reported and tested for (i)in vitroPGP features, (ii) whole genome sequence analysis, and (iii) its effects on root microbiome, plant growth and on the expression of different plant genes in greenhouse experiments. The potential use of thisP. chlororaphisstrain as a plant probiotic is discussed.
4sUDRB-sequencing for genome-wide transcription bursting quantification in breast cancer cells
Authors: Beckman William F. , Lermo Jiménez Miguel Ángel , Moerland Perry D. , Westerhoff Hans V. , Verschure Pernette J.
Published: December 2020

Epigenetics maintains cell-identity specific gene-expression patterns. However, within a population of isogenic cells of the same identity, a substantial variability in gene expression and responsiveness is still observed. Transcription bursting is a substantial source of this gene-expression variability or ‘noise’, contributing to phenotypic heterogeneity and potentially driving both physiological and pathological processes such as differentiation or tumorigenesis and drug resistance. Identification of transcription-bursting dynamics at a genome-wide scale has been restricted to inferring bursts in mRNA production computationally from the heterogeneity of mRNA levels in single cell transcriptomic data. Systematic characterisation of the genomic and epigenetic chromatin context of genes with defined transcription bursting behaviour has been incomplete. Here, we measured the bursting of transcription itself by genome-wide nascent RNA sequencing of breast cancer MCF-7 cells upon synchronisation of transcription with a transcription elongation inhibitor and by calibration using live cell imaging of nascent PP7-taggedGREB1transcription. Comparing across the entire genome, we find transcription bursting to be ubiquitous, with burst sizes of up to 160 transcripts. Transcription bursting is strongly correlated with steady state gene expression between genes, whereas both burst frequency and nascent transcript degradation only correlate weakly. Individual genes deviate strongly from this trend and engage both in anomalous burst size and frequency. We find that the presence of the TATA box or Inr sequence within gene promoters are significantly associated with a larger burst size, as are promoter-associated YY1 and E2F1 transcription-factor binding motifs. Enrichment of the transcription start site with epigenetic marks such as H3K79me2 and H3K27ac is also strongly associated with the transcription burst size. Finally, we show that in these MCF-7 breast-cancer cells, genes with a larger transcription burst size exhibit a larger immediate transcriptional response following endocrine drug treatment. Our genome-wide transcription-bursting analysis method paves the way to elucidate the dynamic role of epigenetic regulation on dynamic transcription in pathophysiology.
Lineage-specific dynamics of erasure of X-upregulation during inactive-X reactivation
Authors: Naik HC , Chandel D , Majumdar S , Arava M , Baro R , Bv H , Hari K , Parichitran  , Avinchal  , Jolly MK , Gayen S
Published: December 2020

In mammals, sex chromosome dosage is compensated through X-chromosome inactivation and active-X upregulation. It is believed that during early development, X-chromosome inactivation and active X upregulation happen in a highly coordinated fashion. However, such coordination between two X-chromosomes in other developmental contexts remains unexplored. Here, we have profiled the coordination between two X-chromosomes in female cells in different developmental contexts and cell types: pre-implantation embryos, embryonic epiblast cells, iPSC reprogramming, germ cell reprogramming, B-cell, and extra-embryonic endoderm stem (XEN) cells. Interestingly, we found that two X-chromosomes in female cells are not always coordinated; instead, it happens in a lineage-specific manner. Specially, while embryonic mouse epiblast cells, iPSC undergo erasure of X-upregulation upon reactivation of the inactive X, germ cells do not. Importantly, we show that the erasure of X-upregulation in epiblast or iPSC is potentially mediated via undifferentiated embryonic transcription Factor 1 (UTF1), which is absent or lowly expressed in late germ cells and therefore, germ cells are unable to erase upregulation. Moreover, we found that partial reactivation of the inactive X is insufficient to drive the erasure of upregulation globally, nor from their counterparts on the active X in XEN and B-cells. Finally, through a phenomenological mathematical model, we show that cross-inhibition between two X-chromosomes can reproduce the dynamics of reactivation and erasure of upregulation. Altogether, our study provides insight into the coordination between two X-chromosomes in female cells in different developmental contexts and related mechanistic aspects.

Abstract Figure
Variation and process of life history evolution in insular dwarfism as revealed by a natural experiment
Authors: Hayashi Shoji , Kubo Mugino O. , Sánchez-Villagra Marcelo R. , Taruno Hiroyuki , Izawa Masako , Shiroma Tsunehiro , Nakano Takayoshi , Fujita Masaki
Published: December 2020

Islands are a classic focus for evolutionary studies. One subject of much interest has been the evolution of “dwarfs”, significantly smaller island mammals relative to their continental counterparts. Although a consensus has been achieved that multivariate ecological causes are behind body size changes, the processes involved remain largely unexplored. Life history variables, including the age of first reproduction, growth rate, and longevity, are probably key to understanding the process of insular dwarfism. The Japanese Archipelago with numerous islands offers a unique natural experiment of evolution into different sizes within the same group of organisms, deer. Thus, we investigated eight deer populations with a total number of 52 individuals exhibiting body size variation, both extant and fossil, to clarify the effect of insularity on life history traits. We applied several methods to both extant and extinct populations to resolve life history changes among deer populations. Skeletochronology, using lines of arrested growth formed in long bones (femur and tibia), successfully reconstructed body growth curves and revealed a gradual change in growth trajectories reflecting the degree of insularity. Slower growth rates with prolonged growth periods in more isolated deer populations were revealed. An extensive examination of bone microstructure further corroborated this fact, with much slower growth and later somatic maturity evident in fossil insular deer isolated for more than 1.5 Myr. Finally, mortality patterns assessed by demographic analysis showed variation among deer populations, with a life history of insular populations shifting toward the “slow life”.
Processive Dynamics of the Usher Assembly Platform During UropathogenicEscherichia coliP Pilus Biogenesis
Authors: Du Minge , Yuan Zuanning , Werneburg Glenn T. , Henderson Nadine S. , Chauhan Hemil , Kovach Amanda , Zhao Gongpu , Johl Jessica , Li Huilin , Thanassi David G.
Published: December 2020

UropathogenicEscherichia coli(UPEC) assemble hair-like surface structures termed pili or fimbriae to initiate infection of the urinary tract. P pili mediate the adherence of UPEC to the kidney epithelium, facilitating bacterial colonization and pyelonephritis1. P pili are assembled through the conserved chaperone-usher (CU) pathway2-4. In this pathway, a dedicated chaperone facilitates the folding of nascent pilus subunits in the periplasm and an integral outer membrane (OM) protein termed the usher provides the assembly platform and secretion channel for the pilus fiber. Much of the structural and functional understanding of the CU pathway has been gained through investigations of type 1 pili, which promote UPEC binding to the bladder epithelium and the development of cystitis5. In contrast, the structural basis for P pilus biogenesis at the usher has remained elusive. This is in part due to the flexible and variable-length P pilus tip fiber, creating structural heterogeneity, as well as difficulties in isolating stable P pilus assembly intermediates from bacteria. Here, we have devised a method to circumvent these hindrances and determined cryo-EM structures of the activated PapC usher in the process of secreting two- and three-subunit P pilus assembly intermediates. These structures show processive steps in P pilus biogenesis, reveal differences between P and type 1 pili, and capture new conformational dynamics of the usher assembly machine.
Evidence that pain sensitivity is rhythmic in humans, mainly driven by the endogenous circadian system and little by sleep
Authors: Daguet I , Raverot V , Bouhassira D , Gronfier C
Published: December 2020

Pain intensity has been reported to fluctuate during the day in some experimental and clinical conditions, but the mechanisms underlying these fluctuations are unknown. Although the circadian timing system is known to regulate a wide range of physiological functions, its implication in pain regulation is unknown. We show here, using highly controlled laboratory constant routine conditions, that pain sensitivity is rhythmic over the 24-hours and strongly controlled by the endogenous circadian timing system. We find that pain sensitivity follows a sinusoidal circadian rhythmicity, with a maximum in the middle of the night and a minimum in the afternoon. We also find a weak homeostatic control of pain sensitivity, with a linear increase over the 34 hours of prolonged wakefulness, which parallels that of sleep pressure. Using mathematical modelling, we describe that the circadian system accounts for 80% of the full magnitude of pain sensitivity over the 24 hours, and that sleep-related processes account for only 20%. This result reveals that nocturnal analgesia is predominantly induced by the circadian system and has been wrongly attributed only to sleep. Our findings highlight the need to consider the time of day in pain assessment, and suggest that personalized circadian medicine may be a promising approach to pain management.

Significance statement

We discovered that sensitivity to pain is rhythmic in healthy humans, that sensitivity is maximal at night and minimal in the afternoon. Contrarily to the current thinking that sleep is the best painkiller, we find that the 24-h rhythmicity of sensitivity to pain is mainly controlled by a biological circadian clock in our body, and very little by our sleep. Our article reveals the neurobiological mechanisms involved in driving the rhythmicity of pain perception in humans, with the main time-piece located in the brain (the suprachiasmatic nuclei in the hypothalamus). Our findings challenge the current vision of pain physiology, and reveal the need to consider time-of-day and internal biological time for pain evaluation and pain management.
The position of single-base deletions in the VNTR sequence of the carboxyl ester lipase (CEL) gene determines pathogenicity
Authors: Gravdal Anny , Xiao Xunjun , Cnop Miriam , Jellas Khadija El , Njølstad Pål R. , Lowe Mark E. , Johansson Bente B. , Molven Anders , Fjeld Karianne
Published: December 2020

Variable number of tandem repeat (VNTR) sequences present in the genome can have functional consequences that contribute to human disease. This is the case for theCELgene, which encodes the digestive enzyme carboxyl ester lipase.CELhas a VNTR located in exon 11, and rare single-base deletions (DELs) within this region cause MODY8, an inherited disorder characterized by exocrine pancreatic dysfunction and diabetes. Here, we have studied how the position of single-base deletions within theCELVNTR affects the protein’s pathogenic properties. We investigated four naturally occurringCELvariants with single-base deletions in different VNTR segments (DEL1, DEL4, DEL9, DEL13), of which only DEL1 and DEL4 have been observed in MODY8 patients. When expressed in a cellular model system, only DEL1 and DEL4 exhibited significantly reduced secretion and increased intracellular aggregation compared to normal CEL. We found that all DEL variants had slightly decreased enzymatic activity and that their level of O-glycosylation was affected. Moreover, only DEL1 and DEL4 significantly increased endoplasmic reticulum (ER) stress. In conclusion,CELsingle-base deletion variants have the highest pathogenic potential when the mutational event has taken place in the proximal VNTR part, resulting in the longest aberrant protein tails. Thus, DEL1 and DEL4 are pathogenicCELvariants, whereas we consider DEL13 as benign and DEL9 as likely benign. These findings have implications for our understanding of howCELmutations cause pancreatic disease through protein misfolding and proteotoxicity, leading to ER stress and activation of the unfolded protein response.
Amino Acids Promote Mitochondrial-Derived Compartment Formation in Mammalian Cells
Authors: Schuler Max-Hinderk , English Alyssa M. , VanderMeer Leah , Shaw Janet M. , Hughes Adam L.
Published: December 2020

We recently identified a new cellular structure in yeast, called the Mitochondrial-Derived Compartment (MDC), that forms on mitochondria in response to amino acid excess. While emerging evidence supports an important function for MDCs in protecting cells from metabolic stress, whether this system exists beyond yeast remains unclear. Here, we show that MDCs are conserved in mammals, and like their yeast counterparts, are responsive to the intracellular amino acid content. Specifically, we find that inhibition of protein translation stimulates formation of dynamic, micron-sized compartments that associate with the mitochondrial network. These compartments are enriched for the carrier receptor Tomm70A and other select mitochondrial outer and inner membrane cargo, associate with the ER membrane, and require the conserved GTPase Miro1 for formation. Mammalian MDCs are responsive to changes in amino acid levels during translation inhibition, and are not activated by other common cellular stressors. Thus, MDCs represent an evolutionarily conserved nutrient-responsive mitochondrial remodeling system.
Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution
Authors: Smith Spenser S. , Chu Daniel , Qu Tiange , Schneider Richard A.
Published: December 2020

Developmental control of jaw length is critical for survival. The jaw skeleton arises from neural crest mesenchyme and previously we demonstrated that these progenitors upregulate bone-resorbing enzymes includingMatrix metalloproteinase 13(Mmp13)when generating short quail beaks versus long duck bills. Inhibiting bone resorption orMmp13increases jaw length. Here, we uncover mechanisms establishing species-specific levels ofMmp13and bone resorption. Quail show greater activation of, and sensitivity toTransforming Growth Factor-Beta(TGFβ) signaling than duck; where mediators like SMADs and targets likeRunx2,which bindMmp13, become elevated. Inhibiting TGFβ signaling decreases bone resorption. We discover a SMAD binding element in the quailMmp13promoter not found in duck and single nucleotide polymorphisms (SNPs) near a RUNX2 binding element that affect expression. Switching the SNPs and SMAD site abolishes TGFβ-sensitivity in the quailMmp13promoter but makes duck responsive. Thus, differential regulation of TGFβ signaling andMmp13promoter structure underlie avian jaw development and evolution.
Postural effects on arm movement variability are idiosyncratic and feedback-dependent
Authors: Phataraphruk Preyaporn , Rahman Qasim , Lakshminarayanan Kishor , Fruchtman Mitchell , Buneo Christopher A.
Published: December 2020

Reaching movements are subject to noise arising during the sensing, planning and execution phases of movement production, which contributes to movement variability. When vision of the moving hand is available, reaching variability appears to be strongly influenced by noise occurring during the specification and/or online updating of movement plans in visual coordinates. In contrast, when vision of the hand is unavailable, variability appears more dependent upon hand movement direction, suggesting a greater influence of execution noise. Given that execution noise acts in part at the muscular level, we hypothesized that reaching variability should depend not only on movement direction but initial arm posture as well. Moreover, given that the effects of execution noise are more apparent when movements are performed without vision of the hand, we reasoned that postural effects would be more evident when visual feedback was withheld. To test these hypotheses, subjects planned memory-guided reaching movements to three frontal plane targets, using either an “adducted” or “abducted” initial arm posture. Movements were then executed with and without hand vision. We found that the effects of initial arm posture on movement variability were idiosyncratic in both visual feedback conditions. In addition, without visual feedback, posture-dependent differences in variability varied with movement extent, growing abruptly larger in magnitude during the terminal phases of movement, and were moderately correlated with differences in mean endpoint positions. The results emphasize the role of factors other than noise (i.e. biomechanics and suboptimal sensorimotor integration) in constraining patterns of movement variability in 3D space.