bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinctive mechanisms of epilepsy-causing mutants discovered by measuring S4 movement in KCNQ2 channels
Authors: Edmond Michaela A. , Hinojo-Perez Andy , Wu Xiaoan , Perez Rodriguez Marta E. , Barro-Soria Rene 
Published: January 2022

AbstractNeuronal KCNQ channels mediate the muscarine-regulated M-current, a key regulator of membrane excitability in the central and peripheral nervous systems. Mutations in KCNQ2 channels cause severe neurodevelopmental disorders, including epileptic encephalopathies. However, the impact that mutations have on channel function remain poorly defined, largely because of our limited understanding of the voltage sensing mechanisms that trigger channel gating. Here, we present measurements of voltage sensor movements in wt-KCNQ2 and channels bearing epilepsy-causing mutations using mutagenesis, cysteine accessibility, and voltage clamp fluorometry (VCF). Cysteine modification reveals that a stretch of 8-9 amino acids in the S4 become exposed upon opening of KCNQ2 channels. VCF shows that the voltage dependence and kinetics of S4 movement and channel opening/closing closely correlate, suggesting an activation scheme in which channel opening does not require multiple voltage-sensor movements. VCF and kinetic modeling reveal different mechanisms by which epilepsy-causing mutations affect KCNQ2 channel voltage-dependent gating. This study provides insight into KCNQ2 channel function, which will aid in uncovering the mechanisms underlying channelopathies.
Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion
Authors: Barth Roman , Shaban Haitham A. 
Published: January 2022

AbstractGene transcription by RNA polymerase II (RNAP II) is a tightly regulated process in the genomic, temporal, and spatial context. Transcriptionally active genes often spatially cluster at RNA Pol II foci, called transcription factories, causing long-range interactions between distal sites of the genome. Recently, we have shown that chromatin exhibits spatially long-range coherently moving regions over the entire nucleus, and transcription enhances this long-range correlated DNA movement. Yet, it remains unclear how the mobility of RNA Pol II molecules is affected by transcription regulation and whether this response depends on the coordinated chromatin movement. We applied our Dense Flow reConstruction and Correlation method to analyze nucleus-wide coherent movements of RNA Pol II in living human cancer cells. We quantify the spatial correlation length of RNA Pol II in the context of DNA motion. We observe a spatially coherent movement of RNA Pol II molecules over ~1 μm, considerably less than for DNA, suggesting that spatially coherent RNA Pol II motion does not solely result from the DNA motion. In contrast to DNA, inducing transcription in quiescent cells decreased the coherent motion of RNA Pol II, while the inhibition of transcription elongation by using DRB slightly increased coherent RNA Pol II motion. The spatially coherent movement of RNA Pol II domains is affected by the transcriptional state and largely independent of the underlying chromatin domains. Our study reveals the nucleus-wide interplay between chromatin and RNA Pol II in the dynamic regulation of chromatin organization.
An ancient role for the Hippo pathway in axis formation and morphogenesis
Authors: Brooun Maria , Salvenmoser Willi , Dana Catherine , Sudol Marius , Steele Robert , Hobmayer Bert , McNeill Helen 
Published: January 2022

SummaryHow did cells of early metazoan organisms first organize themselves to form a body axis? The canonical Wnt pathway has been shown to be sufficient for induction of axis in Cnidaria, a sister group to Bilateria, and is important in bilaterian axis formation. Here, we provide experimental evidence that in cnidarian Hydra the Hippo pathway regulates the formation of a new axis during budding upstream of the Wnt pathway. The target of Hippo pathway, the transcriptional co-activator YAP, inhibits the initiation of budding in Hydra, and is regulated by Hydra LATS. In addition, we show functions of Hippo pathway in regulation of actin organization and cell proliferation in Hydra. We hypothesize that Hippo pathway served as a link between continuous cell division, cell density and axis formation early in metazoan evolution.
A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus
Authors: Jenks Jennifer A. , Amin Sharmi , Kumar Amit , Sponholtz Madeline R. , Wrapp Daniel , Venkatayogi Sravani , Tu Joshua , McLellan Jason S. , Wiehe Kevin , Permar Sallie R. 
Published: January 2022

AbstractCytomegalovirus (CMV) is a leading cause of infant hearing loss and neurodevelopmental delay, but vaccine candidates have faced challenges eliciting neutralizing antibodies. One of the most well-studied targets for CMV vaccines is the viral fusogen glycoprotein B (gB), which is required for viral entry into host cells. Within gB, antigenic domain 2 site 1 (AD-2S1) is a target of potently neutralizing antibodies, but gB-based candidate vaccines have yet to elicit robust responses against this region. We mapped the genealogy of B cells encoding potently neutralizing anti-gB AD-2S1 antibodies from their inferred unmutated common ancestor (UCA) and characterized the binding and function of early lineage ancestors. Remarkably, we found that the single amino acid heavy chain mutation A33N, an improbable mutation rarely generated by somatic hypermutation machinery, conferred broad CMV neutralization to the UCA antibody. Structural studies revealed that this mutation mediated key contacts with the gB AD-2S1 epitope. Collectively, these results provide insight into potently neutralizing gB-directed antibody evolution and a foundation for designing next-generation CMV vaccines.One-sentence summaryThis manuscript identifies an early B cell lineage mutation that confers neutralizing function to antibodies targeting CMV fusogen gB.
A genetically-defined population in the lateral and ventrolateral periaqueductal gray selectively promotes flight to safety
Authors: La-Vu Mimi , Sethi Ekayana , Maesta-Pereira Sandra , Schuette Peter J , Tobias Brooke C , Reis Fernando MCV , Wang Weisheng , Leonard Saskia J , Lin Lilly , Adhikari Avishek 
Published: January 2022

AbstractWhen encountering external threats, survival depends on the engagement of appropriate defensive reactions to minimize harm. There are major clinical implications for identifying the neural circuitry and activation patterns that produce such defensive reactions, as maladaptive overactivation of these circuits underlies pathological human anxiety and fear responses. A compelling body of work has linked activation of large glutamatergic neuronal populations in the midbrain periaqueductal gray (PAG) to defensive reactions such as freezing, flight and threat-induced analgesia. These pioneering data have firmly established that the overarching functional organization axis of the PAG is along anatomically-defined columnar boundaries. Accordingly, broad activation of the dorsolateral column induces flight, while activation of the lateral or ventrolateral (l and vl) columns induces freezing. However, the PAG contains a diverse arrangement of cell types that vary in neurochemical profile and location. How these cell types contribute to defensive responses remains largely unknown, indicating that targeting sparse, genetically-defined populations can lead to a deeper understanding of how the PAG generates a wide array of behaviors. Though several prior works showed that broad excitation of the lPAG or vlPAG causes freezing, we found that activation of lateral and ventrolateral PAG (l/vlPAG) cholecystokinin-expressing (cck) cells selectively causes flight to safer regions within an environment. Furthermore, inhibition of l/vlPAG-cck cells reduces avoidance of a predatory threat without altering other defensive behaviors like freezing. Lastly, l/vlPAG-cck activity increases away from threat and during movements towards safer locations. In contrast, activating l/vlPAG cells pan-neuronally promoted freezing and these cells were activated near threat. These data underscore the importance of investigating genetically-identified PAG cells. Using this approach, we found a sparse population of cck-expressing l/vlPAG cells that have distinct and opposing function and neural activation motifs compared to the broader local ensemble defined solely by columnar anatomical boundaries. Thus, in addition to the anatomical columnar architecture of the APG, the molecular identity of PAG cells may confer an additional axis of functional organization, revealing unexplored functional heterogeneity.
The Intrinsically Disordered Region of Coronins Fine-tunes Oligomerization and Actin Polymerization
Authors: Han Xiao , Hu Zixin , Surya Wahyu , Ma Qianqian , Zhou Feng , Nordenskiöld Lars , Torres Jaume , Lu Lanyuan , Miao Yansong 
Published: January 2022

SummaryCoronins are highly conserved actin-binding proteins (ABPs) in the eukaryotic kingdom for polymerizing actin cytoskeleton. The biochemical activity of coronins is primarily mediated by the structural N-terminal β-propeller and the C-terminal helical coiled-coil (CC) domains, but less is known about the function of a middle nonconserved region, the “unique region (UR)”. The coronin UR is an intrinsically disordered region (IDR). Herein, we demonstrate that the low complexity of the UR is a conserved signature of the coronin protein family, and the UR/IDR exhibits a striking evolutionary correlated pattern associated with sequence length. By analyzing the role of the IDR in coronins via coarse-grained simulations, we reveal that evolutionary selection of IDR length is coupled with the oligomerization of IDR-containing proteins (IDPs) to provide optimal functional output. By integrating biochemical and cell biology experiments and protein engineering, we found that the IDR regulates Crn1 biochemical activity, both in vivo and in vitro, by fine-tuning CC domain oligomerization and maintaining Crn1 in a tetrameric state. The IDR-guided optimization of Crn1 oligomerization is critical for Arp2/3-mediated actin polymerization.
Genomic databanks and targeted assays help characterise domestic mosquito incursions
Authors: Schmidt Thomas L. , Endersby-Harshman Nancy , Kurucz Nina , Pettit William , Krause Vicki L , Ehlers Gerhard , Muzari Mutizwa Odwell , Currie Bart J , Hoffmann Ary A 
Published: January 2022

AbstractBiosecurity strategies that aim to restrict the spread of invasive pests can benefit from knowing where new incursions have come from. This knowledge can be acquired using genomic databanks, by comparing genetic variation in incursion samples against reference samples. Here we use genomic databanks to investigate domestic incursions of two mosquito species in Australia, and assess the performance of genomic tracing methods when databank samples were collected some time ago or are genetically similar. We used a deep learning method to trace a 2021 invasion of Aedes aegypti in Tennant Creek, Northern Territory, to Townsville, Queensland, and to trace two years of Ae. albopictus incursions to two specific islands in the Torres Strait. We observed high precision of tracing despite 30-70 generations separating incursion and reference samples. Targeted assays also provided additional information on the origin of the Tennant Creek Ae. aegypti, in this case by comparing Wolbachia infection data and mitochondrial DNA variation. Patterns of relatedness and inbreeding indicated that Tennant Creek was likely invaded by one family of Ae. aegypti, whereas Torres Strait incursions involved distinct kinship groups. Our results highlight the value of genomic databanks that remain informative over years and for a range of biological conditions, and demonstrate how additional targeted assays (e.g. Wolbachia) can improve inferences.Key MessageGenomic tracing can provide valuable information on pest incursions and new invasions.Evolution will lead to increasing differences between databanks and extant populations.We tested how well genomic databanks could trace incursions sampled 30-70 generations later and where genetic differentiation was low.We show that tracing methods are robust for a wide range of conditions, and report specific incursion origins for two Aedes species.Our results suggest that genomic databanks will remain informative over years and for a range of invasive systems.
Intra-granuloma accumulation and inflammatory differentiation of neutrophils underlie mycobacterial ESX-1-mediated immunopathology
Authors: Lienard Julia , Munke Kristina , Wulff Line , Da Silva Clément , Vandamme Julien , Laschanzky Katie , Joeris Thorsten , Agace William , Carlsson Fredric 
Published: January 2022

AbstractThe conserved ESX-1 type VII secretion system is a major virulence determinant of pathogenic mycobacteria, including Mycobacterium tuberculosis and Mycobacterium marinum. ESX-1 is known to interact with infected macrophages, but its potential roles in regulating other host cells and immunopathology have remained largely unexplored. Using a murine M. marinum infection model we identify neutrophils and Ly6C+MHCII+ monocytes as the main cellular reservoirs for the bacteria. We show that ESX-1 promotes intra-granuloma accumulation of neutrophils and that neutrophils have a previously unrecognized required role in executing ESX-1-mediated pathology. To explore if ESX-1 also regulates the function of recruited neutrophils we performed single cell RNA-seq analysis indicating that ESX-1 drives newly recruited uninfected neutrophils into an inflammatory phenotype via an extrinsic mechanism. In contrast, monocytes restricted the accumulation of neutrophils and immunopathology, demonstrating a major host-protective function for monocytes specifically by suppressing ESX-1-mediated neutrophilic inflammation. iNOS activity was required for the suppressive mechanism and we identified Ly6C+MHCII+ monocytes as the main iNOS-expressing cell type in the infected tissue. These results suggest that ESX-1 mediates immunopathology by driving neutrophil accumulation and phenotypic differentiation in the infected tissue, and they demonstrate an antagonistic interplay between monocytes and neutrophils by which monocytes suppress host-detrimental neutrophilic inflammation.Author SummaryThe ESX-1 type VII secretion system is required for virulence of pathogenic mycobacteria, including Mycobacterium tuberculosis. ESX-1 interacts with infected macrophages, but its potential roles in regulating other host cells and immunopathology have remained largely unexplored. We demonstrate that ESX-1 promotes immunopathology by driving intra-granuloma accumulation of neutrophils, which upon arrival adopt an inflammatory phenotype in an ESX-1-dependent manner. In contrast, monocytes limited the accumulation of neutrophils and neutrophil-mediated pathology via an iNOS-dependent mechanism, suggesting a major host-protective function for monocytes specifically by restricting ESX-1-mediated neutrophilic inflammation. These findings provide insight into how ESX-1 promotes disease, and they reveal an antagonistic functional relationship between monocytes and neutrophils that may regulate immunopathology not only in mycobacterial infection, but also in other infections as well as in inflammatory conditions and cancer.
Safety and immunogenicity of Pfizer/BioNTech SARS-CoV-2 mRNA third booster vaccine against SARS-CoV-2 Omicron variant in Japanese healthcare workers
Authors: Seki Yohei , Yoshihara Yasuo , Nojima Kiyoko , Momose Haruka , Fukushi Shuetsu , Moriyama Saya , Wagatsuma Ayumi , Numata Narumi , Sasaki Kyohei , Kuzuoka Tomoyo , Yato Yoshiyuki , Takahashi Yoshimasa , Maeda Ken , Suzuki Tadaki , Mizukami Takuo , Hamaguchi Isao 
Published: January 2022

SUMMARYBackgroundThe Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in Japan in November 2021. This variant contains up to 36 mutations in the spike protein, the target of neutralizing antibodies, and can escape vaccine-induced immunity. The third booster vaccination campaign began with healthcare workers and high-risk groups. The safety and immunogenicity of third booster vaccination against Omicrons remain unknown.MethodsIn total, 272 healthcare workers were evaluated for their long-term safety and immunogenicity. Here, we established vaccine panels to evaluate the safety and immunogenicity against variants of concern (VOCs), including the Omicron variant, using a live virus microneutralization assay.FindingsTwo-dose vaccination induced robust anti-spike antibodies and neutralization titers (NTs) against the ancestral strain WK-521, whereas NTs in VOCs were significantly decreased. Within 93–247 days of the second vaccine dose, NTs against Omicron were completely abolished in up to 80% of individuals among the vaccine panels. The third booster vaccination induced a robust increase in anti-spike antibodies and NTs against the WK-521, Delta, and Omicron variants. The breadth of humoral immunity and cross-reactivity with Omicron increased. The cytokine signature and adverse event rate remained unchanged after three-dose vaccination.ConclusionsThe third vaccination dose is safe and effective against Omicron infection.FundingThis study was supported by grants from AMED (Grant Number JP21fk0108104 and JP21mk0102146).
Genomic and transcriptomic characterization of Delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)
Authors: Kotwa Jonathon D. , Lobb Briallen , Massé Ariane , Gagnier Marianne , Aftanas Patryk , Banerjee Arinjay , Banete Andra , Blais-Savoie Juliette , Bowman Jeff , Buchanan Tore , Chee Hsien-Yao , Kruczkiewicz Peter , Maguire Finlay , McGeer Allison J. , Nirmalarajah Kuganya , Soos Catherine , Yip Lily , Lindsay L. Robbin , Doxey Andrew C. , Lung Oliver , Pickering Bradley , Mubareka Samira 
Published: January 2022

AbstractWhite-tailed deer are susceptible to SARS-CoV-2 and represent a highly important species for surveillance. Nasal swabs and retropharyngeal lymph nodes from white-tailed deer (n=258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and transcriptomics to further characterize infection and investigate host response to infection. We detected Delta SARS-CoV-2 (AY.44) in deer from the Estrie region; sequences clustered with human sequences from GISAID collected in October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 encoding a truncated protein were detected. Host expression patterns in SARS-CoV-2 infected deer were associated with the innate immune response, including signalling pathways related to anti-viral, pro- and anti-inflammatory signalling, and host damage. Our findings provide preliminary insights of host response to SARS-CoV-2 infection in deer and underscores the importance of ongoing surveillance of key wildlife species for SARS-CoV-2.
Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells
Authors: Zhao Lili , Zhao Qun , An Yuxin , Gao Hang , Zhang Weijie , Gong Zhou , Liu Xiaolong , Zhao Baofeng , Liang Zhen , Tang Chun , Zhang Lihua , Zhang Yukui 
Published: January 2022

AbstractThe protein structures and interactions that maintain and regulate cellular processes in different subcellular organelles are heterogeneous and dynamic. However, it remains challenging to characterize the subcellular specificity and translocation of protein complexes in terms of conformation and interactions. Herein, we developed a spatially resolved protein complex profiling approach by biocompatible chemical cross-linking in living cells (SPACX) to monitor the dynamics of protein conformation, interactions and translocation. The advancement of fast capturing protein complexes in the physiological state, coupled with efficient enrichment of the cross-linked peptides, ensured deep-coverage analysis of the protein interactome in living cells. By ensemble structure refinement with cross-linking restraints, subcellular-specific conformation heterogeneity was identified for PTEN. PTEN displayed a broader range of dynamic conformation changes on the dual specificity domains in the nucleus than in the cytoplasm. Moreover, based on conformational differences, different interacting assemblies involving 25 cytoplasm-exclusively and 18 nucleus-exclusively PTEN-interacting proteins were found to account for diverse biological functions. Upon ubiquitin-proteasome system (UPS) stress, the assembly of PTEN and its interacting partners changed obviously during translocation. We newly identified 36 PTEN-interacting proteins, which were found to be highly enriched in functional pathways closely related to cell apoptosis. Inspiringly, the interactions among PTEN isoforms and their interacting proteins were accessible by the determination of sequence-unique cross-linking interfaces for direct interactions. All these results indicate the promise of SPACX to elucidate the functional heterogeneity of proteins in individual subcellular sociology.
Omicron variant of SARS-CoV-2 exhibits an increased resilience to the antiviral type I interferon response
Authors: Shalamova Lyudmila , Felgenhauer Ulrike , Schaubmar Andreas R. , Büttner Kathrin , Widera Marek , Ciesek Sandra , Weber Friedemann 
Published: January 2022

AbstractThe new variant of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype strain (B.1) with respect to their interactions with the antiviral type I interferon (IFN-alpha/beta) response in infected cells. Our data indicate that Omicron has gained an elevated capability to suppress IFN-beta induction upon infection and to better withstand the antiviral state imposed by exogenously added IFN-alpha.
Central role of Prominin-1 in lipid rafts during liver regeneration
Authors: Bahn Myeong-Suk , Yu Dong-Min , Lee Myoungwoo , Jo Sung-Je , Lee Ji-Won , Lee Hyun , Kim Arum , Hong Jeong-Ho , Kim Jun Seok , Koo Seung-Hoi , Lee Jae-Seon , Ko Young-Gyu 
Published: January 2022

AbstractProminin-1 (PROM1), a lipid raft protein, is required for maintaining cancer stem cell properties in hepatocarcinoma cell lines, but its physiological roles in the liver have not been well studied. Here, we investigated the role of PROM1 in lipid rafts with a precise molecular mechanism during liver regeneration. We found that the expression of PROM1 increased during liver regeneration after 2/3 partial hepatectomy (PHx) or CCl4injection. Interestingly, hepatocyte proliferation and liver regeneration were attenuated in liver-specificProm1knockout (Prom1LKO) mice compared to wild-type (Prom1f/f) mice. Detailed mechanistic studies revealed that PROM1 interacted with the interleukin-6 signal transducer glycoprotein 130 (GP130) and confined GP130 to lipid rafts so that STAT3 signaling by IL-6 was effectively activated. Moreover, the overexpression of the glycosylphosphatidylinsositol (GPI)-anchored first extracellular domain of PROM1 (PROM1GPI-EX1), which is a domain that binds to GP130, rescued the proliferation of hepatocytes and liver regeneration inProm1LKOmice. PROM1 is upregulated in hepatocytes during liver regeneration, and upregulated PROM1 recruits GP130 into lipid rafts and activates the IL6-GP130-STAT3 axis. Thus, we conclude that PROM1 plays an important role in lipid rafts during liver regeneration and might be a promising target for therapeutic applications of liver transplantation.