bluuebunny/crossref_metadata_2025 huggingface dataset:
Subcortical brain segmentation in 5-year-old children: validation of FSL-FIRST and FreeSurfer against manual segmentation
Authors: Lidauer Kristian , Pulli Elmo P. , Copeland Anni , Silver Eero , Kumpulainen Venla , Hashempour Niloofar , Merisaari Harri , Saunavaara Jani , Parkkola Riitta , Lähdesmäki Tuire , Saukko Ekaterina , Nolvi Saara , Kataja Eeva-Leena , Karlsson Linnea , Karlsson Hasse , Tuulari Jetro J.
Published: May 2021

Developing accurate subcortical volumetric quantification tools is crucial for neurodevelopmental studies, as they could reduce the need for challenging and time-consuming manual segmentation. In this study the accuracy of two automated segmentation tools, FSL-FIRST (with three different boundary correction settings) and FreeSurfer were compared against manual segmentation of subcortical nuclei, including the hippocampus, amygdala, thalamus, putamen, globus pallidus, caudate and nucleus accumbens, using volumetric and correlation analyses in 80 5-year-olds.

Both FSL-FIRST and FreeSurfer overestimated the volume on all structures except the caudate, and the accuracy varied depending on the structure. Small structures such as the amygdala and nucleus accumbens, which are visually difficult to distinguish, produced significant overestimations and weaker correlations with all automated methods. Larger and more readily distinguishable structures such as the caudate and putamen produced notably lower overestimations and stronger correlations. Overall, the segmentations performed by FSL-FIRST’s Default pipeline were the most accurate, while FreeSurfer’s results were weaker across the structures.

In line with prior studies, the accuracy of automated segmentation tools was imperfect with respect to manually defined structures. However, apart from amygdala and nucleus accumbens, FSL-FIRST’s agreement could be considered satisfactory (Pearson correlation > 0.74, Intraclass correlation coefficient (ICC) > 0.68 and Dice Score coefficient (DSC) > 0.87) with highest values for the striatal structures (putamen, globus pallidus and caudate) (Pearson correlation > 0.77, ICC > 0.87 and DSC > 0.88, respectively). Overall, automated segmentation tools do not always provide satisfactory results, and careful visual inspection of the automated segmentations is strongly advised.
Combination of a Sindbis-SARS-CoV-2 spike vaccine and αOX40 antibody elicits protective immunity against SARS-CoV-2 induced disease and potentiates long-term SARS-CoV-2-specific humoral and T-cell immunity
Authors: Scaglione Antonella , Opp Silvana , Hurtado Alicia , Lin Ziyan , Pampeno Christine , Noval Maria G , Thannickal Sara A. , Stapleford Kenneth A. , Meruelo Daniel
Published: May 2021

The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 is a major global public threat. Currently, a worldwide effort has been mounted to generate billions of effective SARS-CoV-2 vaccine doses to immunize the world’s population at record speeds. However, there is still demand for alternative effective vaccines that rapidly confer long-term protection and rely upon cost-effective, easily scaled-up manufacturing. Here, we present a Sindbis alphavirus vector (SV), transiently expressing the SARS-CoV-2 spike protein (SV.Spike), combined with the OX40 immunostimulatory antibody (αOX40) as a novel, highly effective vaccine approach. We show that SV.Spike plus αOX40 elicits long-lasting neutralizing antibodies and a vigorous T-cell response in mice. Protein binding, immunohistochemical and cellular infection assays all show that vaccinated mice sera inhibits spike functions. Immunophenotyping, RNA Seq transcriptome profiles and metabolic analysis indicate a reprogramming of T-cells in vaccinated mice. Activated T-cells were found to mobilize to lung tissue. Most importantly, SV.Spike plus αOX40 provided robust immune protection against infection with authentic coronavirus in transgenic mice expressing the human ACE2 receptor (hACE2-Tg). Finally, our immunization strategy induced strong effector memory response, potentiating protective immunity against re-exposure to SARS-CoV-2 spike protein. Our results show the potential of a new Sindbis virus-based vaccine platform to counteract waning immune response that can be used as a new candidate to combat SARS-CoV-2. Given the strong T-cell responses elicited, our vaccine is likely to be effective against variants that are proving challenging, as well as, serve as a platform to develop a broader spectrum pancoronavirus vaccine. Similarly, the vaccine approach is likely to be applicable to other pathogens.
Evaluating the risk of SARS-CoV-2 transmission to bats using a decision analytical framework
Authors: Cook Jonathan D. , Campbell Grant Evan H. , Coleman Jeremy T. H. , Sleeman Jonathan M. , Runge Michael C.
Published: May 2021

Preventing wildlife disease outbreaks is a priority issue for natural resource agencies, and management decisions can be urgent, especially in epidemic circumstances. With the emergence of SARS-CoV-2, wildlife agencies were concerned whether the activities they authorize might increase the risk of viral transmission from humans to North American bats but had a limited amount of time in which to make decisions. We provide a description of how decision analysis provides a powerful framework to analyze and re-analyze complex natural resource management problems as knowledge evolves. Coupled with expert judgment and avenues for the rapid release of information, risk assessment can provide timely scientific information for evolving decisions. In April 2020, the first rapid risk assessment was conducted to evaluate the risk of transmission of SARS-CoV-2 from humans to North American bats.

Based on the best available information, and relying heavily on formal expert judgment, the risk assessment found a small possibility of transmission during summer work activities. Following that assessment, additional knowledge and data emerged, such as bat viral challenge studies, that further elucidated the risks of human-to-bat transmission and culminated in a second risk assessment in the fall of 2020. We update the first SARS-CoV-2 risk assessment with new estimates of little brown bat (Myotis lucifugus) susceptibility and new management alternatives, using findings from the prior two risk assessments and other empirical studies. We highlight the strengths of decision analysis and expert judgment not only to frame decisions and produce useful science in a timely manner, but also to serve as a framework to reassess risk as understanding improves. For SARS-CoV-2 risk, new knowledge led to an 88% decrease in the median number of bats estimated to be infected per 1000 encountered when compared to earlier results. The use of facemasks during, or a negative COVID-19 test prior to, bat encounters further reduced those risks. Using a combination of decision analysis, expert judgment, rapid risk assessment, and efficient modes of information distribution, we provide timely science support to decision makers for summer bat work in North America.
A Biologically Interpretable Graph Convolutional Network to Link Genetic Risk Pathways and Neuroimaging Markers of Disease
Authors: Ghosal Sayan , Chen Qiang , Pergola Giulio , Goldman Aaron L. , Ulrich William , Weinberger Daniel R. , Venkataraman Archana
Published: May 2021

Abstract

We propose a novel end-to-end framework for whole-brain and whole-genome imaging-genetics. Our genetics network uses hierarchical graph convolution and pooling operations to embed subject-level data onto a low-dimensional latent space. The hierarchical network implicitly tracks the convergence of genetic risk across well-established biological pathways, while an attention mechanism automatically identifies the salient edges of this network at the subject level. In parallel, our imaging network projects multimodal data onto a set of latent embeddings. For interpretability, we implement a Bayesian feature selection strategy to extract the discriminative imaging biomarkers; these feature weights are optimized alongside the other model parameters. We couple the imaging and genetic embeddings with a predictor network, to ensure that the learned representations are linked to phenotype. We evaluate our framework on a schizophrenia dataset that includes two functional MRI paradigms and gene scores derived from Single Nucleotide Polymorphism data. Using repeated 10-fold cross-validation, we show that our imaging-genetics fusion achieves the better classification performance than state-of-the-art baselines. In an exploratory analysis, we further show that the biomarkers identified by our model are reproducible and closely associated with deficits in schizophrenia.
Historical biogeography and phylogeography ofIndoplanorbis exustus
Authors: Sil Maitreya , Mahveen Juveriya , Roy Abhishikta , Praveen Karanth K. , Aravind Neelavara Ananthram
Published: May 2021

The history of a lineage is intertwined with the history of the landscape it resides in. Here we showcase how the geo-tectonic and climatic evolution in South Asia and surrounding landmasses have shaped the biogeographic history ofIndoplanorbis exustus, a tropical Asian, freshwater, pulmonated snail. We amplified partial COI gene fragment from all over India and combined this with a larger dataset from South and Southeast Asia to carry out phylogenetic reconstruction, species delimitation analysis, and population genetic analyses. Two nuclear genes were also amplified from one individual per putative species to carry out divergence dating and ancestral area reconstruction analyses. The results suggest thatIndoplanorbisdispersed out of Africa into India during Eocene. Furthermore, molecular data suggestsIndoplanorbisis a species complex consisting of multiple putative species. The primary diversification took place in Northern Indian plains or the Northeast India. The speciation events appear to be primarily allopatric caused by a series of aridification events starting from late Miocene to early Pleistocene. None of the species seemed to have any underlying genetic structure suggestive of high vagility. All the species underwent population fluctuations during the Pleistocene likely driven by the Quaternary climatic fluctuations.
Impact of ploidy and pathogen life cycle on resistance durability
Authors: Saubin Méline , De Mita Stéphane , Zhu Xujia , Sudret Bruno , Halkett Fabien
Published: May 2021

The breeding of resistant hosts based on the gene-for-gene interaction is crucial to address epidemics of plant pathogens in agroecosystems. Resistant host deployment strategies are developed and studied worldwide to decrease the probability of resistance breakdown and increase the resistance durability in various pathosystems. A major component of deployment strategies is the proportion of resistant hosts in the landscape. However, the impact of this proportion on resistance durability remains unclear for diploid pathogens with complex life cycles. In this study, we modelled pathogen population dynamics and genetic evolution at the virulence locus to assess the impact of the ploidy (haploid or diploid) and the pathogen’s life cycle (with or without host alternation) on resistance durability. Ploidy has a strong impact on evolutionary trajectories, with much greater stochasticity and delayed times of resistance breakdown for diploids. This result emphasises the importance of genetic drift in this system: as the virulent allele is recessive, positive selection on resistant hosts only applies to homozygous (virulent) individuals, which may lead to population collapse at low frequencies of the virulent allele. We also observed differences in the effect of host deployment depending on the pathogen’s life cycle. With host alternation, the probability that the pathogen population collapses strongly increases with the proportion of resistant hosts in the landscape. Therefore, resistance breakdown events occurring at high proportions of resistant hosts frequently amount to evolutionary rescue. Last, life cycles correspond to two selection regimes: without host alternation (soft selection) the resistance breakdown is mainly driven by the migration rate. Conversely, host alternation (hard selection) resembles an all-or-nothing game, with stochastic trajectories caused by the recurrent allele redistributions on the alternate host.
Federated Multi-Site Normative Modeling using Hierarchical Bayesian Regression
Authors: Kia Seyed Mostafa , Huijsdens Hester , Rutherford Saige , Dinga Richard , Wolfers Thomas , Mennes Maarten , Andreassen Ole A. , Westlye Lars T. , Beckmann Christian F. , Marquand Andre F.
Published: May 2021

Abstract

Clinical neuroimaging data availability has grown substantially in the last decade, providing the potential for studying heterogeneity in clinical cohorts on a previously unprecedented scale. Normative modeling is an emerging statistical tool for dissecting heterogeneity in complex brain disorders. However, its application remains technically challenging due to medical data privacy issues and difficulties in dealing with nuisance variation, such as the variability in the image acquisition process. Here, we introduce a federated probabilistic framework using hierarchical Bayesian regression (HBR) for multi-site normative modeling. The proposed method completes the life-cycle of normative modeling by providing the possibilities to learn, update, and adapt the model parameters on decentralized neuroimaging data. Our experimental results confirm the superiority of HBR in deriving more accurate normative ranges on large multi-site neuroimaging datasets compared to the current standard methods. In addition, our approach provides the possibility to recalibrate and reuse the learned model on local datasets and even on datasets with very small sample sizes. The proposed federated framework closes the technical loop for applying normative modeling across multiple sites in a decentralized manner. This will facilitate applications of normative modeling as a medical tool for screening the biological deviations in individuals affected by complex illnesses such as mental disorders.
Structure-based Classification of Tauopathies
Authors: Shi Yang , Zhang Wenjuan , Yang Yang , Murzin Alexey , Falcon Benjamin , Kotecha Abhay , van Beers Mike , Tarutani Airi , Kametani Fuyuki , Garringer Holly J. , Vidal Ruben , Hallinan Grace I. , Lashley Tammaryn , Saito Yuko , Murayama Shigeo , Yoshida Mari , Tanaka Hidetomo , Kakita Akiyoshi , Ikeuchi Takeshi , Robinson Andrew C. , Mann David M.A. , Kovacs Gabor G. , Revesz Tamas , Ghetti Bernardino , Hasegawa Masato , Goedert Michel , Scheres Sjors H.W.
Published: May 2021

Ordered assembly of the tau protein into filaments characterizes multiple neurodegenerative diseases, which are called tauopathies. We previously reported that by electron cryo-microscopy (cryo-EM), tau filament structures from Alzheimer’s disease (1,2), chronic traumatic encephalopathy (CTE) (3), Pick’s disease (4) and corticobasal degeneration (CBD) (5) are distinct. Here we show that the structures of tau filaments from typical and atypical progressive supranuclear palsy (PSP), the most common tauopathy after Alzheimer’s disease, define a previously unknown, three-layered fold. Moreover, the tau filament structures from globular glial tauopathy (GGT, Types I and II) are similar to those from PSP. The tau filament fold of argyrophilic grain disease (AGD) differs from the above and resembles the four-layered CBD fold. The majority of tau filaments from aging-related tau astrogliopathy (ARTAG) also have the AGD fold. Surprisingly, tau protofilament structures from inherited cases with mutations +3/+16 in intron 10 of MAPT, the microtubule-associated protein tau gene, are identical to those from AGD, suggesting that a relative overproduction of four-repeat tau can give rise to the AGD fold. Finally, tau filament structures from cases of familial British dementia (FBD) and familial Danish dementia (FDD) are the same as those from Alzheimer’s disease and primary age-related tauopathy (PART). These structures provide the basis for a classification of tauopathies that also allows identification of new entities, as we show here for a case diagnosed as PSP, but with abundant spherical 4R tau inclusions in limbic and other brain areas. The structures of the tau fold of this new disease (Limbic-predominant Neuronal inclusion body 4R Tauopathy, LNT) were intermediate between those of GGT and PSP.
Decomposition of the SARS-CoV-2-ACE2 interface reveals a common trend among emerging viral variants
Authors: Socher Eileen , Conrad Marcus , Heger Lukas , Paulsen Friedrich , Sticht Heinrich , Zunke Friederike , Arnold Philipp
Published: May 2021

New viral variants of the SARS-CoV-2 virus show enhanced infectivity compared to wild type, resulting in an altered pandemic situation in affected areas. These variants are the B.1.1.7 (United Kingdom), B.1.1.7 with the additional E484K mutation, the B.1.351 variant (South Africa) and the P.1 variant (Brazil). Understanding the binding modalities between these viral variants and the host cell receptor ACE2 allows depicting changes, but also common motifs of virus-host cell interaction. The trimeric spike protein expressed at the viral surface contains the receptor-binding domain (RBD) that forms the molecular interface with ACE2. All the above-mentioned variants carry between one and three amino acid exchanges within the interface-forming region of the RBD, thereby altering the binding interface with ACE2. Using molecular dynamics simulations and decomposition of the interaction energies between the RBD and ACE2, we identified phenylalanine 486, glutamine 498, threonine 500 and tyrosine 505 as important interface-forming residues across viral variants. We also suggest a reduced binding energy between RBD and ACE2 in viral variants with higher infectivity, attributed to residue-specific differences in electrostatic interaction energy. Importantly, individual amino acid exchanges not only influence the affected position, but also alter the conformation of surrounding residues and affect their interaction potential as well. We demonstrate how computational methods can help to identify changed as well as common motifs across viral variants. These identified motifs might play a crucial role, in the strategical development of therapeutic interventions against the fast mutating SARS-CoV-2 virus.

Significance Statement

The COVID-19 pandemic caused by the SARS-CoV-2 virus has significantly changed our lives. To date, there is a lack of neutralizing drugs that specifically target SARS-CoV-2. Hope lies in newly developed vaccines that effectively prevent severe cases of acute respiratory syndrome. However, emerging viral variants escape vaccine-induced immune-protection. Therefore, identification of appropriate molecular targets across viral variants is important for the development of second- and third-generation vaccines and inhibitory antibodies. In this study, we identify residues across viral variants that are important for viral binding to the host cell. As such residues cannot be replaced without diminishing infectivity of the virus, these residues represent primary targets for intervention, for example by neutralizing antibodies.
A universal, open-source, high-performance tool for automated sleep staging
Authors: Vallat Raphael , Walker Matthew P.
Published: May 2021

The creation of a completely automated sleep-scoring system that is highly accurate, flexible, well validated, free and simple to use by anyone has yet to be accomplished. In part, this is due to the difficulty of use of existing algorithms, algorithms having been trained on too small samples, and paywall demotivation. Here we describe a novel algorithm trained and validated on +27,000 hours of polysomnographic sleep recordings across heterogeneous populations around the world. This tool offers high sleep-staging accuracy matching or exceeding human accuracy and interscorer agreement no matter the population kind. The software is easy to use, computationally low-demanding, open source, and free. Such software has the potential to facilitate broad adoption of automated sleep staging with the hope of becoming an industry standard.
Pharmacological activation of PIEZO1 in human red blood cells prevents Plasmodium falciparum invasion
Authors: Lohia Rakhee , Le Guet Jordy , Berry Laurence , Guizouarn Hélène , Bernal Roberto , Cerdan Rachel , Abkarian Manouk , Douguet Dominique , Honoré Eric , Wengelnik Kai
Published: May 2021

An inherited gain-of–function variant (E756 del) in the mechanosensitive cationic channel PIEZO1 was recently shown to confer a significant protection against severe malaria. Here, we demonstrate in vitro that human red blood cell (RBC) infection by Plasmodium falciparum is prevented by the pharmacological activation of PIEZO1. The PIEZO1 activator Yoda1 inhibits RBC invasion, without affecting parasite intraerythrocytic growth, division or egress. RBC dehydration, echinocytosis and intracellular Na+/K+ imbalance are unrelated to the mechanism of protection. Inhibition of invasion is maintained, even after a prolonged wash out of Yoda1. Similarly, the chemically unrelated activators Jedi1 and Jedi2 potently inhibit parasitemia, further indicating a PIEZO1-dependent mechanism. Notably, Yoda1 treatment significantly reduced RBC surface receptors of P. falciparum, and decreased merozoite attachment and subsequent RBC deformation. Altogether these data indicate that the pharmacological activation of Piezo1 in human RBCs inhibits malaria infection by impairing P. falciparum invasion.
The Dual Mechanisms of Cognitive Control dataset, a theoretically-guided within-subject task fMRI battery
Authors: Etzel Joset A. , Brough Rachel E. , Freund Michael C. , Kizhner Alexander , Lin Yanli , Singh Matthew F. , Tang Rongxiang , Tay Allison , Wang Anxu , Braver Todd S.
Published: May 2021

Cognitive control is a critical higher mental function, which is subject to considerable individual variation, and is impaired in a range of mental health disorders. We describe here the initial release of Dual Mechanisms of Cognitive Control (DMCC) project data, the DMCC55B dataset, with 55 healthy unrelated young adult participants. Each participant performed four well-established cognitive control tasks (AX-CPT, Cued Task-Switching, Sternberg Working Memory, and Stroop) while undergoing functional MRI scanning. The dataset includes a range of state and trait self-report questionnaires, as well as behavioural tasks assessing individual differences in cognitive ability. The DMCC project is on-going and features additional components (e.g., related participants, manipulations of cognitive control mode, resting state fMRI, longitudinal testing) that will be publicly released following study completion. This DMCC55B subset is released early with the aim of encouraging wider use and greater benefit to the scientific community. The DMCC55B dataset is suitable for benchmarking and methods exploration, as well as analyses of task performance and individual differences.
Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium
Authors: Mehregan Aujan , Pérez-Conesa Sergio , Zhuang Yuxuan , Elbahnsi Ahmad , Pasini Diletta , Lindahl Erik , Howard Rebecca J , Ulens Chris , Delemotte Lucie
Published: May 2021

SARS-CoV-2 contains four structural proteins in its genome. These proteins aid in the assembly and budding of new virions at the ER-Golgi intermediate compartment (ERGIC). Current fundamental research efforts largely focus on one of these proteins – the spike (S) protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other structural proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length envelope (E) protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca2+, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.
Manganese transport by Streptococcus sanguinis in acidic conditions and its impact on growth in vitro and in vivo
Authors: Puccio Tanya , Schultz Alexander C. , Lizarraga Claudia A. , Bryant Ashley S. , Culp David J. , Burne Robert A. , Kitten Todd
Published: May 2021

Streptococcus sanguinis is an oral commensal and an etiological agent of infective endocarditis. Previous studies have identified the SsaACB manganese transporter as essential for endocarditis virulence; however, the significance of SsaACB in the oral environment has never been examined. Here we report that a ΔssaACB mutant of strain SK36 exhibits reduced growth and manganese uptake under acidic conditions. Further studies revealed that these deficits resulted from the decreased activity of TmpA, shown in the accompanying paper to function as a ZIP-family manganese transporter. Transcriptomic analysis of fermentor-grown cultures of SK36 WT and ΔssaACB strains identified pH-dependent changes related to carbon catabolite repression in both strains, though their magnitude was generally greater in the mutant. In strain VMC66, which possesses a MntH transporter, loss of SsaACB did not significantly alter growth or cellular manganese levels under the same conditions. Interestingly, there were only modest differences between SK36 and its ΔssaACB mutant in competition with Streptococcus mutans in vitro and in a murine oral colonization model. Our results suggest that the heterogeneity of the oral environment may provide a rationale for the variety of manganese transporters found in S. sanguinis and point to strategies for enhancing the safety of oral probiotics.

Graphical Abstract

Depiction of methods. Streptococcal strains used are depicted at the top. The four methods illustrated are: 1. S. sanguinis cells were grown in media at pH 7.3 and pH 6.2 and quantified by plating. 2. S. sanguinis cells were grown in a fermentor vessel for RNA-sequencing and metal analysis. 3. S. sanguinis and S. mutans cells were grown in 12-well plates singly or in competition, then plated and the pH of the media measured. 4. S. sanguinis and S. mutans cells were inoculated into the mouths of mice. Oral swabs and dental biofilms from molars were assayed for bacterial composition by qPCR. (Biorender)
The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression
Authors: Mendez Aaron S. , Ly Michael , González-Sánchez Angélica M. , Hartenian Ella , Ingolia Nicholas T. , Cate Jamie H. , Glaunsinger Britt A.
Published: May 2021

Nonstructural protein 1 (nsp1) is the first viral protein synthesized during coronavirus (CoV) infection and is a key virulence factor that dampens the innate immune response. It restricts cellular gene expression through a combination of inhibiting translation by blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We performed a detailed structure-guided mutational analysis of CoV-2 nsp1 coupled with in vitro and cell-based functional assays, revealing insight into how it coordinates these activities against host but not viral mRNA. We found that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, thereby enhancing its restriction of host gene expression. These residues are also critical for the ability of mRNA containing the CoV-2 leader sequence to escape translational repression. Notably, we identify CoV-2 nsp1 mutants that gain the ability to repress translation of viral leader-containing transcripts. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in CoV-2 nsp1 could attenuate the virus.
Novel antibodies for the simple and efficient enrichment of native O-GlcNAc modified peptides
Authors: Burt Rajan A. , Dejanovic Borislav , Peckham Hayley J. , Lee Kimberly A. , Li Xiang , Ounadjela Johain R. , Rao Anjana , Malaker Stacy A. , Carr Steven A. , Myers Samuel A.
Published: May 2021

Antibodies against post-translational modifications (PTMs) such as lysine acetylation, ubiquitin remnants, or phosphotyrosine have resulted in significant advances in our understanding of the fundamental roles of PTMs in biology. However, the roles of a number of PTMs remain largely unexplored due to the lack of robust enrichment reagents. The addition of N-acetylglucosamine to serine and threonine residues (O-GlcNAc) by the O-GlcNAc transferase (OGT) is a PTM implicated in numerous biological processes and disease states but with limited techniques for its study. Here, we evaluate a new mixture of anti-O-GlcNAc monoclonal antibodies for the immunoprecipitation of native O-GlcNAcylated peptides from cells and tissues. The anti-O-GlcNAc antibodies display good sensitivity and high specificity toward O-GlcNAc-modified peptides, and do not recognize O-GalNAc or GlcNAc in extended glycans. Applying this antibody-based enrichment strategy to synaptosomes from mouse brain tissue samples, we identified over 1,300 unique O-GlcNAc-modified peptides and over 1,000 sites using just a fraction of sample preparation and instrument time required in other landmark investigations of O-GlcNAcylation. Our rapid and robust method greatly simplifies the analysis of O-GlcNAc signaling and will help to elucidate the role of this challenging PTM in health and disease.
Frontal language areas do not emerge in the absence of temporal language areas: A case study of an individual born without a left temporal lobe
Authors: Tuckute Greta , Paunov Alexander , Kean Hope , Small Hannah , Mineroff Zachary , Blank Idan , Fedorenko Evelina
Published: May 2021

Language relies on a left-lateralized fronto-temporal brain network. How this network emerges ontogenetically remains debated. We asked whether frontal language areas emerge in the absence of temporal language areas through a ‘deep-data’ investigation of an individual (EG) born without her left temporal lobe. Using fMRI methods that have been validated to elicit reliable individual-level responses, we find that—as expected for early left hemisphere damage—EG has a fully functional language network in her right hemisphere (comparable to that in n=145 controls) and performs normally on language assessments. However, we detect no response to language in EG’s left frontal lobe (replicated across two sessions, 3 years apart). Another network—the multiple demand network—is robustly present in frontal lobes bilaterally, suggesting that EG’s left frontal cortex can support non-linguistic cognition. The existence of temporal language areas therefore appears to be a prerequisite for the emergence of the frontal language areas.
Computational genomic analysis of the lung tissue microenvironment in COVID-19 patients
Authors: Bhuvaneshwar Krithika , Madhavan Subha , Gusev Yuriy
Published: May 2021

The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has affected over 170 million people, and caused over 3.5 million deaths throughout the world as of May 2021. Although over 150 million people around the world have recovered from this disease, the long term effects of the disease are still under study. A year after the start of the pandemic, data from COVID-19 recovered patients shows multiple organs affected with a broad spectrum of manifestations. Long term effects of SARS-CoV-2 infection includes fatigue, chest pain, cellular damage, and robust innate immune response with inflammatory cytokine production. More clinical studies and clinical trials are needed to not only document, but also to understand and determine the factors that predispose certain people to the long term side effects of his infection.

In this manuscript, our goal was to explore the multidimensional landscape of infected lung tissue microenvironment to better understand complex interactions between SARS-CoV-2 viral infection, immune response and the lungs microbiome of COVID-19 patients. Each sample was analyzed with several machine learning tools allowing simultaneous detection and quantification of viral RNA amount at genome and gene level; human gene expression and fractions of major types of immune cells, as well as metagenomic analysis of bacterial and viral abundance. To contrast and compare specific viral response to SARS-COV-2 we have analyzed deep sequencing data from additional cohort of patients infected with NL63 strain of corona virus.

Our correlation analysis of three types of measurements in patients i.e. fraction of viral RNA (at genome and gene level), Human RNA (transcripts and gene level) and bacterial RNA (metagenomic analysis), showed significant correlation between viral load as well as level of specific viral gene expression with the fractions of immune cells present in lung lavage as well as with abundance of major fractions of lung microbiome in COVID-19 patients.

Our exploratory study has provided novel insights into complex regulatory signaling interactions and correlative patterns between the viral infection, inhibition of innate and adaptive immune response as well as microbiome landscape of the lung tissue. These initial findings could provide better understanding of the diverse dynamics of immune response and the side effects of the SARS-CoV-2 infection.
Variomes: a high recall search engine to support the curation of genomic variants
Authors: Pasche Emilie , Mottaz Anaïs , Caucheteur Déborah , Gobeill Julien , Michel Pierre-André , Ruch Patrick
Published: May 2021

Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system searches within three pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles andClinicalTrials.govclinical trials. A variant synonym generator is used to increase the comprehensiveness of the set of retrieved documents. We then apply different strategies to rank the publications. We assess the search effectiveness of the system using different experimental settings. Experimental setting 1: The literature retrieval task is tuned and evaluated using the TREC Precision Medicine 2018 and 2019 benchmarks consisting respectively in 50 and 40 topics. Almost two thirds (62%) of the publications returned in the top-5 are relevant for clinical decision-support. Experimental setting 2: The evaluation of the variant prioritization task is based on a manually-created benchmark composed of eight patients for a total of 756 variants. For each patient, we used both their complete set of variants and tumor board reports. Our approach enabled identifying 81.8% of clinically actionable variants in the top-3. Experimental setting 3: A comparison of Variomes with LitVar, a well-known search engine for genetic variants is performed. Variomes was able to retrieve on average 90.8% of the content, while LitVar retrieved on average 58.6%. Out of the 9.2% articles, which are “missed” by Variomes, a per error analysis suggests that they are artefacts. To conclude, we are proposing here a competitive system to facilitate the curation of variants for personalized medicine.
Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes
Authors: Bhardwaj Taniya , Gadhave Kundlik , Kapuganti Shivani K , Kumar Prateek , Brotzakis Zacharias Faidon , Saumya Kumar Udit , Nayak Namyashree , Kumar Ankur , Garg Neha , Vendruscolo Michele , Giri Rajanish
Published: May 2021

The phenomenon of protein aggregation is associated with a wide range of human diseases. Our knowledge on the aggregation behaviour of viral proteins, however, is still rather limited. Here, we investigated this behaviour in the the SARS-CoV and SARS-CoV-2 proteomes. An initial analysis using a panel of sequence-based predictors suggested the presence of multiple aggregation-prone regions in these proteomes, and revealed an enhanced aggregation propensity in some SARS-CoV-2 proteins. We then studied the in vitro aggregation of predicted aggregation-prone SARS-CoV-2 proteins, including the signal sequence peptide and fusion peptide 1 of the spike protein, a peptide from the NSP6 protein (NSP6-p), the ORF10 protein, and the NSP11 protein. Our results show that these peptides and proteins form aggregates via a nucleation-dependent mechanism. Moreover, we demonstrated that the aggregates of NSP11 are toxic to mammalian cell cultures. These findings provide evidence about the aggregation of proteins in the SARS-CoV-2 proteome.

Significance

The aggregation of proteins is linked with human disease in a variety of ways. In the case of viral infections, one could expect that the aberrant aggregation of viral proteins may damage the host cells, and also that viral particles may trigger the misfolding and aggregation of host proteins, resulting in damage to the host organism. Here we investigate the aggregation propensity of SARS-CoV-2 proteins and show that many of them can form aggregates that are potentially cytotoxic. In perspective, these results suggest that a better understanding of the effects of viruses on the human protein homeostasis system could help future therapeutic efforts.
Transposable elements drive the evolution of genome streamlining
Authors: van Dijk Bram , Bertels Frederic , Stolk Lianne , Takeuchi Nobuto , Rainey Paul B.
Published: May 2021

Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that co-evolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can drive the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock-paper-scissor dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but delivers lineage-level benefits. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause.
Pre-therapeutic Microglia Activation and Sex Determine Therapy Effects of Chronic Immunomodulation
Authors: Biechele Gloria , Blume Tanja , Deussing Maximilian , Zott Benedikt , Shi Yuan , Xiang Xianyuan , Franzmeier Nicolai , Kleinberger Gernot , Peters Finn , Ochs Katharina , Focke Carola , Sacher Christian , Wind Karin , Schmidt Claudio , Lindner Simon , Gildehaus Franz-Josef , Eckenweber Florian , Beyer Leonie , von Ungern-Sternberg Barbara , Bartenstein Peter , Baumann Karlheinz , Dorostkar Mario M. , Rominger Axel , Cumming Paul , Willem Michael , Adelsberger Helmuth , Herms Jochen , Brendel Matthias
Published: May 2021

Modulation of the innate immune system is emerging as a promising therapeutic strategy against Alzheimer’s disease (AD). However, determinants of a beneficial therapeutic effect are ill-understood. Thus, we investigated the potential of 18 kDa translocator protein positron-emission-tomography (TSPO-PET) for assessment of microglial activation in mouse brain before and during chronic immunomodulation. Serial TSPO-PET was performed during five months of chronic microglia modulation by stimulation of peroxisome proliferator-activated receptor (PPAR)-γ with pioglitazone in two different mouse models of AD (PS2APP,AppNL-G-F). Using mixed statistical models on longitudinal TSPO-PET data, we tested for effects of therapy and sex on treatment response. We tested correlations of baseline with longitudinal measures of TSPO-PET, and correlations between PET results with spatial learning performance and β-amyloid accumulation of individual mice. Immunohistochemistry was used to determine the molecular source of the TSPO-PET signal. Pioglitazone-treated female PS2APP andAppNL-G-Fmice showed attenuation of the longitudinal increases in TSPO-PET signal when compared to vehicle controls, whereas treated maleAppNL-G-Fmice showed the opposite effect. Baseline TSPO-PET strongly predicted changes in microglial activation in treated mice (R=−0.874, p<0.0001) but not in vehicle controls (R=−0.356, p=0.081). Reduced TSPO-PET signal upon treatment was associated with better spatial learning and higher fibrillar β-amyloid accumulation. Immunohistochemistry confirmed activated microglia to be the source of the TSPO-PET signal (R=0.952, p<0.0001). TSPO-PET represents a sensitive biomarker for monitoring of immunomodulation and closely reflects activated microglia. Pre-therapeutic assessment of baseline microglial activation and sex are strong predictors of individual immunomodulation effects and could serve for responder stratification.
Distinct regulation of tonic GABAergic inhibition by NMDA receptor subtypes
Authors: Wu Kunwei , Castellano David , Tian Qingjun , Lu Wei
Published: May 2021

Tonic inhibition mediated by extrasynaptic γ-aminobutyric acid type A receptors (GABAARs) play important roles in the regulation of various brain functions. However, the regulatory mechanisms for tonic inhibition remain largely unknown. Here we report distinct actions of GluN2A- and GluN2B-containing subtypes of NMDA receptors (NMDARs) on tonic inhibition in hippocampal neurons. Mechanistically, GluN2A- and GluN2B-containing NMDARs play differential roles in α5-GABAAR internalization. Additionally, GluN2A-, but not GluN2B-, containing receptors are required for the homeostatic potentiation of tonic inhibition. In an acute seizure model induced by kainic acid, tonic inhibition is decreased during acute seizures, while it is increased 24 h later, and these alterations are dependent on the distinct GluN2-containing NMDARs. Collectively, these data reveal a critical link between NMDARs and extrasynaptic GABAARs in both physiological and pathological conditions.
Arthropods and the evolution of RNA viruses
Authors: Chang Tianyi , Hirai Junya , Hunt Brian P. V. , Suttle Curtis A.
Published: May 2021

Many viruses of arthropods also infect other organisms including humans, sometimes with devastating consequences. Yet, for the vast diversity of arthropods, their associated viruses remain unexplored. Here, we mined meta-transcriptomes from 711 arthropod species, including insects, arachnids, myriapods, and crustaceans, and uncovered more than 1400 previously unknown RNA viruses, representing 822 novel evolutionary groups at a level between species and genus. These newly found viral groups fill major evolutionary gaps within the five branches of RNA viruses, bridging the evolution of viruses infecting early and later diverging eukaryotes. Additionally, co-phylogenetic analysis implies that RNA viruses of arthropods commonly co-evolved with their hosts. Our analyses indicate that arthropods have played a central role in the macroevolution of RNA viruses by serving as reservoirs in which viruses co-evolved with arthropods while being exchanged with a vast diversity of organisms.
Efficient biallelic knock-in in mouse embryonic stem cells by in vivo-linearization of donor and transient inhibition of DNA Polymerase θ/DNA-PK
Authors: Arai Daisuke , Nakao Yoichi
Published: May 2021

CRISPR/Cas9-mediated homology-directed repair (HDR) is used for error-free targeted knock-in of foreign donor DNA. However, the low efficiency of HDR-mediated knock-in hinders establishment of knock-in clones. Double-strand breaks (DSBs) induced by CRISPR/Cas9 are preferentially repaired by non-homologous end joining (NHEJ) or microhomology-mediated end joining (MMEJ) before HDR can occur, thereby preventing HDR-mediated knock-in. NHEJ/MMEJ also cause random integrations, which give rise to false-positive knock-in events, or silently disrupt the genome. In this study, we optimized an HDR-mediated knock-in method for mouse embryonic stem cells (mESCs). We succeeded in improving efficiency of HDR-mediated knock-in of a plasmid donor while almost completely suppressing NHEJ/MMEJ-based integration by combining in vivo-linearization of the donor plasmid, transient knockdown of DNA Polymerase θ, and chemical inhibition of DNA-dependent protein kinase (DNA-PK) by M3814. This method also dramatically improved the efficiency of biallelic knock-in; at the Rosa26a locus, 95% of HDR-mediated knock-in clones were biallelic. We designate this method BiPoD (Biallelic knock-in assisted by Pol θ and DNA-PK inhibition). BiPoD achieved simultaneous efficient biallelic knock-in into two loci. BiPoD, therefore, enables rapid and easy establishment of biallelic knock-in mESC lines.
Epigenetic regulation of innate immune memory in microglia
Authors: Zhang Xiaoming , Kracht Laura , Lerario Antonio M. , Dubbelaar Marissa L. , Brouwer Nieske , Wesseling Evelyn M. , Boddeke Erik W.G.M. , Eggen Bart J.L. , Kooistra Susanne M.
Published: May 2021

Microglia are the tissue-resident macrophages of the CNS. They originate in the yolk sac, colonize the CNS during embryonic development and form a self-sustaining population with limited turnover. A consequence of their relative slow turnover is that microglia can serve as a long-term memory for inflammatory or neurodegenerative events. We characterized the epigenomes and transcriptomes of microglia exposed to different stimuli; an endotoxin challenge (LPS) and genotoxic stress (DNA repair deficiency-induced accelerated aging). Whereas the enrichment of permissive epigenetic marks at enhancer regions explains training (hyperresponsiveness) of primed microglia to LPS challenge, the tolerized response of microglia seems to be regulated by loss of permissive epigenetic marks. Here, we identify that inflammatory stimuli and accelerated aging because of genotoxic stress activate distinct gene networks. These gene networks and associated biological processes are partially overlapping, which is likely driven by specific transcription factor networks, resulting in altered epigenetic signatures and distinct functional (desensitized vs. primed) microglia phenotypes.