bluuebunny/crossref_metadata_2025 huggingface dataset:
Symptoms network analysis of serious mental illness: A cross disasters comparison
Authors: Levin Yafit , Rahel Bachem , Goodwin Robin , Ben-Ezra Menachem
Published: April 2021

Background

The Kessler Psychological Distress Scale (K-6) has been used worldwide in community epidemiological surveys and served as a screening measure for serious mental illness in the general population. We take a novel approach by examining the symptoms network of the K-6 and the exploration of differences between three types of disasters: Nature related, Terror attacks, and COVID-19.

Aims

To explore the K-6 symptoms network and its structure replication across the three types of disasters.

Methods

A network analysis of psychological distress symptoms as assessed by the K-6 was conducted using data from 9,271 participants from different disaster samples: Terror (n = 5842), COVID-19 (n = 2428), and Nature related (n = 1001).

Results

While there were extensive connections between items across all disaster samples, network structure differed across the disaster types. While after a nature related disaster and the COVID-19 pandemic depression- and anxiety-items were interconnected, a terror attack resulted in more separated manifestations of anxiety and depression. Centrality analysis showed “depressed/no cheering up” to be the node with the highest strength centrality in all networks; in the Nature-related network, “restless or fidgety” was also highly central.

Conclusions

Results provide evidence of different psychological distress structures in different disasters. Depending on the type of disaster, trauma-focused interventions may need to be augmented, with specific components directed at depression and/or anxiety.
Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling
Authors: Salas Lucas A , Zhang Ze , Koestler Devin C , Butler Rondi A , Hansen Helen M , Molinaro Annette M , Wiencke John K , Kelsey Karl T , Christensen Brock C
Published: April 2021

DNA methylation microarrays can be employed to interrogate cell-type composition in complex tissues. Here, we expand reference-based deconvolution of blood DNA methylation to include 12 leukocyte subtypes (neutrophils, eosinophils, basophils, monocytes, B cells, CD4+ and CD8+ naïve and memory cells, natural killer, and T regulatory cells). Including derived variables, our method provides up to 56 immune profile variables. The IDOL (IDentifying Optimal Libraries) algorithm was used to identify libraries for deconvolution of DNA methylation data both for current and retrospective platforms. The accuracy of deconvolution estimates obtained using our enhanced libraries was validated using artificial mixtures, and whole-blood DNA methylation with known cellular composition from flow cytometry. We applied our libraries to deconvolve cancer, aging, and autoimmune disease datasets. In conclusion, these libraries enable a detailed representation of immune-cell profiles in blood using only DNA and facilitate a standardized, thorough investigation of the immune system in human health and disease.
RESIC: A tool for comprehensive adenosine to inosine RNA Editing Site Identification and Classification
Authors: Light Dean , Haas Roni , Yazbak Mahmoud , Elfand Tal , Blau Tal , Lamm Ayelet T.
Published: April 2021

Adenosine to inosine (A-to-I) RNA editing, the most prevalent type of RNA editing in metazoans, is carried out by adenosine deaminases (ADARs) in double-stranded RNA regions. Several computational approaches have been recently developed to identify A-to-I RNA editing sites from sequencing data, each addressing a particular issue. Here we present RESIC, an efficient pipeline that combines several approaches for the detection and classification of RNA editing sites. The pipeline can be used for all organisms and can use any number of RNA-sequencing datasets as input. RESIC provides 1. The detection of editing sites in both repetitive and non-repetitive genomic regions; 2. The identification of hyper-edited regions; 3. Optional exclusion of polymorphism sites to increase reliability, based on DNA, and ADAR-mutant RNA sequencing datasets, or SNP databases. We demonstrate the utility of RESIC by applying it to human, successfully overlapping and extending the list of known putative editing sites. We further tested changes in the patterns of A-to-I RNA editing, and RNA abundance of ADAR enzymes, following SARS-CoV-2 infection in human cell lines. Our results suggest that upon SARS-CoV-2 infection, compared to mock, the number of hyper editing sites is increased, and in agreement, the activity of ADAR1, which catalyzes hyper-editing, is enhanced. These results imply the involvement of A-to-I RNA editing in conceiving the unpredicted phenotype of COVID-19 disease. RESIC code is open-source and is easily extendable.
A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and sidechain flexibility
Authors: Varela Daniel , Karlin Vera , André Ingemar
Published: April 2021

Protein complex formation is encoded by specific interactions at the atomic scale, but the computational cost of modeling proteins at this level often requires the use of simplified energy models and limited conformational flexibility. In particular, the use of all-atom energy functions, backbone and sidechain flexibility results in rugged energy landscapes that are difficult to explore. In this study we develop a protein-protein docking algorithm, EvoDOCK, that combine the strength of a differential evolution algorithm for efficient exploration of the global search space with the benefits of a local optimization method to refine detailed atomic interactions. EvoDOCK enabled accurate and fast local and global protein-protein docking using an all-atom energy function with side-chain flexibility. Comparison with a standard method built on Monte Carlo optimization demonstrated improved accuracy and with increases in computational speed of up to 35 times. The evolutionary algorithm also enabled efficient atomistic docking with backbone flexibility.
SLIT2-ROBO signaling in tumor-associated microglia/macrophages drives glioblastoma immunosuppression and vascular dysmorphia
Authors: Geraldo Luiz Henrique , Xu Yunling , Jacob Laurent , Fragner Laurence Pibouin , Rao Rohit , Maissa Nawal , Verreault Maïté , Lemaire Nolwenn , Knosp Camille , Lesaffre Corinne , Daubon Thomas , Dejaegher Joost , Solie Lien , Rudewicz Justine , Viel Thomas , Tavitian Bertrand , De Vleeschouwer Steven , Sanson Marc , Bikfalvi Andreas , Idbaih Ahmed , Lu Q. Richard , Souza Lima Flavia Regina , Thomas Jean-Leon , Eichmann Anne , Mathivet Thomas
Published: April 2021

SLIT2 is a secreted polypeptide that guides migration of cells expressing ROBO1&2 receptors. Herein, we investigated SLIT2/ROBO signaling effects in gliomas. In patients with glioblastoma (GBM),SLIT2expression increased with malignant progression and correlated with poor survival and immunosuppression. Knockdown ofSLIT2in mouse glioma cells and patient derived GBM xenografts reduced tumor growth and synergized with immunotherapy to prolong survival. Tumor cellSLIT2knockdown inhibited macrophage invasion and promoted a cytotoxic gene expression profile, which improved tumor vessel function and enhanced efficacy of chemotherapy and immunotherapy. Mechanistically, SLIT2 promoted microglia/macrophage chemotaxis and tumor-supportive polarization via ROBO1&2-mediated PI3Kγ activation. MacrophageRobo1&2deletion and systemic SLIT2 trap delivery mimickedSLIT2knockdown effects on tumor growth and the tumor microenvironment (TME), revealing SLIT2 signaling through macrophage ROBOs as a novel regulator of the GBM microenvironment and a potential immunotherapeutic target for brain tumors.
Safety and efficacy of C9ORF72-repeat RNA nuclear export inhibition in amyotrophic lateral sclerosis
Authors: Castelli Lydia M. , Cutillo Luisa , Souza Cleide Dos Santos , Sanchez-Martinez Alvaro , Granata Ilaria , Myszczynska Monika A. , Heath Paul R. , Livesey Matthew R. , Ning Ke , Azzouz Mimoun , Shaw Pamela J. , Guarracino Mario R. , Whitworth Alexander J. , Ferraiuolo Laura , Milo Marta , Hautbergue Guillaume M.
Published: April 2021

Background

Loss of motor neurons in amyotrophic lateral sclerosis (ALS) leads to progressive paralysis and death. Dysregulation of thousands of RNA molecules with roles in multiple cellular pathways hinders the identification of ALS-causing alterations over downstream changes secondary to the neurodegenerative process. How many and which of these pathological gene expression changes require therapeutic normalisation remains a fundamental question.

Methods

Here, we investigated genome-wide RNA changes in C9ORF72-ALS patient-derived neurons and Drosophila, as well as upon neuroprotection taking advantage of our gene therapy approach which specifically inhibits the SRSF1-dependent nuclear export of pathological C9ORF72-repeat transcripts. This is a critical study to evaluate (i) the overall safety and efficacy of the partial depletion of SRSF1, a member of a protein family involved itself in gene expression, and (ii) a unique opportunity to identify neuroprotective RNA changes.

Results

Our study demonstrates that manipulation of 362 transcripts out of 2,257 pathological changes in C9ORF72-ALS patient-derived neurons is sufficient to confer neuroprotection upon partial depletion of SRSF1. In particular, expression of 90 disease-altered transcripts is fully reverted upon neuroprotection leading to the characterisation of a human C9ORF72-ALS disease-modifying gene expression signature. These findings were further investigated in vivo in diseased and neuroprotected Drosophila transcriptomes, highlighting a list of 21 neuroprotective changes conserved with 16 human orthologues in patient-derived neurons. We also functionally validated the high therapeutic potential of one of these disease-modifying transcripts, demonstrating that inhibition of ALS-upregulated human KCNN1-3 (Drosophila SK) voltage-gated potassium channel orthologs mitigates degeneration of human motor neurons as well as Drosophila motor deficits.

Conclusions

Strikingly, manipulating the expression levels of a small proportion of RNAs is sufficient to induce a therapeutic effect, further indicating that the SRSF1-targeted gene therapy approach is safe in the above preclinical models as it does not disrupt globally gene expression. The efficacy of this intervention is also validated at genome-wide level with therapeutically-induced RNA changes involved in the vast majority of biological processes affected in C9ORF72-ALS. Finally, the identification of a characteristic signature with key RNA changes modified in both the disease state and upon neuroprotection also provides potential new therapeutic targets and biomarkers.
Investigating the roles ofListeria monocytogenesperoxidases in growth and virulence
Authors: Cesinger Monica R. , Schwardt Nicole H. , Halsey Cortney R. , Thomason Maureen K. , Reniere Michelle L.
Published: April 2021

Bacteria have necessarily evolved a protective arsenal of proteins to contend with peroxides and other reactive oxygen species generated in aerobic environments.Listeria monocytogenesencounters an onslaught of peroxide both in the environment and during infection of the mammalian host, where it is the causative agent of the foodborne illness listeriosis. Despite the importance of peroxide for the immune response to bacterial infection, the strategy by whichL. monocytogenesprotects against peroxide toxicity has yet to be illuminated. Here, we investigated the expression and essentiality of all the peroxidase-encoding genes duringL. monocytogenesgrowthin vitroand during infection of murine cells in tissue culture. We found thatchdCandkatwere required for aerobic growthin vitro, andfriandahpAwere each required forL. monocytogenesto survive acute peroxide stress. Despite increased expression offri, ahpA, andkatduring infection of macrophages, onlyfriproved necessary for cytosolic growth and intercellular spread. In contrast, the proteins encoded bylmo0367, lmo0983, tpx, lmo1609, andohrAwere dispensable for aerobic growth, acute peroxide detoxification, and infection. Together, our results provide insight into the multifacetedL. monocytogenesperoxide detoxification strategy and demonstrate thatL. monocytogenesencodes a functionally diverse set of peroxidase enzymes.
Tissue-resident FOLR2+macrophages associate with tumor-infiltrating CD8+T cells and with increased survival of breast cancer patients
Authors: Ramos Rodrigo Nalio , Missolo-Koussou Yoann , Gerber-Ferder Yohan , Bromley Christian , Bugatti Mattia , Núñez Nicolas Gonzalo , Tosello Jimena Boari , Richer Wilfrid , Denizeau Jordan , Sedlik Christine , Caudana Pamela , Kotsias Fiorella , Niborski Leticia Laura , Viel Sophie , Bohec Mylène , Lameiras Sonia , Baulande Sylvain , Lesage Laëtitia , Nicolas André , Meseure Didier , Vincent-Salomon Anne , Reyal Fabien , Dutertre Charles-Antoine , Ginhoux Florent , Vimeux Lene , Donnadieu Emmanuel , Buttard Bénédicte , Galon Jérôme , Zelenay Santiago , Vermi William , Guermonprez Pierre , Piaggio Eliane , Helft Julie
Published: April 2021

Macrophage infiltration is a hallmark of solid cancers and overall macrophage infiltration is correlated with lower patient survival and resistance to therapy. However, tumor-associated macrophages are phenotypically and functionally heterogeneous. Specific tumor-associated macrophage subsets might be endowed with antagonistic role on cancer progression and on the development of anti-tumor immunity. For instance, monocyte-derived TREM2+tumor-associated macrophages have pro-tumorigenic and immunosuppressive functions. Here, we identify a discrete population of FOLR2+tumor-associated macrophages positively correlating with patient survival in breast cancer. FOLR2+macrophages are evolutionarily conserved across species and populate human and murine healthy mammary gland. Moreover, FOLR2+macrophages co-localize with lymphoid aggregates containing CD8+T cells in breast cancer and across ten other types of cancers. This study highlights antagonistic roles for tumor-associated macrophage subsets and paves the way for subset-specific therapeutic interventions in macrophages-based cancer therapies.
Public-good driven release of heterogeneous resources leads to genotypic diversification of an isogenic yeast population in melibiose
Authors: Mahilkar Anjali , Alugoju Phaniendra , Kavatalkar Vijendra , Rajeshkannan E. , Bhat Paike Jayadeva , Saini Supreet
Published: April 2021

Adaptive diversification of an isogenic population, and its molecular basis has been a subject of a number of studies in the last few years. Microbial populations offer a relatively convenient model system to study this question. In this context, an isogenic population of bacteria (E. coli,B. subtilis, andPseudomonas) has been shown to lead to genetic diversification in the population, when propagated for a number of generations. This diversification is known to occur when the individuals in the population have access to two or more resources/environments, which are separated either temporally or spatially. Here, we report adaptive diversification in an isogenic population of yeast,S. cerevisiae, when propagated in an environment containing melibiose as the carbon source. The diversification is driven due to a public good, enzyme α-galactosidase, leading to hydrolysis of melibiose into two distinct resources, glucose and galactose. The diversification is driven by a mutations at a single locus, in theGAL3gene in the GAL/MEL regulon in the yeast.
Preservation of collagen in the soft tissues of frozen mammoths
Authors: Hattori Shunji , Kiriyama-Tanaka Tomomi , Kusubata Masashi , Taga Yuki , Ebihara Testuya , Imai Katsuyuki , Miura Mitsutaka , Mezaki Yoshihiro , Tikhonov Alexei , Senoo Haruki
Published: April 2021

We investigated the characteristics of extracellular matrix (ECM) in the soft tissue of two frozen baby woolly mammoths (Mammuthus primigenius) that died and were buried in Siberian permafrost approximately 40,000 years ago. Morphological and biochemical analyses of mammoth lung and liver demonstrated that those soft tissues were preserved at the gross anatomical and histological levels. The ultrastructure of ECM components, namely a fibrillar structure with a collagen-characteristic pattern of cross-striation, was clearly visible with transmission and scanning electron microscopy. Type I and type IV collagens were detected by immunohistochemical observation. Quantitative amino acid analysis of liver and lung tissues of the baby mammoths indicated that collagenous protein is selectively preserved in these tissues as a main protein. Type I and type III collagens were detected as major components by means of liquid chromatography–mass spectrometry analysis after digestion with trypsin. These results indicate that the triple helical collagen molecule, which is resistant to proteinase digestion, has been preserved in the soft tissues of these frozen mammoths for 40,000 years.
The Seroprevalence of SARS-CoV-2 in Europe: A Systematic Review
Authors: Vaselli Natasha Marcella , Hungerford Daniel , Shenton Ben , Khashkhusha Arwa , Cunliffe Nigel A. , French Neil
Published: April 2021

Background

A year following the onset of the COVID-19 pandemic, new infections and deaths continue to increase in Europe. Serological studies, through providing evidence of past infection, can aid understanding of the population dynamics of SARS-CoV-2 infection.

Objectives

This systematic review of SARS-CoV-2 seroprevalence studies in Europe was undertaken to inform public health strategies including vaccination, that aim to accelerate population immunity.

Methods

We searched the databases Web of Science, MEDLINE, EMBASE, SCOPUS, Cochrane Database of Systematic Reviews and grey literature sources for studies reporting seroprevalence of SARS-CoV-2 antibodies in Europe published between 01/12/2019 - 30/09/20. We provide a narrative synthesis of included studies. Studies were categorized into subgroups including healthcare workers (HCWs), community, outbreaks, pregnancy and children/school. Due to heterogeneity in other subgroups, we only performed a random effects meta-analysis of the seroprevalence amongst HCWs stratified by their country.

Results

109 studies were included spanning 17 European countries, that estimated the seroprevalence of SAR-CoV2 from samples obtained between November 2019 – August 2020. A total of 53/109 studies included HCWs with a reported seroprevalence among HCWs ranging from 0.7% to 45.3%, which did not differ significantly by country. In community studies significant heterogeneity was reported in the seroprevalence among different age groups and the majority of studies reported there was no significant difference by gender.

Conclusion

This review demonstrates a wide heterogeneity in reported seroprevalence of SARS-CoV-2 antibodies between populations. Continued evaluation of seroprevalence is required to understand the impact of public health measures and inform interventions including vaccination programmes.
Rapid diversification of the Australian Amitermes group during late Cenozoic climate change
Authors: Heimburger Bastian , Schardt Leonie , Brandt Alexander , Scheu Stefan , Hartke Tamara R.
Published: April 2021

Late Cenozoic climate change led to the progressive aridification of Australia over the past 15 million years. This gradual biome turnover fundamentally changed Australia’s ecosystems, opening new niches and prompting diversification of plants and animals. One example is the Australian Amitermes Group (AAG), consisting of the Australian Amitermes and affiliated genera. Although it represents the most speciose and diverse higher termite group in Australia, little is known about its evolutionary history. We used ancestral range reconstruction and diversification analyses to illuminate 1) the origin and phylogenetic relationships of the AAG, 2) biogeographical processes leading to the current continent-wide distribution, and 3) timing and pattern of diversification in the context of late Cenozoic climate change. By estimating the first time-calibrated phylogeny, we show that the AAG is a monophyletic group, whose ancestor arrived ~11-10 million years ago from Southeast Asia. Ancestral range reconstruction indicates that Australia’s monsoon region was the launching point for a continental radiation that has been shaped by range expansions and within-area speciation rather than vicariance. We found that multiple arid species diversified from mesic and tropical ancestors in the Plio-Pleistocene, but also observed diversification in the opposite direction. Finally, we show that two pulses of rapid diversification coincided with past climate change during the late Miocene and early Pliocene. Consistent with rapid diversification, species accumulation slowed, likely caused by progressive niche saturation. This study provides a stepping stone for predicting the future response of Australia’s termite fauna in the face of human-mediated climate change.
High intensity muscle stimulation activates a systemic Nrf2-mediated redox stress response
Authors: Ostrom Ethan L. , Valencia Ana P. , Marcinek David J. , Traustadóttir Tinna
Published: April 2021

Introduction

High intensity exercise is an increasingly popular mode of exercise to elicit similar or greater adaptive responses compared to traditional moderate intensity continuous exercise. However, the molecular mechanisms underlying these adaptive responses are still unclear. The purpose of this pilot study was to compare high and low intensity contractile stimulus on the Nrf2-mediated redox stress response in mouse skeletal muscle.

Methods

An intra-animal design was used to control for variations in individual responses to muscle stimulation by using a stimulated limb (STIM) and comparing to the contralateral unstimulated control limb (CON). High Intensity (HI – 100Hz), Low Intensity (LI – 50Hz), and Naïve Control (NC – Mock stimulation vs CON) groups were used to compare these effects on Nrf2-ARE binding, Keap1 protein content, and downstream gene and protein expression of Nrf2 target genes.

Results

Muscle stimulation significantly increased Nrf2-ARE binding in LI-STIM compared to LI-CON (p = 0.0098), while Nrf2-ARE binding was elevated in both HI-CON and HI-STIM compared to NC (p = 0.0007). The Nrf2-ARE results were mirrored in the downregulation of Keap1, where Keap1 expression in HI-CON and HI-STIM were both significantly lower than NC (p = 0.008) and decreased in LI-STIM compared to LI-CON (p = 0.015). In addition, stimulation increased NQO1 protein compared to contralateral control regardless of stimulation intensity (p = 0.019).

Conclusions

Taken together, these data suggest a systemic redox signaling exerkine is activating Nrf2-ARE binding and is intensity gated, where Nrf2-ARE activation in contralateral control limbs were only seen in the HI group. Other research in exercise induced Nrf2 signaling support the general finding that Nrf2 is activated in peripheral tissues in response to exercise, however the specific exerkine responsible for the systemic signaling effects is not known. Future work should aim to delineate these redox sensitive systemic signaling mechanisms.
Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features
Authors: Rayon Teresa , Maizels Rory J. , Barrington Christopher , Briscoe James
Published: April 2021

The spinal cord receives input from peripheral sensory neurons and controls motor output by regulating muscle innervating motor neurons. These functions are carried out by neural circuits comprising molecularly and physiologically distinct neuronal subtypes that are generated in a characteristic spatial-temporal arrangement from progenitors in the embryonic neural tube. The systematic mapping of gene expression in mouse embryos has provided insight into the diversity and complexity of cells in the neural tube. For human embryos, however, less information has been available. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions in four human embryos of Carnegie Stages (CS) CS12, CS14, CS17 and CS19 from Gestational Weeks (W) 4-7. In total we recovered the transcriptomes of 71,219 cells. Analysis of progenitor and neuronal populations from the neural tube, as well as cells of the peripheral nervous system, in dorsal root ganglia adjacent to the neural tube, identified dozens of distinct cell types and facilitated the reconstruction of the differentiation pathways of specific neuronal subtypes. Comparison with existing mouse datasets revealed the overall similarity of mouse and human neural tube development while highlighting specific features that differed between species. These data provide a catalogue of gene expression and cell type identity in the developing neural tube that will support future studies of sensory and motor control systems and can be explored athttps://shiny.crick.ac.uk/scviewer/neuraltube/.
CCR4 blockade leads to clinical activity and prolongs survival in a canine model of advanced prostate cancer
Authors: Maeda Shingo , Motegi Tomoki , Iio Aki , Kaji Kenjiro , Goto-Koshino Yuko , Eto Shotaro , Ikeda Namiko , Nakagawa Takayuki , Nishimura Ryohei , Yonezawa Tomohiro , Momoi Yasuyuki
Published: April 2021

Targeting regulatory T cell (Treg) infiltration is an emerging strategy for cancer immunotherapy. However, the efficacy of this strategy in advanced prostate cancer remains unclear. Here, we describe the therapeutic efficacy of this strategy in a canine model of advanced prostate cancer. We used dogs with naturally occurring prostate cancer to study the molecular mechanism underlying Treg infiltration into tumor tissues and the effect of anti-Treg treatment. We found that tumor-infiltrating Tregs were associated with poor prognosis in dogs bearing spontaneous prostate cancer. RNA sequencing and protein analyses showed that Treg infiltration was mediated by interaction between the tumor-producing chemokine, CCL17, and the receptor CCR4 expressed on Tregs. Dogs with advanced prostate cancer responded to mogamulizumab, a monoclonal antibody targeting CCR4, with improved survival and low incidence of clinically relevant adverse events. Exploratory analyses showed urinary CCL17 concentration and BRAFV595Emutation to be independently predictive of the response to mogamulizumab. Analysis of a publicly available transcriptomic dataset of human prostate cancer showed that the CCL17/CCR4 axis correlated with the Treg marker, Foxp3. In silico survival analyses showed that high expression of CCL17 was associated with poor prognosis. Immunohistochemistry confirmed that tumor-infiltrating Tregs expressed CCR4 in human patients with prostate cancer. These findings suggest that anti-Treg treatment through the blocking of CCR4 is a promising therapeutic approach for advanced prostate cancer.

One Sentence Summary

Targeting regulatory T cell infiltration by CCR4 blockade induces objective responses and improves survival in a canine model of prostate cancer.
Epitope profiling of coronavirus-binding antibodies using computational structural modelling
Authors: Robinson Sarah A. , Raybould Matthew I. J. , Schneider Constantin , Wong Wing Ki , Marks Claire , Deane Charlotte M.
Published: April 2021

Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. It is well-established in the literature that sequence-based clonal clustering can identify antibodies with similar epitope complementarity. However, there is growing evidence that antibodies from markedly different lineages but with similar structures can engage the same epitope with near-identical binding modes. Here, we describe a novel computational method for epitope profiling based on structural modelling and clustering, and show how it can identify sequence-dissimilar antibodies that engage the same epitope. We start by searching for evidence of structural conservation across the latest solved SARS-CoV-2—binding antibody crystal structures. Despite the relatively small number of solved structures, we find numerous examples of sequence-diverse but structurally-similar coronavirus-binding antibodies engaging the same epitope. We therefore developed a high-throughput structural modeling and clustering method to identify functionally-similar antibodies across the set of thousands of coronavirus-binding antibody sequences in the Coronavirus Antibody Database (CoV-AbDab). In the resulting multiple-occupancy structural clusters, 92% bind to consistent domains based on CoV-AbDab metadata. Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than would be suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis.
Midbrain organoids with anSNCAgene triplication model key features of synucleinopathy
Authors: Mohamed Nguyen-Vi , Sirois Julien , Ramamurthy Janani , Mathur Meghna , Lépine Paula , Deneault Eric , Maussion Gilles , Nicouleau Michael , Chen Carol X.-Q. , Abdian Narges , Soubannier Vincent , Cai Eddie , Nami Harris , Thomas Rhalena A. , Tabatabaei Mahdieh , Beitel Lenore K. , Dolt Karamjit Singh , Karamchandani Jason , Kunath Tilo , Fon Edward A. , Durcan Thomas M.
Published: April 2021

SNCA,the first gene associated with Parkinson’s disease, encodes the α-synuclein (α-syn) protein, the predominant component within pathological inclusions termed Lewy bodies (LBs). The presence of LBs is one of the classical hallmarks found in the brain of patients with Parkinson’s disease, and LBs have also been observed in patients with other synucleinopathies. However, the study of α-syn pathology in cells has relied largely on two-dimensional culture models, which typically lack the cellular diversity and complex spatial environment found in the brain. Here, to address this gap, we use 3D midbrain organoids (hMOs), differentiated from human induced pluripotent stem cells derived from patients carrying a triplication of theSNCAgene and from CRISPR/Cas9 corrected isogenic control iPSCs. These hMOs recapitulate key features of α-syn pathology observed in the brains of patients with synucleinopathies. In particular, we find thatSNCAtriplication hMOs express elevated levels of α-syn and exhibit an age-dependent increase in α-syn aggregation, manifested by the presence of both oligomeric and phosphorylated forms of α-syn. These phosphorylated α-syn aggregates were found in both neurons and glial cells and their time-dependent accumulation correlated with a selective reduction in dopaminergic neuron numbers. Thus, hMOs from patients carrying SNCA gene multiplication can reliably model key pathological features of Parkinson’s disease and provide a powerful system to study the pathogenesis of synucleinopathies.
Molecular determinants of phase separation forDrosophilaDNA replication licensing factors
Authors: Parker Matthew W. , Kao Jonchee , Huang Alvin , Berger James M. , Botchan Michael R.
Published: April 2021

Liquid-liquid phase separation (LLPS) of intrinsically disordered regions (IDRs) in proteins can drive the formation of membraneless compartments in cells. Phase-separated structures enrich for specific partner proteins and exclude others. We have shown that the IDRs of metazoan DNA replication initiators drive DNA-dependent phase separationin vitroand chromosome bindingin vivo, and that initiator condensates selectively recruit specific partner proteins. How initiator IDRs facilitate LLPS and maintain compositional specificity is unknown. UsingD. melanogaster (Dm)Cdt1 as a model initiation factor, we show that phase separation results from a synergy between electrostatic DNA-bridging interactions and hydrophobic inter-IDR contacts. Both sets of interactions depend on sequence composition (but not sequence order), are resistant to 1,6- hexanediol, and do not depend on aromaticity. These findings demonstrate that distinct sets of interactions drive self-assembly and condensate specificity across different phase-separating systems and advance efforts to predict IDR LLPS propensity and specificitya priori.
Proteomic analysis of the role of the quality control protease LONP1 in mitochondrial protein aggregation
Authors: Pollecker Karen , Sylvester Marc , Voos Wolfgang
Published: April 2021

The mitochondrial matrix protease LONP1 is an essential part of the organellar protein quality control system. LONP1 has been shown to be involved in respiration control and apoptosis. Furthermore, a reduction in LONP1 level correlates with ageing processes. Up to now, the effects of a LONP1 defect were mostly studied by utilizing transient, siRNA-mediated knockdown approaches. We generated a new cellular model system for studying the impact of LONP1 on mitochondrial protein homeostasis by a CRISPR/Cas-mediated genetic knockdown (gKD). These cells show a stable reduction of LONP1 along with a mild phenotype characterized by absent morphological differences and only small negative effects on mitochondrial functions under normal culture conditions. To assess the consequences of a permanent LONP1 depletion on the mitochondrial proteome, we analyzed the alterations of protein levels by quantitative mass spectrometry, demonstrating small adaptive changes, in particular concerning mitochondrial protein biogenesis. In an additional proteomic analysis, we determined the temperature-dependent aggregation behavior of mitochondrial proteins and its dependence on a reduction of LONP1 activity, demonstrating the important role of the protease for mitochondrial protein homeostasis in mammalian cells. We identified a significant number of mitochondrial proteins that are affected by LONP1 activity concerning their stress-induced solubility. Taken together, our results suggest a very good applicability of the LONP1 gKD cell line as a model system for human ageing processes.
The Akt-mTOR pathway drives myelin sheath growth by regulating cap-dependent translation
Authors: Fedder-Semmes Karlie N. , Appel Bruce
Published: April 2021

In the vertebrate central nervous system, oligodendrocytes produce myelin, a specialized proteolipid rich membrane, to insulate and support axons. Individual oligodendrocytes wrap multiple axons with myelin sheaths of variable lengths and thicknesses. Myelin grows at the distal ends of oligodendrocyte processes and multiple lines of work have provided evidence that mRNAs and RNA binding proteins localize to myelin, together supporting a model where local translation controls myelin sheath growth. What signal transduction mechanisms could control this? One strong candidate is the Akt-mTOR pathway, a major cellular signaling hub that coordinates transcription, translation, metabolism, and cytoskeletal organization. Here, using zebrafish as a model system, we found that Akt-mTOR signaling promotes myelin sheath growth and stability during development. Through cell-specific manipulations to oligodendrocytes, we show that the Akt-mTOR pathway drives cap-dependent translation to promote myelination and that restoration of cap-dependent translation is sufficient to rescue myelin deficits in mTOR loss-of-function animals. Moreover, an mTOR-dependent translational regulator co-localized with mRNA encoding a canonically myelin-translated protein in vivo and bioinformatic investigation revealed numerous putative translational targets in the myelin transcriptome. Together, these data raise the possibility that Akt-mTOR signaling in nascent myelin sheaths promotes sheath growth via translation of myelin-resident mRNAs during development.

SIGNIFICANCE STATEMENT

In the brain and spinal cord oligodendrocytes extend processes that tightly wrap axons with myelin, a protein and lipid rich membrane that increases electrical impulses and provides trophic support. Myelin membrane grows dramatically following initial axon wrapping in a process that demands protein and lipid synthesis. How protein and lipid synthesis is coordinated with the need for myelin to be generated in certain locations remains unknown. Our study reveals that the Akt-mTOR signaling pathway promotes myelin sheath growth by regulating protein translation. Because we found translational regulators of the Akt-mTOR pathway in myelin, our data raise the possibility Akt-mTOR activity regulates translation in myelin sheaths to deliver myelin on demand to the places it is needed.
Long-read whole genome analysis of human single cells
Authors: Hård Joanna , Mold Jeff E , Eisfeldt Jesper , Tellgren-Roth Christian , Häggqvist Susana , Bunikis Ignas , Contreras-Lopez Orlando , Chin Chen-Shan , Nordlund Jessica , Rubin Carl-Johan , Feuk Lars , Michaëlsson Jakob , Ameur Adam
Published: April 2021

With long-read sequencing, we have entered an era where individual genomes are routinely assembled to near completion and where complex genetic variation can efficiently be resolved. Here, we demonstrate that long reads can be applied to study the genomic architecture of individual human cells. Clonally expanded CD8+ T-cells from a human donor were used as starting material for a droplet-based multiple displacement amplification (dMDA) to generate long molecules with minimal amplification bias. PacBio HiFi sequencing generated up to 20 Gb data and 40% genome coverage per single cell. The data allowed for accurate detection and haplotype phasing of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, including in genomic regions inaccessible by short reads. Somatic SNVs were detected in the nuclear genome and mitochondrial DNA. An average of 1278 high-confidence SVs per cell were discovered in the PacBio data, nearly four times as many compared to those found in Illumina dMDA data from clonally related cells. Single-cellde novoassembly resulted in a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, the work presented here demonstrates the utility of whole genome amplification combined with long-read sequencing toward the characterization of the full spectrum of genetic variation at the single-cell level.
Mediodorsal thalamus is critical for updating during extra-dimensional shifts but not reversals in the attentional set-shifting task
Authors: Ouhaz Zakaria , Perry Brook AL , Nakamura Kouichi , Mitchell Anna S
Published: April 2021

Cognitive flexibility, attributed to frontal cortex, is vital for navigating the complexities of everyday life. The mediodorsal thalamus (MD), interconnected to frontal cortex, may influence cognitive flexibility. Here male rats performed an attentional set-shifting task measuring intra-dimensional and extra-dimensional shifts in sensory discriminations. MD lesion rats needed more trials to learn the rewarded sensory dimension. However, once the choice response strategy was established, learning further two-choice discriminations in the same sensory dimension, and reversals of the reward contingencies in the same dimension, were unimpaired. Critically though, MD lesion rats were impaired during the extra-dimensional shift, when they must rapidly update the optimal choice response strategy. Behavioral analyses showed MD lesion rats had significantly reduced correct within trial second choice responses. This evidence shows transfer of information via the MD is critical when monitoring and rapid within trial updates in established choice response strategies are required after there is a rule change.

Significance statement

We demonstrate for the first time that rodent mediodorsal (MD) thalamus is a critical node when choice response strategies need to change rapidly after a within session rule change but not after reversals of reward contingencies during reward guided learning. MD interactions with orbitofrontal cortex are critical for value based learning, while MD interactions with medial prefrontal cortex are critical for rapid within trial updating of optimal choice response rules. MD interactions with the orbitofrontal cortex are not always necessary for reversal learning.
From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance
Authors: Ortuño Francisco M , Loucera Carlos , Casimiro-Soriguer Carlos S. , Lepe Jose A. , Martinez Pedro Camacho , Diaz Laura Merino , de Salazar Adolfo , Chueca Natalia , García Federico , Perez-Florido Javier , Dopazo Joaquin
Published: April 2021

Background

the current SARS-CoV-2 pandemic has emphasized the utility of viral whole genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is increasingly producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and therefore useless, sequences. However, viral sequences evolve in the context of a complex phylogeny and therefore different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.

Results

We developed impuSARS, an application that includes Minimac, the most widely used strategy for genomic data imputation and, taking advantage of the enormous amount of SARS-CoV-2 whole genome sequences available, a reference panel containing 239,301 sequences was built. The impuSARS application was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing) showing great fidelity when reconstructing the original sequences. The impuSARS application is also able to impute whole genomes from commercial kits covering less than 20% of the genome or only from theSpikeprotein with a precision of 0.96. It also recovers the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (< 20%)

Conclusions

imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. impuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole genome sequencing.
Commissioning and operation status of the MAX IV 3 GeV storage ring vacuum system
Authors: Grabski Marek , Al-Dmour Eshraq
Published: April 2021

The 3 GeV electron storage ring of the MAX IV laboratory is the first storage-ring-based synchrotron radiation facility with the inner surface of almost all the vacuum chambers along its circumference coated with non-evaporable getter (NEG) thin film. The coating provides a low dynamic outgassing rate and pumping of active gases. As the NEG coating was applied on an unprecedented scale, there were doubts concerning the storage ring performance. Fast conditioning of the vacuum system and over five years of reliable accelerator operation have demonstrated that the chosen design proved to be good and does not impose limits on the operation. The vacuum system performance is comparable with or better than that of other similar facilities around the world, where conventional designs were implemented. Observed pressure levels are low, and the electron beam lifetime is long and not limited by residual gas density. A summary of the vacuum performance is presented.
Horse Trading: Food Sourcing in the Twenty-First Century
Authors: Walker Russell
Published: April 2021

In January 2013, Irish authorities were the first to uncover the year's first food sourcing scandal: horsemeat sold as beef on supermarket shelves. It was not long before regulators and retailers realized the problem was truly a continental one. The incident involved French exporters, Luxembourger production facilities, Cypriot and Dutch meat traders, British and Swedish retailers, and Romanian horsemeat. Food service providers and retailers were forced to test beef products to ensure they were horse-free, pulling products that contained traces of equine meat. British supermarkets alone disposed of an estimated 10 million “beef” burgers in the wake of the scandal.

This case is an example of the challenges of managing the complex global supply chains that make up the modern food industry. In this class discussion, students will use concepts from management, economics, and public policy to assess the damage of this event and to analyze strategies for preventing similar incidents in the future.
Office Space, A Company's Frontier: The Corporate Decision to Buy or Lease
Authors: Furfine Craig
Published: April 2021

Markus Steuer, director of real estate at Drechtal Pharmaceuticals, must decide where his firm should locate in the immediate future. Drechtal was currently leasing space in seven different buildings, yet the company anticipated a dramatic increase in headcount should its first oncology drug, Trianoline, be approved by Swissmedic. The potential increased demand for space initiated Steuer's investigation of whether it was optimal to continue to lease space or whether or not it should invest in its own corporate headquarters. With its current leases set to expire over the coming 24 months, it was an opportune time to consider Drechtal's options.
Chipotle Mexican Grill: Food with Integrity?
Authors: Walker Russell , Merkley Greg
Published: April 2021

By any measure, Chipotle Mexican Grill was a success story in the restaurant business. It grew from one location in 1993 to over 2,000 locations by 2016 and essentially created the fast casual dining category. Its stock appreciated more than 1,000% in the ten years following its 2006 IPO.

However, after more than 20 years without a major reported food safety incident, Chipotle was revealed as the source of multiple outbreaks of illness from norovirus, salmonella, and E. coli that sickened nearly 600 people in 13 states in 2015. The company closed stores, spent several months under investigation by the U.S. Centers for Disease Control and Prevention (CDC) and other health organizations, and faced a criminal investigation in connection with the incidents.

After a much-publicized closing of all of its stores on February 8, 2016, and numerous changes to its food sourcing and preparation practices, Chipotle tried to win back customers with dramatically increased advertising and free food promotions.

However, on April 26, the chain announced its first-ever quarterly loss as a public company. Same-store sales for the first quarter were 29.7% lower than in the previous year. Operating margins fell from 27.5% to 6.8% over the same period, and the company's share price was down 41% from its summer 2015 high.