bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of SOS-inducing agents on the expression of ArtAB toxin gene in Salmonella enterica and Salmonella bongori
Authors: Miura Shou , Tamamura Yukino , Takayasu Mariko , Sasaki Miwa , Nishimura Natsuko , Tokugawa Kanetaka , Suwa Izumi , Murata Ryo , Akiba Masato , Kusumoto Masahiro , Uchida Ikuo
Published: June 2020

Salmonella entericasubspeciesentericaserovar Typhimurium (S. Typhimurium) definitive phage type 104 (DT104),S. entericasubspeciesentericaserovar Worthington (S. Worthington) andS. bongoriproduce ArtA and ArtB (ArtAB) toxin homologues, which catalyse ADP-ribosylation of pertussis toxin-sensitive G protein. ArtAB gene (artAB) is encoded on prophage in DT104 and its expression is induced by mitomycin C (MTC) and hydrogen peroxide (H2O2) that trigger the bacterial SOS response. Although the genetic regulatory mechanism associated withartABexpression is not characterized, it is thought to be associated with prophage induction, which occurs when the RecA-mediated SOS response is triggered. Here we show that subinhibitory concentration of quinolone antibiotics that are SOS-inducing agents, also induce ArtAB production in theseSalmonellastrains. Both MTC and fluoroquinolone antibiotics such as enrofloxacin-inducedartAandrecAtranscription andartAB-encoding prophage (ArtAB-prophage) in DT104 andS. Worthington. However, inS. bongori, which harboursartABgenes on incomplete prophage,artAtranscription was induced by MTC and enrofloxacin, but prophage induction was not observed. Taken together, these results suggest that SOS response followed by induction ofartABtranscription is essential for ArtAB production. H2O2-mediated induction of ArtAB prophage and efficient production of ArtAB was observed in DT104 but not inS. Worthington andS. bongori. Therefore, induction ofartABexpression with H2O2is strain-specific, and the mode of action of H2O2as an SOS-inducing agent might be different from those of MTC and quinolone antibiotics.
A novelin vitro Caenorhabditis eleganstranscription system
Authors: Wibisono Phillip , Liu Yiyong , Sun Jingru
Published: June 2020

Caenorhabditis elegansis an excellent model organism for biological research, but its contributions to biochemical elucidation of eukaryotic transcription mechanisms have been limited. One of the biggest obstacles for biochemical studies ofC. elegansis the high difficulty of preparing functionally active nuclear extract due to its thick surrounding cuticle. By employing Balch homogenization, we have achieved effective disruption of larval and adult worms and have obtained functionally active nuclear extract through subcellular fractionation.In vitrotranscription reactions were successfully re-constituted using such nuclear extract. Furthermore, two non-radioactive detection methods, PCR and qRT-PCR, have been adapted into our system to qualitatively and quantitatively detect transcription, respectively. Using this system to assess how pathogen infection affectsC. eleganstranscription revealed thatPseudomonas aeruginosainfection increased transcription activity. Ourin vitrosystem is useful for biochemically studyingC. eleganstranscription mechanisms and gene expression regulations. The effective preparation of functionally active nuclear extract in our system fills a technical gap in biochemical studies ofC. elegansand will expand the usefulness of this model organism in addressing many biological questions beyond transcription.
InstantDL - An easy-to-use deep learning pipeline for image segmentation and classification
Authors: Waibel Dominik , Boushehri Sayedali Shetab , Marr Carsten
Published: June 2020

Motivation

Deep learning contributes to uncovering and understanding molecular and cellular processes with highly performant image computing algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate, consistent and fast data processing. However, published algorithms mostly solve only one specific problem and they often require expert skills and a considerable computer science and machine learning background for application.

Results

We have thus developed a deep learning pipeline called InstantDL for four common image processing tasks: semantic segmentation, instance segmentation, pixel-wise regression and classification. InstantDL enables experts and non-experts to apply state-of-the-art deep learning algorithms to biomedical image data with minimal effort. To make the pipeline robust, we have automated and standardized workflows and extensively tested it in different scenarios. Moreover, it allows to assess the uncertainty of predictions. We have benchmarked InstantDL on seven publicly available datasets achieving competitive performance without any parameter tuning. For customization of the pipeline to specific tasks, all code is easily accessible.

Availability and Implementation

InstantDL is available under the terms of MIT licence. It can be found on GitHub:https://github.com/marrlab/InstantDL

Contact

carsten.marr@helmholtz-muenchen.de
Oral epithelial expression of angiotensin converting enzyme-2: Implications for COVID-19 diagnosis and prognosis
Authors: Srinivasan Mythily , Zunt Susan L , Goldblatt Lawrence I
Published: June 2020

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) uses the angiotensin converting enzyme (ACE)-2 as the host receptor for target cell entry. The extent and distribution of ACE-2 has been associated with the clinical symptoms of coronavirus disease (COVID)-19. Here we show by immunofluorescence analysis that the ACE2 is abundantly expressed in oral mucosa, particularly in the surface epithelial cells suggesting that these cells could represent sites of entry for SARS-CoV-2. Further, together with the reports on ACE2 ectodomain shedding, we discuss the rationale for the hypothesis that the ACE-2 measurement in saliva could be a marker for COVID-19 infection during early phase following SARS-CoV-2 exposure.
CD209L/L-SIGN and CD209/DC-SIGN act as receptors for SARS-CoV-2
Authors: Amraei Razie , Yin Wenqing , Napoleon Marc A. , Suder Ellen L. , Berrigan Jacob , Zhao Qing , Olejnik Judith , Chandler Kevin Brown , Xia Chaoshuang , Feldman Jared , Hauser Blake M. , Caradonna Timothy M. , Schmidt Aaron G. , Gummuluru Suryaram , Muhlberger Elke , Chitalia Vipul , Costello Catherine E. , Rahimi Nader
Published: June 2020

As the COVID-19 pandemic continues to spread, investigating the processes underlying the interactions between SARS-CoV-2 and its hosts is of high importance. Here, we report the identification of CD209L/L-SIGN and the related protein CD209/DC-SIGN as receptors capable of mediating SARS-CoV-2 entry into human cells. Immunofluorescence staining of human tissues revealed prominent expression of CD209L in the lung and kidney epithelium and endothelium. Multiple biochemical assays using a purified recombinant SARS-CoV-2 spike receptor binding domain (S-RBD) or S1 encompassing both NTB and RBD and ectopically expressed CD209L and CD209 revealed that CD209L and CD209 interact with S-RBD. CD209L contains twoN-glycosylation sequons, at sites N92 and N361, but we determined that only site N92 is occupied. Removal of theN-glycosylation at this site enhances the binding of S-RBD with CD209L. CD209L also interacts with ACE2, suggesting a role for heterodimerization of CD209L and ACE2 in SARS-CoV-2 entry and infection in cell types where both are present. Furthermore, we demonstrate that human endothelial cells are permissive to SARS-CoV-2 infection and interference with CD209L activity by knockdown strategy or with soluble CD209L inhibits virus entry. Our observations demonstrate that CD209L and CD209 serve as alternative receptors for SARS-CoV-2 in disease-relevant cell types, including the vascular system. This property is particularly important in tissues where ACE2 has low expression or is absent, and may have implications for antiviral drug development.
epiGBS2: an improved protocol and automated snakemake workflow for highly multiplexed reduced representation bisulfite sequencing
Authors: Gawehns Fleur , Postuma Maarten , van Gurp Thomas P. , Wagemaker Niels C. A. M. , Fatma Samar , Van Antro Morgane , Mateman Christa , Milanovic-Ivanovic Slavica , van Oers Kees , Grosse Ivo , Vergeer Philippine , Verhoeven Koen J. F.
Published: June 2020

epiGBS is an existing reduced representation bisulfite sequencing method to determine cytosine methylation and genetic polymorphismsde novo. Here, we present epiGBS2, an improved epiGBS laboratory protocol and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. epiGBS2 decreases costs and time investment and increases user-friendliness and reproducibility. The library protocol was adjusted to allow for a flexible choice of restriction enzymes and a double digest. Instead of fully methylated adapters, semi-methylated adapters are now used. The bioinformatics pipeline was improved in speed and integrated in the snakemake workflow management system, which now makes the pipeline easy to execute, modular, and parameter settings flexible. We also provide a detailed description of the laboratory protocol, an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo-knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.3819996), and example output.
Characterization of a gene-trap knockout mouse model ofScn2aencoding voltage-gated sodium channel Nav1.2
Authors: Eaton Muriel , Zhang Jingliang , Ma Zhixiong , Park Anthony C. , Lietzke Emma , Romero Chloé Maricela , Liu Yushuang , Coleman Emily Rose , Chen Xiaoling , Xiao Tiange , Huang Zhuo , Skarnes William C. , Koss Wendy A. , Yang Yang
Published: June 2020

Recent large-scale genomic studies have revealedSCN2Aas one of the most frequently mutated gene in patients with neurodevelopmental disorders including autism spectrum disorder and intellectual disability.SCN2Aencodes for voltage-gated sodium channel isoform 1.2 (Nav1.2), which is mainly expressed in the central nervous system and responsible for the propagation of neuronal action potentials. Homozygous knockout (null) ofScn2ais perinatal lethal, whereas heterozygous knockout ofScn2aresults in mild behavior abnormalities. To achieve a more substantial, but not complete, reduction ofScn2aexpression, we characterized aScn2adeficient mouse model using a targeted gene trap knockout (gtKO) strategy to recapitulate loss-of-functionSCN2Adisorders. This model produces viable homozygous mice (Scn2agtKO/gtKO) that can survive to adulthood, with markedly low but detectable Nav1.2 expression. AlthoughScn2agtKO/gtKOadult mice possess normal olfactory, taste, hearing, and mechanical sensitivity, they have decreased thermal and cold tolerance. Innate behaviors are profoundly impaired including impaired nesting, marble burying, and mating. These mice also have increased food and water intake with subsequent increases in fecal excretion of more but smaller fecal boli. This novelScn2agene trap knockout mouse thus provides a unique model to study pathophysiology associated withScn2adeficiency.
A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2
Authors: Karathanou Konstantina , Lazaratos Michalis , Bertalan Éva , Siemers Malte , Buzar Krzysztof , Schertler Gebhard F.X. , del Val Coral , Bondar Ana-Nicoleta
Published: June 2020

Corona virus spike protein S is a large homo-trimeric protein embedded in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, has a relatively large H-bond cluster at the receptor binding domain, and a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding.
Spatiotemporal whole-brain dynamics of auditory patterns recognition
Authors: Bonetti L. , Brattico E. , Carlomagno F. , Cabral J. , Stevner A. , Deco G. , Whybrow P.C. , Pearce M. , Pantazis D. , Vuust P. , Kringelbach M.L
Published: June 2020

Music is a non-verbal human language, built on logical structures and articulated in balanced hierarchies between sounds, offering excellent opportunities to explore how the brain creates meaning for complex spatiotemporal auditory patterns. Using the high temporal resolution of magnetoencephalography in 70 participants, we investigated their unfolding brain dynamics during the recognition of previously memorized J.S. Bach’s musical patterns from prelude in C minor BWV 847 compared to novel patterns matched in terms of entropy and information content. Remarkably, the recognition of the memorized music ignited a widespread brain network comprising primary auditory cortex, superior temporal gyrus, insula, frontal operculum, cingulate gyrus, orbitofrontal cortex, basal ganglia, thalamus and hippocampus. Furthermore, measures of both brain activity and functional connectivity presented an overall increase over time, following the evolution and unfolding of the memorized musical patterns. Specifically, while the auditory cortex responded mainly to the first tones of the patterns, the activity and synchronization of higher-order brain areas such as cingulate, frontal operculum, hippocampus and orbitofrontal cortex largely increased over time, arguably representing the key whole-brain mechanisms for conscious recognition of auditory patterns as predicted by the global neuronal workspace hypothesis. In conclusion, our study described the fine-grained whole-brain activity and functional connectivity dynamics responsible for processing and recognition of previously memorized music. Further, the study highlights how the use of musical patterns in combination with a wide array of analytical tools and neuroscientific measures spanning from decoding to fast neural phase synchronization can shed new light on meaningful, complex cognitive processes.
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2
Authors: Custódio Tânia F. , Das Hrishikesh , Sheward Daniel J , Hanke Leo , Pazicky Samuel , Pieprzyk Joanna , Sorgenfrei Michèle , Schroer Martin , Gruzinov Andrey , Jeffries Cy , Graewert Melissa , Svergun Dmitri , Dobrev Nikolay , Remans Kim , Seeger Markus A. , McInerney Gerald M , Murrell Ben , Hällberg B. Martin , Löw Christian
Published: June 2020

The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC50of 0.6 µg/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed a novel conformation of the spike where two RBDs are in the ‘up’ ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.
Rapid molecular evolution ofSpiroplasmasymbionts ofDrosophila
Authors: Gerth Michael , Martinez-Montoya Humberto , Ramirez Paulino , Masson Florent , Griffin Joanne S. , Aramayo Rodolfo , Siozios Stefanos , Lemaitre Bruno , Mateos Mariana , Hurst Gregory D.D.
Published: June 2020

Spiroplasmaare a group of Mollicutes whose members include plant pathogens, insect pathogens, and endosymbionts of animals.Spiroplasmaphenotypes have been repeatedly observed to be spontaneously lost inDrosophilacultures, and several studies have documented a high genomic turnover inSpiroplasmasymbionts and plant pathogens. These observations suggest thatSpiroplasmaevolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns ofSpiroplasma poulsonii, a natural symbiont ofDrosophila. We analysed genomic evolution ofsHy within flies, andsMel withinin vitroculture over several years. We observed thatS. poulsoniisubstitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair locimutSandmutLis conserved acrossSpiroplasmaand likely contributes to elevated substitution rates. Further, the closely related strainssMel andsHy (>99.5% sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation insHy, a protective symbiont ofDrosophila hydei. Finally, comparison across diverseSpiroplasmalineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in severalSpiroplasmalineages and other endosymbionts. Overall, our results highlight the peculiar nature ofSpiroplasmagenome evolution, which may explain unusual features of its evolutionary ecology.
TIR-1/SARM1 Inhibits Axon Regeneration
Authors: Julian Victoria , Byrne Alexandra B.
Published: June 2020

An injured axon has two choices, regenerate or degenerate. In many neurons, the result is catastrophic axon degeneration and a failure to regenerate. To coerce the injured nervous system to regenerate, the molecular mechanisms that regulate both axon regeneration and degeneration need to be defined. We found that TIR-1/SARM1, a key regulator of axon degeneration, inhibits regeneration of injured motor axons. Loss oftir-1function both reduces the frequency with which severed axon fragments degenerate and increases the frequency of axon regeneration. The increased regeneration intir-1mutants is not a secondary consequence of its effects on degeneration. Rather, TIR-1 carries out each of these opposing functions cell autonomously by regulating independent downstream genetic pathways. While promoting axon degeneration with the DLK-1 mitogen activated protein kinase (MAPK) signaling cascade, TIR-1 inhibits axon regeneration by activating the NSY-1/ASK1 MAPK signaling cascade. Our finding that TIR-1 regulates both axon regeneration and degeneration provides critical insight into how axons coordinately regulate the two key responses to injury, consequently informing approaches to manipulate the balance between these responses towards repair.
Bridging the gap – Spontaneous fluctuations shape stimulus-evoked spectral power
Authors: Wainio-Theberge Soren , Wolff Annemarie , Northoff Georg
Published: June 2020

Spontaneous fluctuations of neural activity have been shown to influence trial-by-trial variation in perceptual, cognitive, and behavioural outcomes. This implies that these fluctuations affect stimulus-related neural processes, and hence should affect stimulus-evoked neural activity. However, the mechanisms by which spontaneous neural activity shapes stimulus-evoked neural activity have rarely been examined. Employing a large-scale magnetoencephalographic dataset, as well as an electroencephalographic replication dataset, we observed that for high-frequency power, high pre-stimulus activity leads to greater evoked desynchronization (negative interaction); in contrast, for low-frequency power, high pre-stimulus activity induces greater event-related synchronization (positive interaction). We show that both positive and negative interactions are manifest primarily in cortical oscillations, rather than scale-free activity, and can also be observed in the time domain. In summary, we demonstrate positive and negative spontaneous-evoked interaction in multiple electrophysiological processes; these mechanisms “bridge the gap” between spontaneous and evoked activity and provide novel insights into how spontaneous activity influences behaviour and cognition.
Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts
Authors: Zhu Kaiyi , Cai Lingyi , Cui Chenqian , Anastassiou Dimitris
Published: June 2020

During the last ten years, many research results have been referring to a particular type of cancer-associated fibroblasts associated with poor prognosis, invasiveness, metastasis and resistance to therapy in multiple cancer types, characterized by a gene expression signature with prominent presence of genes COL11A1, THBS2 and INHBA. Identifying the underlying biological mechanisms responsible for their creation may facilitate the discovery of targets for potential pan-cancer therapeutics. Using a novel computational approach for single-cell gene expression data analysis identifying the dominant cell populations in a sequence of samples from patients at various stages, we conclude that these fibroblasts are produced by a pan-cancer cellular transition originating from a particular type of adipose-derived stromal cells naturally present in the stromal vascular fraction of normal adipose tissue, having a characteristic gene expression signature. Focusing on a rich pancreatic cancer dataset, we provide a detailed description of the continuous modification of the gene expression profiles of cells as they transition from APOD-expressing adipose-derived stromal cells to COL11A1-expressing cancer-associated fibroblasts, identifying the key genes that participate in this transition. These results also provide an explanation to the well-known fact that the adipose microenvironment contributes to cancer progression.

Author summary

Computational analysis of rich gene expression data at the single-cell level from cancer biopsies can lead to biological discoveries about the nature of the disease. Using a computational methodology that identifies the gene expression profile of the dominant cell population for a particular cell type in the microenvironment of tumors, we observed that there is a remarkably continuous modification of this profile among patients, corresponding to a cellular transition. Specifically, we found that the starting point of this transition has a unique characteristic signature corresponding to cells that are naturally residing in normal adipose tissue. We also found that the endpoint of the transition has another characteristic signature corresponding to a particular type of cancer-associated fibroblasts with prominent expression of gene COL11A1, which has been found strongly associated with invasiveness, metastasis and resistance to therapy in multiple cancer types. Our results provide an explanation to the well-known fact that the adipose tissue contributes to cancer progression, shedding light on the biological mechanism by which tumor cells interact with the adipose microenvironment. We provide a detailed description of the changing profile during the transition, identifying associated genes as potential targets for pan-cancer therapeutics inhibiting the underlying mechanism.
Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosome
Authors: Wang Zhiyong , Xiao Shijun , Cai Mingyi , Han Zhaofang , Li Wanbo , Xie Yangjie , Xu Guicai , Lin Aiqiang , Zhang Yan , Ye Kun , Luo Huiyu , Liao Mengxiang , Han Fang , Liu Xiande , Zhang Dongling , Wang Qiurong , Wang Bi , Li Weiming , Li Jiong-Tang
Published: June 2020

Autosomal origins of heterogametic sex chromosomes have been inferred frequently from suppressed recombination and gene degeneration manifested in incompletely differentiated sex chromosomes. However, the initial transition of an autosome region to a proto-sex locus has been not explored in depth. By assembling and analyzing a chromosome-level draft genome, we found a recent (evolved 0.26 million years ago), highly homologous, anddmrt1containing sex-determination locus with slightly reduced recombination in large yellow croaker (Larimichthys crocea), a teleost species with genetic sex determination (GSD) and with undifferentiated sex chromosomes. We observed genomic homology and polymorphic segregation of the proto-sex locus between sexes. Expression ofdmrt1showed a stepwise increase in the development of testis, but not in the ovary. We infer that the inception of the proto-sex locus involves a few divergences in nucleotide sequences and slight suppression of recombination in an autosome region. In androgen-induced sex reversal of genetic females, in addition todmrt1, genes in the conserveddmrt1cluster, and the rest of the sex determination network were activated. We provided evidence that broad functional links were shared by genetic sex determination and environmental sex reversal.
Gene expression imputation provides insight into the genetic architecture of frontotemporal dementia
Authors: Reus Lianne M. , Pasaniuc Bogdan , Posthuma Danielle , Boltz Toni ,   International FTD-Genomics Consortium (IFGC), Pijnenburg Yolande A.L. , Ophoff Roel A
Published: June 2020

The etiology of genetically sporadic frontotemporal dementia is poorly understood. Although genome-wide association studies for frontotemporal dementia have identified a small number of candidate risk regions, most of the risk genes remain largely unknown. To identify candidate genes with predicted expression levels associated with frontotemporal dementia, we integrated genome-wide summary statistics with external reference gene expression data, using a transcriptome-wide association studies approach.

FUSION software was used to leverage summary statistics on frontotemporal dementia (n=2,340 cases, n=7,252 controls) and clinical subtypes (behavioral variant frontotemporal dementia n=1,337 cases/2,754 controls; semantic dementia n=308 cases/616 controls; progressive non-fluent aphasia n=269 cases/538 controls, frontotemporal dementia with motor neuron disease n=200 cases/400 controls) from the International Frontotemporal Dementia Genomics Consortium with 53 expression quantitative loci tissue type panels (n=12,205 from five consortia). Significance was assessed using a 5% false discovery rate threshold. We identified 73 significant gene-tissue associations for frontotemporal dementia, representing 44 unique genes in 34 tissue types. Most significant findings were derived from dorsolateral prefrontal cortex splicing data (n=19 genes, 26%). Furthermore, the 17q21.31 inversion locus contained 23 significant associations, representing six unique genes whose predicted expression associated with frontotemporal dementia. Other top hits includedSEC22Bon chromosome 1, a gene involved in vesicle trafficking,TRGV5on chromosome 17 andZNF302on chromosome 19. A single gene finding was observed for behavioral variant frontotemporal dementia (i.e.,RAB38on chromosome 11) with evidence from multiple tissue types. For the other clinical subtypes no significant associations were observed.

We used transcriptome-wide association studies to prioritize candidate genes for frontotemporal dementia and identified a number of specific genes, including potential novel candidate genes (such asSEC22B) and previously reported risk regions (e.g., 17q.21.31). Most significant associations were observed in the dorsolateral prefrontal cortex, despite the modest sample size of the gene expression reference panel of this tissue type. This suggests that our findings are specific to frontotemporal dementia and are likely to be biologically relevant highlights of genes at different frontotemporal dementia risk loci that are contributing to the disease pathology.
Locomotor deficits in ALS mice are paralleled by loss of V1-interneuron-connections onto fast motor neurons
Authors: Allodi Ilary , Montañana-Rosell Roser , Selvan Raghavendra , Löw Peter , Kiehn Ole
Published: June 2020

ALS is characterized by progressive inability to execute movements. Motor neurons innervating fast-twitch muscle fibers exhibit preferential degeneration. The reason for differential vulnerability of fast motor neurons, and its consequence on motor output is not known. Here, we show that fast motor neurons receive more inhibitory synaptic inputs than slow motor neurons, and loss of inhibitory synapses onto fast motor neurons precedes disease progression in theSOD1G93Amouse model of ALS. Loss of inhibitory synapses on fast motor neurons is accounted for by a loss of synapses from inhibitory V1 spinal interneurons. Deficits in V1-motor neuron connectivity appear prior to motor neuron death and are paralleled by development of specificSOD1G93Alocomotor deficits. These distinctSOD1G93Alocomotor deficits are phenocopied by silencing of inhibitory V1 spinal interneurons in wild-type mice. Silencing inhibitory V1 spinal interneurons does not exacerbateSOD1G93Alocomotor deficits, suggesting phenotypic pathway interaction. Our study identifies a potential cell non-autonomous source of motor neuronal vulnerability in ALS, and links ALS-induced changes in locomotor phenotypes to inhibitory V1 interneurons.
A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing
Authors: Kellner Max J. , Ross James J. , Schnabl Jakob , Dekens Marcus P.S. , Heinen Robert , Grishkovskaya Irina , Bauer Benedikt , Stadlmann Johannes , Menéndez-Arias Luis , Straw Andrew D. , Fritsche-Polanz Robert , Traugott Marianna , Seitz Tamara , Zoufaly Alexander , Födinger Manuela , Wenisch Christoph , Zuber Johannes ,   Vienna Covid-19 Detection Initiative (VCDI), Pauli Andrea , Brennecke Julius
Published: June 2020

Global efforts to combat the Covid-19 pandemic caused by SARS-CoV-2 still heavily rely on RT-qPCR-based diagnostic tests. However, their high cost, moderate throughput and reliance on sophisticated equipment limit widespread implementation. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative detection method that has the potential to overcome these limitations. We present a rapid, robust, sensitive and versatile RT-LAMP based SARS-CoV-2 detection assay. Our forty-minute procedure bypasses a dedicated RNA isolation step, is insensitive to carry-over contamination, and uses a hydroxynaphthol blue (HNB)-based colorimetric readout, which allows robust SARS-CoV-2 detection from various sample types. Based on this assay, we have substantially increased sensitivity and scalability by a simple nucleic acid enrichment step (bead-LAMP), established a pipette-free version for home testing (HomeDip-LAMP), and developed open source enzymes that can be produced in any molecular biology setting. Our advanced, universally applicable RT-LAMP assay is a major step towards population-scale SARS-CoV-2 testing.
Data integration uncovers the metabolic bases of phenotypic variation in yeast
Authors: Petrizzelli Marianyela , de Vienne Dominique , Nidelet Thibault , Noûs Camille , Dillmann Christine
Published: June 2020

The relationship between different levels of integration is a key feature for understanding the genotype-phenotype map.

Here, we describe a novel method of integrated data analysis that incorporates protein abundance data into constraint-based modeling to elucidate the biological mechanisms underlying phenotypic variation. Specifically, we studied yeast genetic diversity at three levels of phenotypic complexity in a population of yeast obtained by pairwise crosses of eleven strains belonging to two species,Saccha-romyces cerevisiaeandS. uvarum. The data included protein abundances, integrated traits (life-history/fermentation) and computational estimates of metabolic fluxes.

Results highlighted that the negative correlation between production traits such as population carrying capacity (K) and traits associated with growth and fermentation rates (Jmax) is explained by a differential usage of energy production pathways: a highKwas associated with high TCA fluxes, while a highJmaxwas associated with high glycolytic fluxes. Enrichment analysis of protein sets confirmed our results.

This powerful approach allowed us to identify the molecular and metabolic bases of integrated trait variation, and therefore has a broad applicability domain.
The Tissue Tropisms and Transstadial Transmission of aRickettsiaEndosymbiont in the Highland Midge,Culicoides impunctatus(Diptera: Ceratopogonidae)
Authors: Pilgrim Jack , Siozios Stefanos , Baylis Matthew , Hurst Gregory D. D.
Published: June 2020

Rickettsiaare a group of intracellular bacteria which can manipulate host reproduction and alter sensitivity to natural enemy attack in a diverse range of arthropods. The maintenance ofRickettsiaendosymbionts in insect populations can be achieved through both vertical and horizontal transmission routes. For example, the presence of the symbiont in the follicle cells and salivary glands ofBemisiawhiteflies allows Belli groupRickettsiatransmission via the germline and plants, respectively. However, the transmission routes of otherRickettsia, such as those in the Torix group of the genus, remain underexplored. Through fluorescencein-situhybridisation (FISH) and transmission electron microscopy (TEM) screening, this study describes the pattern of TorixRickettsiatissue tropisms in the highland midge,Culicoides impunctatus(Diptera: Ceratopogonidae). Of note is high intensity of infection of the ovarian suspensory ligament, suggestive of a novel germline targeting strategy. Additionally, localisation of the symbiont in tissues of several developmental stages suggests transstadial transmission is a major route of ensuring maintenance ofRickettsiawithinC. impunctatuspopulations. Aside from providing insights into transmission strategies,Rickettsiapresence in the fat body of larvae indicates potential host fitness and vector capacity impacts to be investigated in the future.

Importance Statement

Microbial symbionts of disease vectors have garnered recent attention due to their ability to alter vectorial capacity. Their consideration as a means of arbovirus control depends on symbiont vertical transmission which leads to spread of the bacteria through a population. Previous work has identified aRickettsiasymbiont present in several vector species of biting midges (Culicoidesspp.), however, symbiont transmission strategies and host effects remain underexplored. In this study, we describe the presence ofRickettsiain the ovarian suspensory ligament and the ovarian epithelial sheath ofCulicoides impunctatus. Infection of these organs suggest the connective tissue surrounding developing eggs is important for ensuring vertical transmission of the symbiont in midges and possibly other insects. Additionally, our results indicateRickettsialocalisation in the fat body ofCulicoides impunctatus. As viruses spread by midges often replicate in the fat body, this implies possible vector competence effects to be further investigated.
Replay bursts coincide with activation of the default mode and parietal alpha network
Authors: Higgins Cameron , Liu Yunzhe , Vidaurre Diego , Kurth-Nelson Zeb , Dolan Ray , Behrens Timothy , Woolrich Mark
Published: June 2020

Our brains at rest spontaneously replay recently acquired information, but how this process is orchestrated to avoid interference with ongoing cognition is an open question. We investigated whether replay coincided with spontaneous patterns of whole brain activity. We found, in two separate datasets, that replay sequences were packaged into transient bursts occurring selectively during activation of the default mode network (DMN) and parietal alpha network. These networks were characterized by widespread synchronized oscillations coupled to increases in ripple band power, mechanisms that coordinate information flow between disparate cortical areas. Our data show a tight correspondence between two widely studied phenomena of neural physiology and suggest the DMN may coordinate replay bursts in a manner that minimizes interference with ongoing cognition.
TheBotrytis cinereaCrh transglycosylae is a cytoplasmic effector triggering plant cell death and defense response
Authors: Bi Kai , Scalschi Loredana , Namrata Jaiswal Gupta , Frid Renana , Zhu Wenjun , Masrati Gal , Mengiste Tesfaye , Sharon Amir
Published: June 2020

Crh proteins catalyze crosslinking of chitin and glucan polymers in the fugal cell wall. We revealed a novel and unexpected role ofBotrytis cinereaBcCrh1 as a cytoplasmic effector and elicitor of plant defense. During saprophytic growth the BcCrh1 protein is localized in vacuoles and ER. Upon plant infection the protein accumulates to high levels in infection cushions, it is then secreted to the apoplast and translocated into plant cells, where it induces cell death and defense responses. Two regions of 53 and 35 amino acids were found sufficient for protein uptake and cell death induction, respectively. Dimerization of BcCrh proteins was necessary for the transglycosylation activity and proper fungal development, while the monomeric proteins was sufficient for induction of cell death.Arabidopsislines expressing thebccrh1gene had reduced sensitivity toB. cinerea,demonstrating the potential use of the protein in plant immunization against necrotrophic pathogens.
The development of attentional control mechanisms in multisensory environments
Authors: Turoman Nora , Tivadar Ruxandra I. , Retsa Chrysa , Maillard Anne M. , Scerif Gaia , Matusz Pawel J.
Published: June 2020

Outside the laboratory, people need to pay attention to relevant objects that are typically multisensory, but it remains poorly understood how the underlying neurocognitive mechanisms develop. We investigated when adult-like mechanisms controlling one’s attentional selection of visual and multisensory objects emerge across childhood. Five-, 7-, and 9-year-olds were compared with adults in their performance on a computer game-like multisensory spatial cueing task, while 129-channel EEG was simultaneously recorded. Markers of attentional control were behavioural spatial cueing effects and the N2pc ERP component (analysed traditionally and using a multivariate electrical neuroimaging framework). In behaviour, adult-like visual attentional control was present from age 7 onwards, whereas multisensory control was absent in all children groups. In EEG, multivariate analyses of the activity over the N2pc time-window revealed stable brain activity patterns in children. Adult-like visual-attentional control EEG patterns were present age 7 onwards, while multisensory control activity patterns were found in 9-year-olds (albeit behavioural measures showed no effects). By combining rigorous yet naturalistic paradigms with multivariate signal analyses, we demonstrated that visual attentional control seems to reach an adult-like state at ~7 years, before adult-like multisensory control, emerging at ~9 years. These results enrich our understanding of how attention in naturalistic settings develops.

Highlights

By age 7, children showed adult-like task-set contingent attentional capture in behaviour

Children’s behavioural data did not show evidence for attentional enhancement for multisensory objects, but 9-year-olds’ EEG topographic patterns elicited by multisensory vs. purely visual distractors differed reliably

Traditional visual attentional event-related potential (ERP) analyses, such as the N2pc, did not detect attentional enhancement for multisensory objects in adults, and visual or multisensory attention in children

Multivariate analyses of ERPs, such as electrical neuroimaging, are more sensitive to the change of attentional control processes over development
SARS-CoV-2 structure and replication characterized byin situcryo-electron tomography
Authors: Klein Steffen , Cortese Mirko , Winter Sophie L. , Wachsmuth-Melm Moritz , Neufeldt Christopher J. , Cerikan Berati , Stanifer Megan L. , Boulant Steeve , Bartenschlager Ralf , Chlanda Petr
Published: June 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state byin situcryo-electron tomography and subtomogram averaging. We directly visualized RNA filaments inside the double membrane vesicles, compartments associated with viral replication. The RNA filaments show a diameter consistent with double-stranded RNA and frequent branching likely representing RNA secondary structures. We found that assembled S trimers in lumenal cisternae do not alone induce membrane bending but laterally reorganize on the envelope during virion assembly. The viral ribonucleoprotein complexes (vRNPs) are accumulated at the curved membrane characteristic for budding sites suggesting that vRNP recruitment is enhanced by membrane curvature. Subtomogram averaging shows that vRNPs are distinct cylindrical assemblies. We propose that the genome is packaged around multiple separate vRNP complexes, thereby allowing incorporation of the unusually large coronavirus genome into the virion while maintaining high steric flexibility between the vRNPs.
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways
Authors: Treveil Agatha , Bohar Balazs , Sudhakar Padhmanand , Gul Lejla , Csabai Luca , Olbei Marton , Poletti Martina , Madgwick Matthew , Andrighetti Tahila , Hautefort Isabelle , Modos Dezso , Korcsmaros Tamas
Published: June 2020

The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context,a prioriinteractions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a cell-type specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis. The workflow is available on GitHub (https://github.com/korcsmarosgroup/ViralLink) in an easily accessible Python wrapper script, or as customisable modular R and Python scripts.

Author summary

Collaborative and multidisciplinary science provides increased value for experimental datasets and speeds the process of discovery. Such ways of working are especially important at present due to the urgency of the SARS-CoV-2 pandemic. Here, we present a systems biology workflow which models the effect of viral proteins on the infected host cell, to aid collaborative and multidisciplinary research. Through integration of gene expression datasets with context-specific and context-agnostic molecular interaction datasets, the workflow can be easily applied to different datasets as they are made available. Application to diverse SARS-CoV-2 datasets will increase our understanding of the mechanistic details of the infection at a cell type specific level, aid drug target discovery and help explain the variety of clinical manifestations of the infection.
Automated video-based heart rate tracking for the anesthetized and behaving monkey
Authors: Froesel Mathilda , Goudard Quentin , Hauser Marc , Gacoin Maëva , Ben Hamed Suliann
Published: June 2020

Background

Heart rate is extremely valuable in the study of complex behaviours and their physiological correlates in non-human primates. However, collecting this information is often challenging, involving either invasive implants or tedious behavioural training.

New Method

In the present study, we implement a Eulerian Video Magnification (EVM) heart tracking method in the macaque monkey combined with wavelet transform. This is based on a measure of image to image fluctuations in skin reflectance due to changes in blood influx.

Results

We show a strong temporal coherence and amplitude match between EVM-based heart tracking and ground truth ECG, from both color (RGB) and infrared (IR) videos, in anesthetized macaques, to a level comparable to what can be achieved in humans. We further show that this method allows to identify consistent heart rate changes following the presentation of conspecific emotional voices or faces.

Comparison with Existing Method(s)

Eulerian Video Magnification (EVM) is used to extract heart rate in humans but has never been applied to non-human primates. Video photoplethysmography allows to extract awake macaques heart rate from RGB videos. In contrast, our method allows to extract awake macaques heart rate from both RGB and IR videos and is particularly resilient to the head motion that can be observed in awake behaving monkeys.

Conclusions

Overall, we believe that this method can be generalized as a tool to track heart rate of the awake behaving monkey, for ethological, behavioural, neuroscience or welfare purposes.

Highlights

Heart rate varies during complex non-human primate (NHP) behaviour and cognition.

We apply Eulerian Video Magnification to track NHP heart rate (EVM-HR).

EVM-HR can be used with RGB & IR videos, and anesthetized or awake NHPs.

NHP EVM-HR vary with emotional content of presented stimuli.

EVM-HR is of interest to ethology, behavioural, neuroscience & welfare purposes.
Dissecting the impact of metabolic environment on three common cancer cell phenotypes
Authors: Kochanowski Karl , Sander Timur , Link Hannes , Chang Jeremy , Altschuler Steven , Wu Lani
Published: June 2020

The impact of different metabolic environments on cancer cell behavior is poorly understood. Here, we systematically altered nutrient composition of cell culture media and examined the impact on three phenotypes—drug-treatment survival, cell migration, and lactate overflow—that are frequently studied in cancer cells. These perturbations across diverse metabolic environments revealed simple relationships between cell growth rate and drug-treatment survival or migration. In contrast, lactate overflow was highly sensitive to changes in sugar availability but largely insensitive to changes in amino acid availability, regardless of the growth rate. Further investigation suggested that the degree of lactate overflow across metabolic environments is largely determined by the cells’ ability to maintain high rates of sugar uptake. This study enabled us to elucidate quantitative relationships between metabolic environment and cancer cell phenotypes, which echo empirical growth laws discovered to govern analogous phenotypes in microbes.