bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mouse model of Bardet-Biedl Syndrome has impaired fear memory, which is rescued by lithium treatment
Authors: Pak Thomas K. , Carter Calvin S. , Zhang Qihong , Huang Sunny C. , Searby Charles , Hsu Ying , Taugher Rebecca , Vogel Tim , Cychosz Christopher C. , Genova Rachel , Moreira Nina , Stevens Hanna , Wemmie John , Pieper Andrew A. , Wang Kai , Sheffield Val C. 
Published: October 2020

AbstractPrimary cilia are microtubule-based organelles present on most cells that regulate many physiological processes, ranging from maintaining energy homeostasis to renal function. However, the role of these structures in the regulation of behavior remains unknown. To study the role of cilia in behavior, we employ mouse models of the human ciliopathy, Bardet-Biedl Syndrome (BBS). Here, we demonstrate that BBS mice have significant impairments in context fear conditioning, a form of associative learning. Moreover, we show that postnatal deletion of BBS gene function, as well as congenital deletion, specifically in the forebrain, impairs context fear conditioning. Analyses indicated that these behavioral impairments are not the result of impaired hippocampal long-term potentiation. However, our results indicate that these behavioral impairments are linked to impaired hippocampal neurogenesis. Two-week treatment with lithium chloride partially restores the proliferation of hippocampal neurons which leads to a rescue of context fear conditioning. Overall, our results identify a novel role of cilia genes in hippocampal neurogenesis and long-term context fear conditioning.Author summaryThe primary cilium is a microtubule-based membranous projection on the cell that is involved in multiple physiological functions. Patients who have cilia dysfunction commonly have intellectual disability. However, it is not known how cilia affect learning and memory. Studying mouse models of a cilia-based intellectual disability can provide insight into learning and memory. One such cilia-based intellectual disability is Bardet-Biedl Syndrome (BBS), which is caused by homozygous and compound heterozygous mutations of BBS genes. We found that a mouse model of BBS (Bbs1M390R/M390Rmice) has learning and memory defects. In addition, we found that other mouse models of BBS have similar learning and memory defects. These BBS mouse models have difficulty associating an environment with an aversive stimulus, a task designed to test context fear memory. This type of memory involves the hippocampus. We found thatBbs1M390R/M390Rmice have decreased cell production in the hippocampus. TreatingBbs1M390R/M390Rmice with a compound (lithium) that increases cell production in the hippocampus improved the learning and memory deficits. Our results demonstrate a potential role for cilia in learning and memory, and indicate that lithium is a potential treatment, requiring further study, for the intellectual disability phenotype of BBS.
Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors
Authors: Mor Michael , Werbner Michal , Alter Joel , Safra Modi , Chomsky Elad , Hada-Neeman Smadar , Polonsky Ksenia , Nowell Cameron J. , Clark Alex E. , Roitburd-Berman Anna , Shalom Noam Ben , Navon Michal , Rafael Dor , Sharim Hila , Kiner Evgeny , Griffis Eric , Gershoni Jonathan M. , Kobiler Oren , Leibel Sandra Lawrynowicz , Zimhony Oren , Carlin Aaron F. , Yaari Gur , Dassau Moshe , Gal-Tanamy Meital , Hagin David , Croker Ben A. , Freund Natalia T. 
Published: October 2020

AbstractThe interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mildversussevere cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe and not mild infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of viral inhibition. B cell receptor (BCR) sequencing revealed two VH genes, VH3-38 and VH3-53, that were enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against live SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and RBD mutagenesis, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.
Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope tag insertion
Authors: Tamura-Sakaguchi Risako , Aruga Rie , Hirose Mika , Ekimoto Toru , Miyake Takuya , Hizukuri Yohei , Oi Rika , Kaneko Mika K. , Kato Yukinari , Akiyama Yoshinori , Ikeguchi Mitsunori , Iwasaki Kenji , Nogi Terukazu 
Published: October 2020

AbstractAntibody labeling has been extensively conducted for structure determination in both x-ray crystallography and EM analysis. However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, we have developed an alternative method to prepare an antibody-complex by inserting an exogenous epitope into the target. We have already demonstrated that the Fab of monoclonal antibody NZ-1 could form a stable complex with the target containing a PA12 tag as an inserted epitope. Nevertheless, we also found that the complex formation through the inserted PA12 tag inevitably caused structural change around the insertion site of the target. Hence, we here attempted to improve the insertion method and consequently discovered that utilization of a PA14 tag significantly reduced the structural change in the target. By adopting a closed ring-like conformation inside the antigen-binding pocket, the inserted PA14 tag had less impact on the folding of the target. Due to this structural property, the PA14 tag could also be inserted into the sterically hindered loop for labeling. Molecular dynamics simulations also indicated that the folding of the target was rigid regardless of the PA14 insertion and the complex formation with the NZ-1 Fab. Using the improved labeling technique, we performed negative-stain EM on a bacterial site-2 protease, which enabled us to approximate the domain arrangement based on the docking mode of the NZ-1 Fab.
Cryo-EM reveals the dynamic interplay between mitochondrial Hsp90 and SdhB folding intermediates
Authors: Liu Yanxin , Elnatan Daniel , Sun Ming , Myasnikov Alexander G. , Agard David A. 
Published: October 2020

AbstractTRAP1 is a mitochondrion specific Hsp90, a ubiquitous chaperone family that mediates the folding and maturation of hundreds of “client” proteins. Through the interaction with client proteins, TRAP1 regulates mitochondrial protein homeostasis, oxidative phosphorylation/glycolysis balance, and plays a critical role in mitochondrial dynamics and disease. However, the molecular mechanism of client protein recognition and remodeling by TRAP1 remains elusive. Here we established the succinate dehydrogenase B subunit (SdhB) from mitochondrial complex II as a client protein for TRAP1 amenable to detailed biochemical and structural investigation. SdhB accelerates the rate of TRAP1 dimer closure and ATP hydrolysis by 5-fold. Cryo-EM structures of the TRAP1:SdhB complex show TRAP1 stabilizes SdhB folding intermediates by trapping an SdhB segment in the TRAP1 lumen. Unexpectedly, client protein binding induces an asymmetric to symmetric transition in the TRAP1 closed state. Our results highlight a client binding mechanism conserved throughout Hsp90s that transcends the need for cochaperones and provide molecular insights into how TRAP1 modulates protein folding within mitochondria. Our structures also suggest a potential role for TRAP1 in Fe-S cluster biogenesis and mitochondrial protein import and will guide small molecule development for therapeutic intervention in specific TRAP1 client interactions.
Single-cell tracking reveals super-spreading cells with high persistence in invasive brain cancer
Authors: Nousi Aimilia , Søgaard Maria Tangen , Jauffred Liselotte 
Published: October 2020

ABSTRACTCell migration is a fundamental characteristic of vital processes such as tissue morphogenesis, wound healing and immune cell homing to lymph nodes and inflamed or infected sites. Therefore, various brain defect diseases, chronic inflammatory diseases as well as tumor formation and metastasis are associated with aberrant or absent cell migration. With embedment of multicellular brain cancer spheroids in Matrigel™ and single-particle tracking, we extracted the paths of cells migrating away from the spheroids. We found that - in contrast to local invasion - single cell migration is independent of the mechanical load exerted by the environment and is characterized by high directionality and persistence. Furthermore, we identified a subpopulation of super-spreading cells with >200-fold longer persistence times than the majority of cells. These results highlight yet another aspect of between-cell heterogeneity in tumors.
Brain Activation-based Filtering: a Scholarly Journal Recommendation Model for Human Neuroimaging Studies
Authors: Kim Junsol 
Published: October 2020

AbstractThe development of noninvasive neuroimaging techniques such as functional magnetic resonance imaging was followed by a large volume of human neuroimaging studies of mental processes, mechanisms, and diseases. Due to the high volume of studies and the large number of journals, it is increasingly challenging for neuroscientists to review existing scholarly journals and find the most suitable journal to publish their studies. Therefore, this paper proposes a scholarly journal recommendation model for human neuroimaging studies called brain activation-based filtering (BAF). Based on the collective matrix factorization technique, BAF recommends journals relevant to the activated brain regions that are described in a given neuroimaging study. For instance, if ‘social brain’ regions such as the dorsomedial prefrontal cortex, precuneus, and temporoparietal junction are activated in a study, BAF recommends relevant social neuroscience journals (e.g.,Social Cognitive and Affective Neuroscience). Five-fold cross-validation shows that BAF predicts journals with a reliable area under the curve score of 0.855. Furthermore, an interactive Google Colab notebook is offered to recommend relevant journals for a novel human neuroimaging study (https://github.com/JunsolKim/brain-activation-based-filtering).
Stimulus-independent neural coding of event semantics: Evidence from cross-sentence fMRI decoding
Authors: Asyraff Aliff , Lemarchand Rafael , Tamm Andres , Hoffman Paul 
Published: October 2020

AbstractMultivariate neuroimaging studies indicate that the brain represents word and object concepts in a format that readily generalises across stimuli. Here we investigated whether this was true for neural representations of simple events described using sentences. Participants viewed sentences describing four events in different ways. Multivariate classifiers were trained to discriminate the four events using a subset of sentences, allowing us to test generalisation to novel sentences. We found that neural patterns in a left-lateralised network of frontal, temporal and parietal regions discriminated events in a way that generalised successfully over changes in the syntactic and lexical properties of the sentences used to describe them. In contrast, decoding in visual areas was sentence-specific and failed to generalise to novel sentences. In the reverse analysis, we tested for decoding of syntactic and lexical structure, independent of the event being described. Regions displaying this coding were limited and largely fell outside the canonical semantic network. Our results indicate that a distributed neural network represents the meaning of event sentences in a way that is robust to changes in their structure and form. They suggest that the semantic system disregards the surface properties of stimuli in order to represent their underlying conceptual significance.
Transmembrane polar relay drives the allosteric regulation for ABCG5/G8 sterol transporter
Authors: Xavier Bala M. , Zein Aiman A. , Venes Angelica , Wang Junmei , Lee Jyh-Yeuan 
Published: October 2020

AbstractThe heterodimeric ATP-binding cassette (ABC) sterol transporter, ABCG5/G8, is responsible for the biliary and transintestinal secretion of cholesterol and dietary plant sterols. Missense mutations of ABCG5/G8 can cause sitosterolemia, a loss-of-function disorder characterized by plant sterol accumulation and premature atherosclerosis. A new molecular framework was recently established by a crystal structure of human ABCG5/G8 and reveals a network of polar and charged amino acids in the core of the transmembrane domains, namely polar relay. In this study, we utilize genetic variants to dissect the mechanistic role of this transmembrane polar relay in controlling ABCG5/G8 function. We demonstrated a sterol-coupled ATPase activity of ABCG5/G8 by cholesteryl hemisuccinate (CHS), a relatively water-soluble cholesterol memetic, and characterized CHS-coupled ATPase activity of three loss-of-function missense variants, R543S, E146Q, and A540F, which are respectively within, in contact with, and distant from the polar relay. The results established anin vitrophenotype of the loss-of-function and missense mutations of ABCG5/G8, showing significantly impaired ATPase activity and loss of energy sufficient to weaken the signal transmission from the transmembrane domains. Our data provide a biochemical evidence underlying the importance of the polar relay and its network in regulating the catalytic activity of ABCG5/G8 sterol transporter.
Globally defining the effects of mutations in a picornavirus capsid
Authors: Mattenberger Florian , Latorre Victor , Tirosh Omer , Stern Adi , Geller Ron 
Published: October 2020

ABSTRACTThe capsids of non-enveloped viruses are highly multimeric and multifunctional protein assemblies that protect the viral genome between infection cycles, dictate host and cell tropism, and mediate evasion of humoral immune responses. As such, capsids play key roles in viral biology and pathogenesis. Despite their importance, a comprehensive understanding of how mutations affect viral fitness across different structural and functional attributes of the capsid is lacking. To address this limitation, we globally define the effects of mutations in the capsid of a human picornavirus, generating a comprehensive dataset encompassing >90% of all possible single amino acid mutations. Moreover, we use this information to identify structural and sequence determinants that accurately predict mutational fitness effects, refine evolutionary analyses, and define the sequence specificity of key capsid encoded motifs. Finally, capitalizing on the sequence requirements identified in our dataset for capsid encoded protease cleavage sites, we implement and validate a bioinformatic approach for identifying novel host proteins targeted by viral proteases. Our findings present the most comprehensive investigation of mutational fitness effects in a picornavirus capsid to date and illuminate important aspects of viral biology, evolution, and host interactions.
Proteoforms of the SARS-CoV-2 nucleocapsid protein are primed to proliferate the virus and attenuate the antibody response
Authors: Lutomski Corinne A. , El-Baba Tarick J. , Bolla Jani R. , Robinson Carol V. 
Published: October 2020

AbstractThe SARS-CoV-2 nucleocapsid (N) protein is the most immunogenic of the structural proteins and plays essential roles in several stages of the virus lifecycle. It is comprised of two major structural domains: the RNA binding domain, which interacts with viral and host RNA, and the oligomerization domain which assembles to form the viral core. Here, we investigate the assembly state and RNA binding properties of the full-length nucleocapsid protein using native mass spectrometry. We find that dimers, and not monomers, of full-length N protein bind RNA, implying that dimers are the functional unit of ribonucleoprotein assembly. In addition, we find that N protein binds RNA with a preference for GGG motifs which are known to form short stem loop structures. Unexpectedly, we found that N undergoes proteolytic processing within the linker region, separating the two major domains. This process results in the formation of at least five proteoforms that we sequenced using electron transfer dissociation, higher-energy collision induced dissociation and corroborated by peptide mapping. The cleavage sites identified are in highly conserved regions leading us to consider the potential roles of the resulting proteoforms. We found that monomers of N-terminal proteoforms bind RNA with the same preference for GGG motifs and that the oligomeric state of a C-terminal proteoform (N156-419) is sensitive to pH. We then tested interactions of the proteoforms with the immunophilin cyclophilin A, a key component in coronavirus replication. We found that N1-209and N1-273bind directly to cyclophilin A, an interaction that is abolished by the approved immunosuppressant drug cyclosporin A. In addition, we found the C-terminal proteoform N156-419generated the highest antibody response in convalescent plasma from patients >6 months from initial COVID-19 diagnosis when compared to the other proteoforms. Overall, the different interactions of N proteoforms with RNA, cyclophilin A, and human antibodies have implications for viral proliferation and vaccine development.
The strength of a NES motif in the nucleocapsid protein of human coronaviruses is related to genus, but not to pathogenic capacity
Authors: Sendino Maria , Omaetxebarria Miren Josu , Rodriguez Jose Antonio 
Published: October 2020

ABSTRACTSeven members of theCoronaviridaefamily infect humans, but only three (SARS-CoV, SARS-CoV-2 and MERS-CoV) cause severe disease with a high case fatality rate. Usingin silicoanalyses (machine learning techniques and comparative genomics), several features associated to coronavirus pathogenicity have been recently proposed, including a potential increase in the strength of a predicted novel nuclear export signal (NES) motif in the nucleocapsid protein.Here, we have used a well-established nuclear export assay to experimentally establish whether the recently proposed nucleocapsid NESs are capable of mediating nuclear export, and to evaluate if their activity correlates with coronavirus pathogenicity.The six NES motifs tested were functional in our assay, but displayed wide differences in export activity. Importantly, these differences in NES strength were not related to strain pathogenicity. Rather, we found that the NESs of the strains belonging to the genusAlphacoronaviruswere markedly stronger than the NESs of the strains belonging to the genusBetacoronavirus.We conclude that, while some of the genomic features recently identifiedin silicocould be crucial contributors to coronavirus pathogenicity, this does not appear to be the case of nucleocapsid NES activity, as it is more closely related to coronavirus genus than to pathogenic capacity.
Structural basis for repurposing a 100-years-old drug suramin for treating COVID-19
Authors: Yin Wanchao , Luan Xiaodong , Li Zhihai , Zhang Leike , Zhou Ziwei , Gao Minqi , Wang Xiaoxi , Zhou Fulai , Shi Jingjing , You Erli , Liu Mingliang , Wang Qingxia , Wang Qingxing , Jiang Yi , Jiang Hualiang , Xiao Gengfu , Yu Xuekui , Zhang Shuyang , Xu H. Eric 
Published: October 2020

SUMMARYThe COVID-19 pandemic by non-stop infections of SARS-CoV-2 has continued to ravage many countries worldwide. Here we report the discovery of suramin, a 100-year-old drug, as a potent inhibitor of the SARS-CoV-2 RNA dependent RNA polymerase (RdRp) through blocking the binding of RNA to the enzyme. In biochemical assays, suramin and its derivatives are at least 20-fold more potent than remdesivir, the currently approved nucleotide drug for COVID-19. The 2.6 Å cryo-EM structure of the viral RdRp bound to suramin reveals two binding sites of suramin, with one site directly blocking the binding of the RNA template strand and the other site clash with the RNA primer strand near the RdRp catalytic active site, therefore inhibiting the viral RNA replication. Furthermore, suramin potently inhibits SARS-CoV-2 duplication in Vero E6 cells. These results provide a structural mechanism for the first non-nucleotide inhibitor of the SARS-CoV-2 RdRp and a rationale for repurposing suramin for treating COVID-19.One Sentence SummaryDiscovery and mechanism of suramin as potent SARS-CoV-2 RNA polymerase inhibitor and its repurposing for treating COVID-19.
Protoplast fusion inBacillusspecies produces frequent, unbiased, genome-wide homologous recombination
Authors: Burdick Leah H. , Streich Jared C. , Vasileva Delyana P. , Klingeman Dawn M. , Chhetri Hari B. , Ellis J. Christopher , Close Dan M. , Jacobson Daniel A. , Michener Joshua K. 
Published: October 2020

ABSTRACTIn eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossedBacillusstrains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Computational analyses suggested that this bias is due to the action of restriction-modification systems whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that the intensity of recombination is uniform across the genome without concentration into hotspots. Unexpectedly, our results revealed that large species-level genetic distance did not affect key recombination parameters. Our study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.