bluuebunny/crossref_metadata_2025_split huggingface dataset:
Body size, not species identity, drives body heating in alpineErebiabutterflies
Authors: Kleckova Irena , Okrouhlik Jan , Svozil Tomas , Matos-Maraví Pável , Klecka Jan 
Published: October 2022

AbstractEfficient thermoregulation is crucial for animals living under fluctuating climatic and weather conditions. We studied the body heating of six butterfly species of the genusErebia(Lepidoptera: Nymphalidae) that co-occur in the European Alps. We tested whether butterfly physical characteristics (body size, wing loading) are responsible for the inter-specific differences in body temperatures recorded previously under natural conditions. We used a thermal camera to measure body heating of wild butterfly individuals in a laboratory experiment with artificial light and heating sources. We revealed that physical characteristics had a small effect on explaining inter-specific differences in mean body temperatures recorded in the field. Our results show that larger butterflies, with higher weight and wing loading, heated up more slowly but reached the same asymptotic body temperature as smaller butterflies. Altogether, our results suggest that differences in body temperatures amongErebiaspecies observed in the field might be caused mainly by species-specific microhabitat use and point towards an important role of active behavioural thermoregulation in adult butterflies. We speculate that microclimate heterogeneity in mountain habitats facilitates behavioural thermoregulation of adults. Similarly, microclimate structuring might also increase survival of less mobile butterfly life stages, i.e., eggs, larvae and pupae. Thus, landscape heterogeneity in management practices may facilitate long term survival of montane invertebrates under increased anthropogenic pressures.
Computational investigation of mechanisms for pH modulation of human chloride channels
Authors: Elverson Kathleen , Freeman Sally , Manson Forbes , Warwicker Jim 
Published: October 2022

AbstractMany transmembrane proteins are modulated by intracellular or extracellular pH. Investigation of pH-dependence generally proceeds by mutagenesis of a wide set of amino acids, guided by properties such as amino acid conservation and structure. This study shows how web-based calculation of pKas allows rapid and effective identification of amino acids of interest with respect to pH-dependence. Commencing with the calcium-activated chloride channel bestrophin 1, the carboxylate ligand structure around calcium sites relaxes in the absence of calcium, consistent with a measured lack of pH-dependence. By contrast, less relaxation in the absence of calcium in TMEM16A, and maintenance of elevated carboxylate sidechain pKas, is suggested to give rise to pH-dependent chloride channel activity. This hypothesis, modulation of calcium/proton coupling and pH-dependent activity through extent of structural relaxation, is shown to apply to the well-characterised cytosolic proteins calmodulin (pH-independent) and calbindin D9k (pH-dependent). Further application of destabilised ionisable charge sites, or electrostatic frustration, is made to other human chloride channels (that are not calcium-activated), ClC-2, GABAA, and GlyR. Experimentally-determined sites of pH modulation are readily identified. The structure-based tool is freely available, allowing users to focus mutagenesis studies, construct hypothetical proton pathways, and derive hypotheses such as the model for control of pH-dependent calcium activation through structural flexibility. Predicting altered pH-dependence for mutations in ion channel disorders can support experimentation and, ultimately, clinical intervention.
Apolipoprotein E2 Promotes Melanoma Growth, Metastasis, and Protein Synthesis via the LRP1 Receptor
Authors: Adaku Nneoma , Ostendorf Benjamin N. , Tavazoie Sohail F. 
Published: October 2022

AbstractThe secreted lipid transporter apolipoprotein E (APOE) plays important roles in atherosclerosis and Alzheimer’s disease and has been implicated as a suppressor of melanoma progression. APOE germline genotype predicts human melanoma outcomes, as APOE4 and APOE2 allele carriers exhibit increased versus reduced melanoma survival, respectively, relative to APOE3 homozygotes. While the APOE4 variant was recently shown to suppress melanoma progression by enhancing anti-tumor immunity, the melanoma cell-intrinsic effects of APOE variants on cancer progression remain poorly characterized. By using a genetically engineered mouse model, we show that human germline APOE genetic variants differentially modulate melanoma growth and metastasis in a melanoma LRP1 receptor-dependent manner. We identify protein synthesis as a tumor cell-intrinsic process differentially modulated by APOE variants, with APOE2 surprisingly promoting translation via LRP1. Our findings reveal a gain-of-function role for the APOE2 variant in melanoma progression, raising important implications for other diseases impacted by APOE genetics.SignificanceOur work reveals that germline APOE variants differentially impact genetically initiated melanoma progression, with APOE2 acting as a promoter of tumor growth, metastasis, and a cell-intrinsic process—protein synthesis. These findings may aid in predicting patient outcomes and may partly explain the protective effect of APOE2 in Alzheimer’s disease.
EMC holdase:CaV1.2/CaVβ3 complex and CaV1.2 channel structures reveal CaV assembly and drug binding mechanisms
Authors: Chen Zhou , Mondal Abhisek , Abderemane-Ali Fayal , Montano José , Zaro Balyn , Minor Daniel L. 
Published: October 2022

AbstractVoltage-gated ion channels (VGICs) comprise multiple structural units whose assembly is required for function1,2. There is scant structural understanding of how VGIC subunits assemble and whether chaperone proteins are required. High-voltage activated calcium channels (CaVs)3,4 are paradigmatic multi-subunit VGICs from electrically excitable tissues whose function and trafficking is powerfully shaped by interactions between pore-forming CaV1 or CaV2 CaVα13 and auxiliary CaVβ5, and CaVα2δ subunits6,7. Here, we present cryo-EM structures of human brain and cardiac CaV1.2 bound with CaVβ3 to a chaperone, the endoplasmic reticulum membrane protein complex (EMC)8,9, and of the isolated CaV1.2/CaVβ3/CaVα2δ-1 channel. These provide an unprecedented view of an EMC holdase:client complex and define EMC sites, the TM and Cyto docks, whose interaction with the client channel cause partial extraction of a pore subunit and splay open the CaVα2δ interaction site. The structures further identify the CaVα2δ binding site for gabapentinoid anti-pain and anti-anxiety drugs6, show that EMC and CaVα2δ channel interactions are mutually exclusive, and indicate that EMC to CaVα2δ handoff involves a Ca2+-dependent step and ordering of multiple CaV1.2 elements. Together, the structures unveil a CaV assembly intermediate and previously unknown EMC client binding sites that have broad implications for biogenesis of VGICs and other membrane proteins.
Integrative multispecies omics reveals a hierarchy of cold-responsive regulatory network launched by circadian components in rosids
Authors: Guo Liangyu , Xu Zhiming , Wang Shuo , Nie Yuqi , Ye Xiaoxue , Jin Xuejiao , Zhu Jianhua , Wu Wenwu 
Published: October 2022

AbstractElucidating regulators and molecular mechanisms underlying gene transcriptional and post-transcriptional co-regulatory network is key to understand plant cold-stress responses. Previous studies were mainly conducted on single species and whether the regulators and mechanisms are conserved across different species remains elusive. Here, we selected three species that diverged at early evolution of rosids (93–115 million years ago) and integrated phylotranscriptome and ChIP/DAP-seq datasets to identify cold-responsive regulators and their regulatory networks. First, we found over ten thousand cold-responsive genes including differentially expressed genes (DEGs) and alternative splicing genes (DASGs) in each species. Among the DEGs, genes encoding a set of transcription factors (TFs) (AP2/ERF, MYB, WRKY, NAC, etc.) and RNA binding proteins (RBPs) (Ribosomal, RRM, DEAD, Helicase_C, etc.) are conserved in cold responses in rosids. Compared to TFs, RBPs show a delayed cold-responsive pattern, likely suggesting a hierarchical regulation of DEGs and DASGs. Between DEGs and DASGs, we identified 259 overlapping DE-DASG orthogroups and interestingly, pathway analysis on each dataset of DEGs, DASGs, and DE-DASGs coincidently shows an enrichment of circadian rhythm. Evidentially, many circadian components are cold-regulated at both transcriptional and post-transcriptional levels. Moreover, we reasoned 226 cold-responsive genes regulated by at least two of five circadian components (CCA1, LHY, RV4, RVE8, and RVE7) in rosids. Finally, we unveiled a conserved hierarchical network in dynamic transcriptional and post-transcriptional regulation of cold-responsive genes launched by circadian components in rosids. Together, our results provide insights into core regulators and mechanisms underlying cold-responsive regulatory network across rosids, despite a long evolutionary history.
Evaluating sickness-induced anxiety versus lethargy at the behavioral and neuronal activity level
Authors: Lanovoi Hunter T. , Oyama Rumi , Carcea Ioana 
Published: October 2022

SummaryIn mammals, inflammatory responses to infections trigger adaptive behavioral changes collectively known as ‘sickness behavior’. Among these, lethargy protects the sick individual by conserving energy, and increased anxiety is believed to prevent exposure to threats. However, the characterization of these conflicting behavioral states in sickness could be an artifact of behavioral assessment, particularly in rodents. We adjusted existing behavioral testing and designed a new paradigm to disambiguate between increased lethargy versus increased anxiety. Our data indicate that in mice sickness induces a significant increase in lethargy but not in anxiety. Further supporting our behavioral results, at the neuronal level we found evidence that sickness activates anxiolytic rather than anxiogenic regions of the amygdala, including oxytocin receptor expressing neurons. Putative mechanisms by which sickness could activate CeA-OTR+ neurons were investigated.
Photosynthetically active radiation is required for seedling growth promotion by volcanic dacitic tuff breccia (Azomite)
Authors: McCue Kent F. , Mehlferber Elijah , Reed Robert , Ortiz Alexis , Ferrel Jon , Khanna Rajnish 
Published: October 2022

AbstractA plant’s growth and development are shaped by its genome and the capacity to negotiate its environment for access to light, water, and nutrients. There is a vital need to understand the interactions between the plant, its physical environment, and the fertilizers used in agriculture. In this study, a commercially available volcanic ash fertilizer, Azomite®, characterized as dacitic (rhyolitic) tuff breccia (DTB), was tested for its effect on promoting early seedling vigor. Early growth and photomorphogenesis processes are well studied in Arabidopsis. Seedling assays under different light conditions were used to dissect the underlying mechanisms involved. These assays are well established and can be translated to agriculturally important crop plants. The volcanic ash fertilizer was tested at different concentrations on seedlings grown on basic media lacking sucrose either in continuous darkness (Dc), continuous Red (Rc), Far-Red (FRc), or White Light (WLc). Micronutrients in the volcanic ash significantly increased seedling growth under Rc and WLc, but not under Dc and FRc, indicating that photosynthetically active radiation (PAR) was required for the observed growth increase. Furthermore, red-light photoreceptor mutant, phyB-9 lacked the growth response, and higher amount of fertilizer reduced growth in all conditions tested. These data suggest that light triggers the ability of the seedling to utilize micronutrients in volcanic ash in a dose-dependent manner. The methods described here can be used to establish mechanisms of activity of various nutrient inputs, and coupled with whole-genome expression profiling, can lead to better insights into optimizing nutrient field applications to improve crop production.
Irx1 and Irx2 play dose-dependent cooperative functions in mammalian development
Authors: Sheybani-Deloui Sepideh , Xu Leo , Hu Lijuan , Yuan Qiongjing , Son Joe Eun , Kim Kyoung-Han , Liu Weifan , Mo Rong , Zhang Xiaoyun , Chi Lijun , Olguin Paul Delgado , Hui Chi-Chung 
Published: October 2022

AbstractIrx1 and Irx2 (Irx1/2) are two closely linked and widely expressed members of the conserved Iroquois homeobox family of transcription factors. Despite mounting evidence suggesting the importance of homologs of these genes in many aspects of vertebrate development and function, the role of Irx1/2 in mammals has remained largely unknown. Here, we used mice carrying our newly generated Irx1flox and Irx1floxIrx2del mutant alleles to perform a stepwise genetic ablation of Irx1 and Irx2 levels. Our analysis revealed reduced postnatal growth and viability of Irx1KO mice with gross histological defects in the lung and gut and demonstrated that ablation of one copy of Irx2 in these mice results in neonatal lethality with exacerbated phenotypic defects. Conversely, while Irx2KO mice appear normal, ablation of one copy of Irx1 in these mutants leads to lethality at weaning. Furthermore, we found that homozygous deletion of both Irx1 and Irx2 results in embryonic lethality by mid-gestation with defective extraembryonic vasculature. Our results illustrate that Irx1 and Irx2 play distinct dose-dependent cooperative functions during both the early and late stages of mouse development.
Modelling the gastrointestinal carriage of Klebsiella pneumoniae infections
Authors: Calderon-Gonzalez Ricardo , Lee Alix , Lopez-Campos Guillermo , Hancock Steven J. , Sa-Pessoa Joana , Dumigan Amy , McMullan Ronan , Campbell Eric L. , Bengoechea Jose A. 
Published: October 2022

ABSTRACTKlebsiella pneumoniae is a leading cause of nosocomial and community acquired infections, making K. pneumoniae the second pathogen associated with the most deaths attributed to any antibiotic resistant infection. K. pneumoniae colonises the nasopharynx and the gastrointestinal tract in an asymptomatic manner without dissemination to other tissues; importantly gastrointestinal colonisation is a requisite for infection. Our understanding of K. pneumoniae colonisation is still based on interrogating mouse models in which animals are pre-treated with antibiotics to disturb the colonisation resistance imposed by the gut microbiome. In these models, infection disseminates to other tissues. Here, we report a murine model to allow for the study of the gastrointestinal colonisation of K. pneumoniae without tissue dissemination. Hypervirulent and antibiotic resistant strains stably colonise the gastrointestinal tract of in an inbred mouse population without antibiotic treatment. The small intestine is the primary site of colonisation followed by a transition to the colon over time without dissemination to other tissues. Our model also mimics the disease dynamics of metastatic K. pneumoniae strains able to disseminate from the gastrointestinal tract to other sterile sites. Colonisation is associated with mild to moderate histopathology, no significant inflammation, and no effect on the richness of the microbiome. Our model recapitulates the clinical scenario in which antibiotic treatment disturbs the colonisation of K. pneumoniae resulting in dissemination to other tissues. Finally, we establish that the capsule polysaccharide is necessary for the colonisation of the large intestine whereas the type VI secretion system contributes to colonisation across the gastrointestinal tract.IMPORTANCEKlebsiella pneumoniae is one of the pathogens sweeping the World in the antibiotic resistance pandemic. Klebsiella colonises the nasopharynx and the gut of healthy subjects in an asymptomatic manner, being gut colonisation a requisite for infection. This makes essential to understand the gastrointestinal carriage to prevent Klebsiella infections. Current research models rely on the perturbation of the gut microbiome by antibiotics, resulting in an invasive infection. Here, we report a new model of K. pneumoniae gut colonisation that recapitulates key features of the asymptomatic human gastrointestinal tract colonisation. In our model, there is no need to disturb the microbiota to achieve stable colonization without dissemination to other tissues. Our model recapitulates the clinical scenario in which antibiotic treatment triggers invasive infection. We envision our model will be an excellent platform to test therapeutics to eliminate Klebsiella asymptomatic colonisation, and to investigate factors enhancing colonisation and invasive infections.
Population-level relative effectiveness of the COVID-19 vaccines and the contribution of naturally acquired immunity
Authors: Shioda Kayoko , Chen Yangping , Collins Matthew H , Lopman Benjamin A 
Published: October 2022

ABSTRACTBackgroundImmune protection against SARS-CoV-2 can be induced by natural infection or vaccination or both. The interaction between vaccine-induced immunity and naturally acquired immunity at the population level has been understudied.MethodsWe used regression models to evaluate whether the impact of COVID-19 vaccines differed across states with different levels of naturally acquired immunity from March 2021 to April 2022 in the United States. Analysis was conducted for three evaluation periods separately (Alpha, Delta, and Omicron waves). As a proxy of the proportion of the population with naturally acquired immunity, we used either the reported seroprevalence or the estimated proportion of the population ever infected in each state.ResultsCOVID-19 mortality decreased as the coverage of ≥1 dose increased among people ≥65 years of age, and this effect did not vary by seroprevalence or the proportion of the total population ever infected. Seroprevalence and the proportion ever infected were not associated with COVID-19 mortality, after controlling for vaccine coverage. These findings were consistent in all evaluation periods.ConclusionsCOVID-19 vaccination was associated with a sustained reduction in mortality at the state level during the Alpha, Delta, and Omicron periods. The effect did not vary by naturally acquired immunity.
Adaptation to spindle assembly checkpoint inhibition through the selection of specific aneuploidies
Authors: Adell Manuel Alonso Y , Klockner Tamara C. , Höfler Rudolf , Wallner Lea , Schmid Julia , Markovic Ana , Martyniak Anastasiia , Campbell Christopher S. 
Published: October 2022

AbstractBoth the presence of an abnormal complement of chromosomes (aneuploidy) and an increased frequency of chromosome missegregation (chromosomal instability) are hallmarks of cancer. Analyses of cancer genome data have identified certain aneuploidy patterns in tumors; however, the bases behind their selection are largely unexplored. By establishing time-resolved long-term adaptation protocols, we found that human cells adapt to persistent spindle assembly checkpoint (SAC) inhibition by acquiring specific chromosome arm gains and losses. Independently adapted populations converge on complex karyotypes, which over time are refined to contain ever smaller chromosomal changes. Of note, the frequencies of chromosome arm gains in adapted cells correlate very well with those detected in cancers, suggesting that our cellular adaptation approach recapitulates selective traits that dictate pan-cancer aneuploidy patterns. We further engineered specific aneuploidies to determine the genetic basis behind the observed karyotype patterns. These experiments demonstrated that the adapted and engineered aneuploid cell lines limit CIN by extending mitotic duration. Heterozygous deletions of key SAC and APC/C genes recapitulated the rescue phenotypes of the monosomic chromosomes. We conclude that aneuploidy-induced gene dosage imbalances of individual mitotic regulators are sufficient for altering mitotic timing to reduce CIN.
AnIn VivoAnalysis of the Functional Motifs of DEAD-box RNA Helicase Me31B inDrosophilaFertility and Germline Development
Authors: Kara Evan , McCambridge Aidan , Proffer Megan , Dilts Carol , Pumnea Brooke , Eshak John , Smith Korey A. , Fielder Isaac , Doyle Dominique A. , Ortega Bianca M. , Mukatash Yousif , Malik Noor , Mohammed Ammaar R. , Govani Deep , Niepielko Matthew G. , Gao Ming 
Published: October 2022

AbstractInDrosophilagermline, Me31B is a putative ATP-dependent, RNA helicase that plays role in post-transcriptional RNA regulation to ensure the correct spatial and temporal expression of the mRNAs, a process crucial for proper germline development and fertility. However, Me31B’sin vivoworking mechanism remains unclear. In this study, we aim to analyze the functions of Me31B’s key domains/motifs to understand how these domains/motifs operate to fulfill the protein’s overall activities. We generatedDrosophilastrains mutant for six important motifs including three ATPase/helicase motifs (DEAD-box, DVLARAK, and HRIGR), the N-terminal domain (N-ter), the C-terminal domain (C-ter), and a protein-binding motif (FDF motif-binding motif). In characterizing these mutants, we observed that the three ATPase/helicase motif mutations cause dominant female sterility which is associated with developmental defects in oogenesis and embryogenesis. Follow-up examination of the DVLARAK motif mutant revealed its abnormalities in germline mRNA localization and transcript level. The Me31B N-ter domain (deletion of C-ter), C-ter domain (deletion of N-ter), and mutation of FDF motif-binding motif led to a decrease in female fertility and abnormal subcellular Me31B localizations in the egg chambers. Moreover, deletion of Me31B N-ter or C-ter motif results in a decrease of Me31B protein levels in the ovaries. This study indicates that these six motifs of Me31B play different roles to contribute to Me31B’s whole-protein functions like ATPase, RNA helicase, protein stability, protein localization, and partner protein binding, which are crucial for germline development and fertility. Considering Me31B protein family’s conserved presence in bothDrosophilagermline and soma (for example, neurons) and in other organisms such as yeast, worm, mouse, and human, the results from this study could expand our understanding of Me31B helicase family’s general working mechanisms in different cell types and species.
Fission-independent compartmentalization of mitochondria during budding yeast cell division
Authors: Yoshii Saori R. , Barral Yves 
Published: October 2022

AbstractLateral diffusion barriers compartmentalize membranes to generate polarity or asymmetrically partition membrane-associated macromolecules. Budding yeasts assemble such barriers in the endoplasmic reticulum (ER) and the outer nuclear envelope at the bud neck to retain aging factors in the mother cell and generate naïve and rejuvenated daughter cells. However, little is known about whether other organelles are similarly compartmentalized. Here, we show that the membranes of mitochondria are laterally compartmentalized at the bud neck and near the cell poles. The barriers in the inner mitochondrial membrane are constitutive, whereas those in the outer membrane form in response to stresses. The strength of mitochondrial diffusion barriers is regulated positively by spatial cues from the septin axis, and negatively by retrograde (RTG) signaling. These data indicate that mitochondria are compartmentalized in a fission-independent manner. We propose that these diffusion barriers may promote mitochondrial polarity and contribute to mitochondrial quality control.