bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Mechanochemical feedback between curved membranes and BAR protein self-organization
Authors: Le Roux Anabel-Lise , Tozzi Caterina , Walani Nikhil , Quiroga Xarxa , Zalvidea Dobryna , Trepat Xavier , Staykova Margarita , Arroyo Marino , Roca-Cusachs Pere
Published: September 2020

In many physiological situations, BAR proteins interact with, and reshape, pre-existing curved membranes, contributing to essential cellular processes. However, the non-equilibrium and timedependent process of reshaping, and its dependence on initial membrane shape, remains largely unknown. Here we explain, both experimentally and through modelling, how a BAR protein dynamically interacts with mechanically bent lipid membranes. We capture protein binding to curved membranes, and characterize a variety of dynamical reshaping events depending on membrane shape and protein arrangement. The events can be generally understood by an isotropic-to-nematic phase transition, in which low curvature templates with isotropic protein orientation progress towards highly curved lipid tubes with nematic protein arrangement. Our findings also apply in cells, where mechanical stretch triggers BAR-protein-membrane interactions that enable potential mechanotransduction mechanisms. Our results characterize and broaden the reshaping processes of BAR proteins on mechanically constrained membranes, demonstrating the interplay between membrane mechanical stimuli and BAR protein response.
The Kappa Opioid Receptor is required for some intermittent alcohol drinking induced changes in stress and threat responding in male C57BL/6J mice
Authors: Hwa Lara S. , Bowling Morgan , Calloway Rachel , Kash Thomas L.
Published: September 2020

The dynorphin/kappa opioid receptor (KOR) system in the brain regulates both stressful experiences and negative, aversive states during withdrawal from drugs of abuse. We explored the role of this system during acute withdrawal from long-term alcohol drinking. Male C57BL/6J mice were subjected to repeated forced swim tests, home cage exposure to a predator odor, and a visual threat after intermittent access to alcohol or water. Systemic injection of KOR antagonist norBNI reversed alcohol-related differences in immobility time during the second swim test and reduced burying behavior in response to predator odor, but did not affect behavioral response to visual threat.

Highlights

Intermittent alcohol drinking changed stress reactions in mice.

KOR antagonist norBNI altered some, but not all, stress responses in alcohol drinkers
Across kingdom biased CYP-mediated metabolism via small-molecule ligands docking on P450 oxidoreductase
Authors: Jensen Simon Bo , Thodberg Sara , Parween Shaheena , Moses Matias E. , Hansen Cecilie C. , Thomsen Johannes , Sletfjerding Magnus B. , Knudsen Camilla , Giudice Rita Del , Lund Philip M. , Castaño Patricia R. , Bustamante Yanet G. , Jørgensen Flemming S. , Pandey Amit V. , Laursen Tomas , Møller Birger Lindberg , Hatzakis Nikos S.
Published: September 2020

Metabolic control is mediated by the dynamic assemblies and function of multiple redox enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates electrons and selectively activates numerous (>50 in humans and >300 in plants) cytochromes P450 (CYPs) controlling metabolism of drugs, steroids and xenobiotics in humans and natural product biosynthesis in plants. The mechanisms underlying POR-mediated CYP metabolism remain poorly understood and to date no ligand binding has been described to regulate the specificity of POR. Here, using a combination of computational modeling and functional assays, we identified ligands that dock on POR and bias its specificity towards CYP redox partners. Single molecule FRET studies revealed ligand docking to alter POR conformational sampling, which resulted in biased activation of metabolic cascades in whole cell assays. We propose the model ofbiased metabolism, a mechanism akin to biased signaling of GPCRs, where ligand docking on POR stabilizes different conformational states that are linked to distinct metabolic outcomes. Biased metabolism may allow designing pathway-specific therapeutics or personalized food suppressing undesired, disease related, metabolic pathways.
Can quantifying morphology and TMEM119 expression distinguish between microglia and infiltrating macrophages after ischemic stroke and reperfusion in male and female mice?
Authors: Young Kimberly F. , Gardner Rebeca , Sariana Victoria , Whitman Susan A. , Bartlett Mitchell J. , Falk Torsten , Morrison Helena W.
Published: September 2020

Background

Ischemic stroke is an acquired brain injury with gender dependent outcomes. A persistent obstacle in understanding the sex-specific neuroinflammatory contributions to ischemic brain injury is distinguishing between resident microglia versus infiltrating macrophages—both phagocytes—and determining cell population specific contributions to injury evolution and recovery processes. Our purpose was to identify microglial and macrophage populations regulated by ischemic stroke using morphology analysis and the presence of microglia transmembrane protein 119 (TMEM119). Second, we examined sex and menopause differences in microglia/macrophage cell populations after an ischemic stroke.

Methods

Male and female, premenopausal and postmenopausal, mice underwent either 60-min of middle cerebral artery occlusion and 24-h of reperfusion or sham surgery. The accelerated ovarian failure model was used to model post-menopause. Brain tissue was collected to quantify infarct area and for immunohistochemistry and western blot methods. Ionized calcium-binding adapter molecule, TMEM119, and confocal microscopy were used to analyze microglia morphology and TMEM119 area in ipsilateral brain regions. Western blot was used to quantify protein quantity.

Results

Post-stroke injury is increased in male and female post-menopause mice versus pre-menopause female mice (p<0.05) with differences primarily occurring in caudal sections. After stroke, microglia underwent a region, but not sex group, dependent transformation into less ramified cells (p<0.0001). However, the number of phagocytic microglia were increased in distal ipsilateral regions of postmenopausal mice versus the other sex groups (p<0.05). The number of TMEM119 positive cells was decreased in proximity to the infarct (p<0.0001) but without a sex group effect. Two key findings prevented distinguishing microglia from systemic macrophages. First, morphological data were not congruent with TMEM119 immunofluorescence data. Cells with severely decreased TMEM119 immunofluorescence were ramified, a distinguishing microglia characteristic. Second, whereas TMEM119 immunofluorescence area decreased in proximity to the infarcted area, TMEM119 protein quantity was unchanged in ipsilateral hemisphere regions using western blot methods.

Conclusions

Our findings suggest that TMEM119 is not a stable microglia marker in male and female mice in the context of ischemic stroke. Until TMEM119 function in the brain is elucidated, its use to distinguish between cell populations following brain injury with cell infiltration is cautioned.
CHARTS: A web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq datasets
Authors: Bernstein Matthew N. , Ni Zijian , Collins Michael , Burkard Mark E. , Kendziorski Christina , Stewart Ron
Published: September 2020

Background

Single-cell RNA-seq (scRNA-seq) enables the profiling of genome-wide gene expression at the single-cell level and in so doing facilitates insight into and information about cellular heterogeneity within a tissue. Perhaps nowhere is this more important than in cancer, where tumor and tumor microenvironment heterogeneity directly impact development, maintenance, and progression of disease. While publicly available scRNA-seq cancer datasets offer unprecedented opportunity to better understand the mechanisms underlying tumor progression, metastasis, drug resistance, and immune evasion, much of the available information has been underutilized, in part, due to the lack of tools available for aggregating and analysing these data.

Results

We present CHARacterizing Tumor Subpopulations (CHARTS), a computational pipeline and web application for analyzing, characterizing, and integrating publicly available scRNA-seq cancer datasets. CHARTS enables the exploration of individual gene expression, cell type, malignancy-status, differentially expressed genes, and gene set enrichment results in subpopulations of cells across multiple tumors and datasets.

Conclusion

CHARTS is an easy to use, comprehensive platform for exploring single-cell subpopulations within tumors across the ever-growing collection of public scRNA-seq cancer datasets. CHARTS is freely available atcharts.morgridge.org.
Engineering Transcriptional Interference through RNA Polymerase Processivity Control
Authors: O’Connor Nolan J. , Bordoy Antoni E. , Chatterjee Anushree
Published: September 2020

Antisense transcription is widespread in all kingdoms of life and has been shown to influence gene expression through transcriptional interference (TI), a phenomenon in which one transcriptional process negatively influences anotherin cis. The processivity, or uninterrupted transcription, of an RNA Polymerase (RNAP) is closely tied to levels of antisense transcription in bacterial genomes, but its influence on TI, while likely important, is not well-characterized. Here we show that TI can be tuned through processivity control via three distinct antitermination strategies: the antibiotic bicyclomycin, phage protein Psu, and ribosome-RNAP coupling. We apply these methods toward TI and tune ribosome-RNAP coupling to produce 38-fold gene repression due to RNAP collisions. We then couple protein roadblock and RNAP collisions to design minimal genetic NAND and NOR logic gates. Together these results show the importance of processivity control for strong TI and demonstrate the potential for TI to create sophisticated switching responses.
Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England
Authors: Moore Ginny , Rickard Helen , Stevenson David , Bou Paz Aranega , Pitman James , Crook Ant , Davies Katherine , Spencer Antony , Burton Chris , Easterbrook Linda , Love Hannah E. , Summers Sian , Welch Stephen R. , Wand Nadina , Thompson Katy-Anne , Pottage Thomas , Richards Kevin S. , Dunning Jake , Bennett Allan
Published: September 2020

Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented.

The presence of SARS-CoV-2 in the air and on environmental surfaces around hospitalised patients, with and without respiratory symptoms, was investigated. Environmental sampling was carried out within eight hospitals in England during the first wave of the COVID-19 outbreak. Samples were analysed using reverse transcription polymerase chain reaction (RT-PCR) and virus isolation assays.

SARS-CoV-2 RNA was detected on 30 (8.9%) of 336 environmental surfaces. Ct values ranged from 28·8 to 39·1 equating to 2·2 × 105 to 59 genomic copies/swab. Concomitant bacterial counts were low, suggesting the cleaning performed by nursing and domestic staff across all eight hospitals was effective. SARS-CoV-2 RNA was detected in four of 55 air samples taken <1 m from four different patients. In all cases, the concentration of viral RNA was low and ranged from <10 to 460 genomic copies per m3 of air. Infectious virus was not recovered from any of the PCR positive samples analysed.

Effective cleaning can reduce the risk of fomite (contact) transmission but some surface types may facilitate the survival, persistence and/or dispersal of SARS-CoV-2. The presence of low or undetectable concentrations of viral RNA in the air supports current guidance on the use of specific PPE ensembles for aerosol and non-aerosol generating procedures.
Over-the-counter Analgesics in Pregnancy and Offspring Neonatal Outcomes: A Retrospective Cohort Study
Authors: Zafeiri Aikaterini , Raja Edwin A. , Mitchell Rod T. , Hay David C. , Bhattacharya Sohinee , Fowler Paul A.
Published: September 2020

Objective

To identify associations between in utero exposure to 5 over-the-counter (OTC) analgesics and adverse neonatal outcomes.

Design

Retrospective cohort study

Setting

Aberdeen UK

Population

151,141 singleton deliveries, 1985 to 2015

Methods

Self-reported, non-prescription, consumption of paracetamol, aspirin, ibuprofen, diclofenac and naproxen during pregnancy and neonatal outcomes were obtained from the Aberdeen Maternity and Neonatal Databank (AMND). Univariable and multivariable regression analyses were performed to investigate associations between analgesic use and offspring neonatal outcomes. Crude (cORs) and adjusted odds ratios (aORs) with 95% confidence intervals (CIs) were reported, indicating the strength of association.

Main Outcome Measures

Premature delivery (<37 weeks), stillbirth, neonatal death, birthweight, standardised birthweight score, neonatal unit admission, APGAR score at 1 and 5 minutes, cryptorchidism, neural tube and amniotic band defects, hypospadias and gastroschisis.

Results

Pregnancies exposed to at least one of the 5 analgesics were significantly independently associated with increased odds for premature delivery <37 weeks (aOR=1.50, 95%CI 1.43-1.58), stillbirth (aOR=1.33, 95%CI 1.15-1.54), neonatal death (aOR=1.56, 95%CI 1.27-1.93), birthweight <2500g (aOR=1.28, 95%CI 1.20-1.37), birthweight >4000g (aOR=1.09, 95%CI 1.05-1.13), admission to neonatal unit (aOR=1.57, 95%CI 1.51-1.64), APGAR score <7 at 1 minute (aOR=1.18, 95%CI 1.13-1.23) and 5 minutes (aOR=1.48, 95%CI 1.35-1.62), neural tube defects (aOR=1.64, 95%CI 1.08-2.47) and hypospadias (aOR=1.27, 95%CI 1.05-1.54 males only).

Conclusions

There was a high prevalence of OTC analgesics use during pregnancy, which steeply increased during the 30-year study period. Analgesic consumption was independently associated with multiple adverse neonatal offspring outcomes. The use of paracetamol in combination with other NSAIDs conferred the highest risk.

Funding

Biotechnology and Biological Sciences Research council (BBSRC) funding under the EASTBIO doctoral training programme.
EXTENDING THE SUSCEPTIBLE-EXPOSED-INFECTED-REMOVED (SEIR) MODEL TO HANDLE THE HIGHfaLSEnEGATIVE RATE ANDsyMPTOM-BASED ADMINISTRATION OF COVID-19 DIAGNOSTIC TESTS:SEIR-fansy
Authors: Bhaduri Ritwik , Kundu Ritoban , Purkayastha Soumik , Kleinsasser Michael , Beesley Lauren J. , Mukherjee Bhramar
Published: September 2020

Abstract

The false negative rate of the diagnostic RT-PCR test for SARS-CoV-2 has been reported to be substantially high. Due to limited availability of testing, only a non-random subset of the population can get tested. Hence, the reported test counts are subject to a large degree of selection bias. We consider an extension of the Susceptible-Exposed-Infected-Removed (SEIR) model under both selection bias and misclassification. We derive closed form expression for the basic reproduction number under such data anomalies using the next generation matrix method. We conduct extensive simulation studies to quantify the effect of misclassification and selection on the resultant estimation and prediction of future case counts. Finally we apply the methods to reported case-death-recovery count data from India, a nation with more than 5 million cases reported over the last seven months. We show that correcting for misclassification and selection can lead to more accurate prediction of case-counts (and death counts) using the observed data as a beta tester. The model also provides an estimate of undetected infections and thus an undereporting factor. For India, the estimated underreporting factor for cases is around 21 and for deaths is around 6. We develop an R-packageSEIR-fansyfor broader dissemination of the methods.
Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer
Authors: Singh Naveen K. , Ray Partha , Carlin Aaron F. , Magallanes Celestine , Morgan Sydney , Laurent Louise C. , Aronoff-Spencer Eliah S. , A. Hall Drew
Published: September 2020

Significant barriers to the diagnosis of latent and acute SARS-CoV-2 infection continue to hamper population-based screening efforts required to contain the COVID-19 pandemic in the absence of effective antiviral therapeutics or vaccines. We report an aptamer-based SARS-CoV-2 salivary antigen assay employing only low-cost reagents ($3.20/test) and an off-the-shelf glucometer. The test was engineered around a glucometer as it is quantitative, easy to use, and the most prevalent piece of diagnostic equipment globally making the test highly scalable with an infrastructure that is already in place. Furthermore, many glucometers connect to smartphones providing an opportunity to integrate with contract tracing apps, medical providers, and electronic medical records. In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads - as benchmarked by RT-qPCR - within one hour, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). We propose that this approach can provide an inexpensive, rapid, and accurate diagnostic for distributed screening of SARS-CoV-2 infection at scale.
When it is available, will we take it? Public perception of hypothetical COVID-19 vaccine in Nigeria
Authors: Adebisi Yusuff Adebayo , Alaran Aishat Jumoke , Bolarinwa Obasanjo Afolabi , Akande-Sholabi Wuraola , Lucero-Prisno Don Eliseo
Published: September 2020

COVID-19 pandemic is a global public health threat facing mankind. There is no specific antiviral treatment for COVID-19, and no vaccine is currently available. This study aims to understand the perception of the public towards hypothetical COVID-19 vaccine in Nigeria. We conducted a cross-sectional survey in August 2020 across the 36 states of Nigeria using an online questionnaire. The questionnaire includes sections on the demographic characteristics of the respondents and their perception regarding hypothetical COVID-19 vaccine. A total of 517 respondents completed and returned the informed consent along with the questionnaire electronically. Data were coded and abstracted into the Microsoft Excel spreadsheet and loaded into the STATA 14 software for final analysis. The results showed that more than half of the respondents were male 294 (56.87%). Most of the respondents (385, 74.47%) intend to take the COVID-19 vaccine when it becomes available. Among the 132 respondents that would not take the COVID-19 vaccine, the major reason for non-acceptance is unreliability of the clinical trials 49 (37.12%), followed by the belief that their immune system is sufficient to combat the virus 36 (27.27%). There are significant association with the respondents age and having reservations toward vaccination [χ2= 19.0389 P-value=0.00] and COVID-19 vaccine acceptance [χ2=24.3316 P-value=0.00]. Furthermore, geographical location and acceptance of the COVID-19 vaccine [χ2=13.7786 P-value=0.02] are significantly associated. Even though the majority of our respondents are willing to take the COVID-19 vaccine, our findings reiterate the need to reassure the public that any vaccine which becomes available is safe and effective.
Risk Assessment of COVID-19 Airborne Infection During Hybrid Learning
Authors: Anchordoqui Luis A. , Chudnovsky Eugene M. , Paul Thomas C.
Published: September 2020

Converging lines of evidence seem to indicate that SARS-CoV-2, the novel coronavirus responsible for the COVID-19 pandemic, can be transmitted from person-to-person via aerosols that waft through the air and accumulate over time. The airborne nature of the virus could be a threat in indoor spaces in general and in particular for in-class education. We provide an assessment of the risk of SARS-CoV-2 infection during a 7-hour school day in elementary schools. We show that existing data are insufficient to establish a low (below 1%) probability of infection with high accuracy. The use of facemasks and social distancing could significantly decrease this risk.
Anti-SARS-CoV-2 IgM and IgG antibodies in health workers in Sergipe, Brazil
Authors: de Melo Mônica Santos , Borges Lysandro Pinto , de Souza Daniela Raguer Valadão , Martins Aline Fagundes , de Rezende Neto José Melquiades , Ribeiro Anderson Alves , Santos Aryanne Araujo , da Invenção Grazielly Bispo , Matos Igor Leonardo Santos , Santos Kezia Alves dos , Souza Nicolas Alessandro Alves , Borges Pâmela Chaves , de Oliveira Makson Gleydson Brito
Published: September 2020

Background

The exponential growth of COVID-19 cases in Brazil is overloading health systems with overcrowding of hospitals and overflowing intensive care units. Increasing infection rates in health professionals can lead to the collapse of the health system and further worsen the pandemic. The aim of this study was to evaluate the seroprevalence of IgM and IgG for SARS-CoV-2 in health workers in Sergipe, Brazil.

Methods

The targeted tests involved health professionals working on the front line to combat COVID-19. The samples were collected in the month of June, in six hospital units in the state of Sergipe.

Results

471 health professionals were tested. Of these, 28 workers (5.95%) tested positive for IgM and 64 (13.59%) tested positive for IgG. 9 workers (1.91%) tested positive for IgM and were also positive for IgG.

Discussion

Health workers must be monitored constantly, because if they are infected, they can spread the virus to colleagues, hospitalized patients and even family members.

Conclusion

Knowing the prevalence of antibodies to the virus in health workers is an important measure of viral spread control.
Quantifying the impact of quarantine duration on COVID-19 transmission
Authors: Ashcroft Peter , Lehtinen Sonja , Bonhoeffer Sebastian
Published: September 2020

The numbers of confirmed cases of SARS-CoV-2 infection are increasing in many places. Consequently, the number of individuals placed into quarantine is increasing too. The large number of individuals in quarantine has high societal and economical costs, as well as infringing on the freedom of the individual. This has led to a vigorous debate about the duration of quarantine, particularly in light of the potentially low specificity of quarantine (i.e. low probability of quarantined individuals indeed being infected). We present a mathematical model that leverages empirically determined distributions of incubation period, infectivity, and generation time to quantify how the duration of quarantine affects transmission. With this model we address the impact of shortening the quarantine for returning travellers and traced contacts of confirmed cases, both in terms of prevented transmission and the ratio of prevented transmission to days spent in quarantine. We also consider the impact of i) test-and-release strategies; ii) additional hygiene measures imposed upon release after a negative test; iii) the development of symptoms during quarantine; iv) the relationship between quarantine duration and adherence; and v) the specificity of quarantine. When considering the benefit versus cost utility of quarantine, we find that the diminishing impact of longer quarantine on transmission prevention may support a quarantine duration below 10 days, particularly for returning travellers. A greater gain of utility can be achieved through a test-and-release strategy, and this can be even further strengthened by imposed hygiene measures post-release. We also find that unless a test-and-release strategy is considered, the specificity of quarantine does not affect the optimal duration of quarantine. Therefore, the argument that we should shorten quarantine because of lack of specificity is misguided.
A Generalized Evolutionary Classifier for Evolutionary Guided Precision Medicine
Authors: McCoy Matthew , Yeang Chen-Hsiang , Parashar Deepak , Beckman Robert A.
Published: September 2020

Background

Current precision medicine (CPM) matches patients to therapies, utilizing traditional biomarker classifiers. Dynamic precision medicine (DPM) is an evolutionary guided precision medicine (EGPM) approach that specifically accounts for intratumoral genetic heterogeneity and evolutionary dynamics. DPM adapts as frequently as every six weeks, plans proactively for future resistance development, and incorporates multiple therapeutic agents. Simulations indicate that DPM can double mean and median survival and significantly improve long-term survival in a cohort of 3 million virtual patients representing a pan-oncology spectrum. Given the cost and invasiveness of monitoring subclones frequently in the DPM paradigm, we sought to determine the value of a DPM window study of only two six-week adaptations (“moves”).

Methods

3 million virtual patients, differing in DPM input parameters of initial subclonal compositions, drug sensitivities, and growth and mutational kinetics, were simulated as previously described. Each virtual patient was treated with CPM, DPM, and DPM for two moves followed by CPM.

Results

The first two DPM moves provide similar benefit to a five-year, 40-move sequence in the full virtual population. In simulations, if the first two moves are identical for DPM and CPM, patients will not benefit from DPM (89% negative predictive value). The patient subset (20%) in which two-move and 40-move DPM sequences are closely similar in outcome has extraordinary predicted benefit (HR-DPM/CPM 0.04).

Conclusions

The first two DPM moves provide most of the clinical benefit of DPM, reducing the duration of required subclonal monitoring. This leads to an evolutionary classifier (EC) that selects patients who will benefit, i.e. those in whom DPM and CPM recommendations differ early. This EC development paradigm may apply to other EGPM approaches despite different underlying assumptions.

CONTEXT SUMMARY

Key objective: Current precision medicine (CPM) performs static matching of biomarker classifiers to therapies. We asked, using computer simulation, whether dynamic precision medicine (DPM), a highly adaptive and proactive evolutionary guided precision medicine (EGPM) paradigm, could benefit patients with only two six-week adaptive treatment periods (“moves”), and still enhance long term survival by preventing late term relapses.

Knowledge generated: Two moves of DPM were highly effective, nearly as effective as 40 moves in the full population. Patients for whom DPM and CPM recommend the same treatment sequence for the first two moves will likely not benefit from DPM.

Relevance: A 2-move DPM paradigm is far more cost-effective and less invasive than a 40-move paradigm, and opens up the neoadjuvant period for studying DPM. The findings establish an evolutionary classifier (EC) for selecting patients who will benefit from DPM. This general approach to developing an EC may work for other EGPM.
Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography
Authors: Bouvette Jonathan , Liu Hsuan-Fu , Du Xiaochen , Zhou Ye , Sikkema Andrew P. , Da Fonseca Rezende E Mello Juliana , Klemm Bradley P. , Huang Rick , Schaaper Roel M. , Borgnia Mario J. , Bartesaghi Alberto
Published: September 2020

Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by an order of magnitude and significantly improve map resolution compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved.
IL-7R signalling activates widespread VHand DHgene usage to drive antibody diversity in bone marrow B cells
Authors: Baizan-Edge Amanda , Stubbs Bryony A. , Stubbington Michael J. T. , Bolland Daniel J. , Tabbada Kristina , Andrews Simon , Corcoran Anne E.
Published: September 2020

Generation of the primary antibody repertoire requires V(D)J recombination of hundreds of gene segments in the immunoglobulin heavy chain (Igh) locus. It has been proposed that interleukin-7 receptor (IL-7R) signalling is necessary for Igh recombination, but this has been challenging to partition from the receptor’s role in B cell survival and proliferation. By generating the first detailed description of the Igh repertoire of murine IL-7Rα-/-bone marrow B cells, we demonstrate that IL-7R signalling profoundly influences VHgene selection during VH-to-DJHrecombination. We find skewing towards usage of 3’ VHgenes duringde novoVH-to-DJHrecombination that is more severe than the fetal liver (FL) B cell repertoire, and we now show a role for IL-7R signalling in DH-to-JHrecombination. Transcriptome and accessibility analyses suggests reduced expression of B lineage-specific transcription factors (TFs) and their targets, and loss of DHand VHantisense transcription in IL-7Rα-/-B cells. These results refute models suggesting that IL-7R signalling is only required for survival and proliferation, and demonstrate a pivotal role in shaping the Igh repertoire by activating underpinning epigenetic mechanisms.
From genotype to phenotype: maintenance of a chemical polymorphism in the context of high geneflow
Authors: Ehlers Bodil K. , Gauthier Perrine , Villesen Palle , Santoni Sylvain , Thompson John D. , Bataillon Thomas
Published: September 2020

A major question in evolution is how to maintain many adaptive phenotypes within a species. In Mediterranean wild thyme, a staggering number of discrete chemical phenotypes (chemotypes) coexist in close geographic proximity. Plant chemotypes are defined by the dominant monoterpene produced in their essential oil. We study the genetics of six distinct chemotypes nested within two well established ecotypes. Ecotypes, and chemotypes within ecotypes, are spatially segregated, and their distribution tracks local differences in the abiotic environment. The ecotypes have undergone a rapid shift in distribution associated with current climate change. Here, combining genomic, phenotypic, and environmental data, we show how the genetics of ecotype determination can allow for such rapid evolutionary response despite high gene flow among ecotypes. Variation in three terpene-synthase loci explains almost all variation in ecotype identity, with one single locus accounting for as much as 78% of it. Phenotypic selection on ecotypes combined with low segregating genotypic redundancy and tight genetic determination leaves a clear footprint at the genomic level: alleles associated with ecotype identity track environmental variation despite extensive gene flow. Different chemotypes, nested within each ecotype, also track environmental variation. However, in contrast to ecotypes, chemotype identity is determined by more loci and show a wider range of genotypic redundancy, which dilutes the impact of phenotypic selection on alleles associated with different chemotypes. Identifying the genetics behind this polymorphism in thyme is a crucial step towards understanding the maintenance of this widespread chemical polymorphism found in many aromaticLamiaceae.
Pharmacological targeting of host chaperones protects from pertussis toxin in vitro and in vivo
Authors: Ernst Katharina , Mittler Ann-Katrin , Winkelmann Veronika , Eberhardt Nina , Anastasia Anna , Sonnabend Michael , Lochbaum Robin , Wirsching Jan , Skerry Ciaran , Carbonetti Nicholas H. , Frick Manfred , Barth Holger
Published: September 2020

Whooping cough is caused byBordetella pertussisthat releases pertussis toxin (PT) which comprises enzyme A-subunit PTS1 and binding/transport B-subunit. After receptor-mediated endocytosis, PT reaches the endoplasmic reticulum from where unfolded PTS1 is transported to the cytosol. PTS1 ADP-ribosylates G-protein α-subunits resulting in increased cAMP signaling. Here, the role of target cell chaperones Hsp90, Hsp70, cyclophilins and FK506-binding proteins for cytosolic PTS1-uptake is characterized in detail. PTS1 specifically and directly interacts with chaperonesin vitroand in cells. Specific pharmacological chaperone inhibition protects CHO-K1, human primary airway basal cells and a fully differentiated airway epithelium from PT-intoxication by reducing cytosolic PTS1-amounts without affecting cell binding or enzyme activity. PT is internalized by human airway epithelium secretory but not ciliated cells and leads to increase of apical surface liquid. Cyclophilin-inhibitors reduced leukocytosis in infant mouse model of pertussis, indicating their promising potential for developing novel therapeutic strategies against whooping cough.
New insights into the paradoxical distribution ofIRC7inSaccharomyces cerevisiaeand its associated phenotypic and genomic landscapes
Authors: Ruiz Javier , de Celis Miguel , Martín-Santamaría María , Benito-Vázquez Iván , Pontes Ana , Lanza Val F. , Sampaio José Paulo , Santos Antonio , Belda Ignacio
Published: September 2020

Biotic and abiotic factors of wine fermentations have led to the accumulation of numerous genomic hallmarks of domestication inSaccharomyces cerevisiaewine strains. Here we have studied the paradoxical distribution of a dominant allele ofIRC7in wine yeast strains. This gene encodes a cysteine-S-β-lyase and presents two alleles: a wild full-length allele (IRC7F) and a mutated one (IRC7S), harboring a 38bp-deletion. Interestingly,IRC7S-coding for a less active enzyme-appears in the great majority of wine strains. Studying its global distribution among phylogenetic clades, we observed thatIRC7Sallele is dominant just in wine strains, having a moderate presence in other domesticated clades (Beer, Bread and Wine-PDM), but being completely absent in wild clades, appearing as a new hallmark of domestication. To explain this paradoxical distribution, we performed anIRC7-rooted phenotypic-wide survey, demonstrating thatIRC7S-homozygous (HS) wine strains have both fitness (lower lag phases and higher growth rates) and competitive (killer toxin resistance, pseudohyphal growth) advantages. Hence, we performed a genome-wide survey across domesticated clades, finding a set of mutations that are conserved among wine strains and potentially associated toIRC7Sallele, which can help to explain the outstanding phenotype of HS strains and their dominant distribution in wines.

Originality-Significance Statement

S. cerevisiaeis one of the best studied microbes due to its industrial importance and its use as a eukaryotic model organism.S. cerevisiaeis also an interesting model for studying the effects of domestication in yeast genomic, phenotype and ecology. The study of how wildS. cerevisiaestrains evolved into a greatly adapted domesticated strains and changed its lifestyle drastically is still of great interest. In the case of wine populations, strains have accumulated numerous hallmarks of domestication in their genome, related with their great phenotypic adaptation to this environment. Here, we report a new hallmark of domestication in wine strains; theIRC7deleted allele (IRC7S) and present the first insights about its unexpected global distribution among phylogenetic clades, understanding the genomic context and the phenotypic implications of this allele in wine strains.
Host-interactor screens ofPhytophthora infestansRXLR proteins reveal vesicle trafficking as a major effector-targeted process
Authors: Petre Benjamin , Contreras Mauricio P. , Bozkurt Tolga O. , Schattat Martin H. , Sklenar Jan , Schornack Sebastian , Abd-El-Haliem Ahmed , Castells-Graells Roger , Lozano-Duran Rosa , Dagdas Yasin F. , Menke Frank L. H. , Jones Alexandra M. E. , Vossen Jack H. , Robatzek Silke , Kamoun Sophien , Win Joe
Published: September 2020

Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogenPhytophthora infestans.To this end, we performed anin plantaprotein-protein interaction screen by transiently expressingP. infestansRXLR effectors inNicotiana benthamianaleaves followed by co-immunoprecipitation (co-IP) and liquid chromatography tandem mass spectrometry (LC-MS/MS). This screen generated an effector-host protein interactome matrix of 59P. infestansRXLR effectors x 586N. benthamianaproteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted byP. infestans.We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and co-localize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles inN. benthamianacells. FYVE positive vesicles also accumulated in leaf cells nearP. infestanshyphae, indicating that the pathogen may enhance endosomal trafficking during infection. We anticipate that the interactome dataset we generated will serve as a useful community resource for functional studies ofP. infestanseffectors and of effector-targeted host processes.
Peripheral sgp130-mediatedtrans-signaling blockade induces obesity and insulin resistance in mice via PPARα suppression
Authors: Lanton Tali , Levkovitch-Siany Orr , Udi Shiran , Tam Joseph , Abramovitch Rinat , Perles Sharon , Williams Evan , Rachmilewitz Jacob , Mor Uria , Elinav Eran , Schmidt-Arras Dirk , Rehman Ateequr , Rosenstiel Philip , Giannou Anastasios , Huber Samuel , Rose-John Stefan , Galun Eithan , Axelrod Jonathan H.
Published: September 2020

IL-6 signaling via its receptor (IL-6R) and co-receptor (gp130) performs multiple roles in regulating metabolic homeostasis. However, gp130 is also expressed systemically in a soluble form (sgp130), which limits soluble IL-6 receptor (sIL-6R)-mediated signaling – also calledtrans-signaling. Here we find that transgenic peripheral sgp130-mediatedtrans-signaling blockade induces mature-onset obesity, while differentially affecting age-dependent behavioral determinants of energy expenditure. In youth,trans-signaling blockade increases feeding associated with reduced leptin sensitivity but increases energy expenditure to maintain metabolic balance. In aging, reduced physical activity predisposes mice to adiposity, adipose tissue macrophage recruitment, hepatosteatosis, hyperglycemia, and insulin resistance. Mechanistically,trans-signaling blockade reduces hepatic Stat3 phosphorylation and suppresses PPARα, associated with miR-21 upregulation, while pharmacological activation of PPARα prevents obesity and hepatosteatosis, and rescues insulin sensitivity. Together these experiments reveal a role for peripheral IL-6trans-signaling in metabolic homeostasis and provide clinical significance to elevated sgp130 levels found in some obese and diabetic patients.
Synaptonemal Complex dimerization regulates chromosome alignment and crossover patterning in meiosis
Authors: Gordon Spencer G. , Kursel Lisa E. , Xu Kewei , Rog Ofer
Published: September 2020

During sexual reproduction the parental homologous chromosomes find each other (pair) and align along their lengths by integrating local sequence homology with large-scale contiguity, thereby allowing for precise exchange of genetic information. The Synaptonemal Complex (SC) is a conserved zipper-like structure that assembles between the homologous chromosomes. This phase-separated interface brings chromosomes together and regulates exchanges between them. However, the molecular mechanisms by which the SC carries out these functions remain poorly understood. Here we isolated and characterized two mutations in the dimerization interface in the middle of the SC zipper inC. elegans. The mutations perturb both chromosome alignment and the regulation of genetic exchanges. Underlying the chromosome-scale phenotypes are distinct alterations to the way SC subunits interact with one another. We propose that the SC brings homologous chromosomes together through two biophysical activities: obligate dimerization that prevents assembly on unpaired chromosomes; and a tendency to phase-separate that extends pairing interactions along the entire length of the chromosomes.
Evolution of fungal community associated with ready-to-eat pineapple during storage under different temperature conditions
Authors: Manthou Evanthia , Coeuret Gwendoline , Chaillou Stephane , Nychas George-John E.
Published: September 2020

The international market of fresh-cut products has witnessed dramatic growth in recent years, stimulated by consumer’s demand for healthy, nutritious and convenient foods. One of the main challenging issues for the quality and safety of these products is the potential microbial spoilage that can significantly reduce their shelf-life. The complete identification of fresh-cut product microbiota together with the evaluation of environmental factors impact on microbial composition is of primary importance. We therefore assessed the fungal communities associated with the spoilage of ready-to-eat (RTE) pineapple using a metagenetic amplicon sequencing approach, based on the ITS2 region. Our results revealed a significant variability on fungal species composition between the different batches of RTE pineapple. The initial microbiota composition was the main influencing factor and determined the progress of spoilage. Temperature and storage time were the secondary factors influencing spoilage and their impact was depending on the initial prevalent fungal species, which showed different responses to the various modifications. Our results strongly suggest that further large-scale sampling of RTE pineapple production should be conducted in order to assess the full biodiversity range of fungal community involved in the spoilage process and for unravelling the impact of important environmental factors shaping the initial microbiota.
Unique features of stimulus-based probabilistic reversal learning
Authors: Harris Carl , Aguirre Claudia , Kolli Saisriya , Das Kanak , Izquierdo Alicia , Soltani Alireza
Published: September 2020

Reversal learning paradigms are widely-used assays of behavioral flexibility with their probabilistic versions being more amenable to studying integration of reward outcomes over time. Prior research suggests differences between initial and reversal learning, including higher learning rates, a greater need for inhibitory control, and more perseveration after reversals. However, it is not well-understood what aspects of stimulus-based reversal learning are unique to reversals, and whether and how observed differences depend on reward probability. Here, we used a visual probabilistic discrimination and reversal learning paradigm where male and female rats selected between a pair of stimuli associated with different reward probabilities. We compared accuracy, rewards collected, omissions, latencies, win-stay/lose-shift strategies, and indices of perseveration across two different reward probability schedules. We found that discrimination and reversal learning are behaviorally more unique than similar: latencies to select the better option, win-stay strategies, and perseveration were of a different pattern in reversal learning compared to discrimination learning. Additionally, fit of choice behavior using reinforcement learning models revealed a lower sensitivity to the difference in subjective reward values (greater exploration) and higher learning rates for the reversal phase. Interestingly, a consistent reward probability group difference emerged with a richer environment associated with longer reward collection latencies than a leaner environment. We also replicated previous reports on sex differences in reversal learning. Future studies should systematically compare the neural correlates of fine-grained behavioral measures to reveal possible dissociations in how the circuitry is recruited in each phase.
IF1 connects obesity and insulin resistance through mitochondrial reprogramming in association with ANT2
Authors: Wang Ying , Guan Yaya , Zhang Jiaojiao , Cao Xinyu , Shen Shuang , Zhong Genshen , Xong Xiwen , Xu Yanhong , Zhang Xiaoying , Wang Hui , Ye Jianping
Published: September 2020

IF1 (ATPIF1) is a nuclear DNA-encoded protein with an activity in the inhibition of catalytic activity of F1Fo-ATP synthase (ATPase), an enzyme for ATP synthesis in mitochondria. A role of IF1 remains unknown in the metabolic disorder in obesity. In this study, IF1 was examined in the diet-induced obese (DIO) mice and a decrease in IF1 protein was observed in several tissues including the skeletal muscle, liver and intestine in the absence of mRNA alteration. Significance of the reduction was investigated in the IF1-KO mice, in which insulin sensitivity was improved in the absence of body weight alteration on Chow diet. On a high fat diet (HFD), the IF1-KO mice gain more body weight as a result of enhanced fat tissue growth. The energy expenditure and locomotion activity were decreased in the KO mice without an alteration in food intake. The increase in insulin sensitivity remained in the obese KO mice. The colon tissue exhibited a resistance to the HFD-induced atrophy with less cell apoptosis and more secretion of GLP-1. Mitochondria exhibited an enhanced ATP production and maximal oxygen consumption without an alteration in the respiratory chain proteins. However, the ATP level was reduced in the fasting condition in the muscle as well as the liver. Mitophagy was enhanced with elevated accumulation of PINK1 and Parkin proteins in the mitochondria. The protein abundance of ADP/ATP translocase 2 (ANT2) was decreased in the inner membrane of mitochondria to account for the reduced apoptosis and enhanced mitophagy. The data suggest that the IF1 reduction in obesity leads to reprogramming of mitochondrial metabolism in a compensatory response to maintain the insulin sensitivity through down-regulation of ANT2 protein.