bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural plasticity of Atg18 oligomers: organization of assembled tubes and scaffolds at the isolation membrane
Authors: Mann Daniel , Fromm Simon A. , Martinez-Sanchez Antonio , Gopaldass Navin , Mayer Andreas , Sachse Carsten 
Published: July 2022

AbstractAutophagy-related protein 18 (Atg18) participates in the elongation of early autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes to the structural coordination of Atg2 and Atg9 at the isolation membrane remains to be understood. Here, we determined the cryo-EM structures of Atg18 organized in helical tubes as well as soluble oligomers. The helical assembly is composed of Atg18 tetramers forming a lozenge cylindrical lattice with remarkable structural similarity to the COPII outer coat. When reconstituted with lipid membranes, using subtomogram averaging we determined tilted Atg18 dimer structures bridging two juxtaposed lipid membranes spaced apart by 80 Å. Together with an AlphaFold Atg18-Atg2 model, we propose that Atg18 oligomers form a structural scaffold coordinating the Atg2 membrane bridge. The observed structural plasticity of Atg18’s oligomeric organization and membrane binding provide a molecular framework for the positioning of downstream components of the autophagy machinery.
DevelopingWolbachia-based disease interventions for an extreme environment
Authors: Ross Perran A. , Elfekih Samia , Collier Sophie , Klein Melissa J. , Lee Su Shyan , Dunn Michael , Jackson Sarah , Zhang Yexin , Axford Jason K. , Gu Xinyue , Nassar Majed S. , Paradkar Prasad N. , Tawfik Essam A. , Jiggins Francis M. , Almalik Abdulaziz M. , Al-Fageeh Mohamed B. , Hoffmann Ary A. 
Published: July 2022

AbstractAedes aegyptimosquitoes carrying self-spreading, virus-blockingWolbachiabacteria are being deployed to suppress dengue transmission. However, there are challenges in applying this technology in extreme environments. We introduced twoWolbachiastrains intoAe. aegyptifrom Saudi Arabia for a release program in the hot coastal city of Jeddah.Wolbachiareduced infection and dissemination of dengue virus (DENV2) in Saudi Arabian mosquitoes and showed complete maternal transmission and cytoplasmic incompatibility.Wolbachiareduced mosquito heat tolerance and egg viability, with theWolbachiastrains showing differential thermal stability.Wolbachiaeffects were similar across mosquito genetic backgrounds but we found evidence of local adaptation, with Saudi Arabian mosquitoes having lower egg viability but higher adult desiccation tolerance than Australian mosquitoes. Genetic background effects will influenceWolbachiainvasion dynamics, reinforcing the need to use local genotypes for mosquito release programs, particularly in extreme environments like Jeddah. Our comprehensive characterization ofWolbachiastrains provides a foundation forWolbachia-based disease interventions in harsh climates.
Multibody kinematic optimisation vs body fat: A performance analysis
Authors: Radhakrishnan Vignesh , Patil Samadhan B , Pelah Adar 
Published: July 2022

AbstractWe have analysed the performance of mulitbody kinematic optimisation methods in reducing soft tissue artefacts for subject data of varying body fat percentages. Multibody kinematic optimisation methods are a critical aspect of movement analysis using musculoskeletal modelling software. By minimising soft tissue artefacts, they help in achieving higher fidelity joint kinematics and dynamics analyses. Prior studies have not examined the performance of multibody kinematic optimisation on subjects of varying body fat percentages. Herein, we: 1) have analysed the efficacy of three different multibody kinematic optimisation methods on varying body fat percentages, 2) implemented a novel weighting scheme to reduce error irrespective of body fat percentages. Residual error using gait data of 50 participants of varying body fat percentages was calculated through inverse kinematic analysis using OpenSim(c) musculoskeletal modelling software. The analysis was repeated using a time-based weighting scheme. The residual error of participants with higher body fat percentages was greater by 30% when compared to residual error of participants of lower body fat percentages. Additionally, time-based weighting scheme reduced residual error by 20% on average compared to constant-value weighting scheme. Our results indicate that multibody kinematic optimisation methods are adversely affected by higher body fat percentages and that time-based weighting can provide higher fidelity movement analysis irrespective of body fat percentages. Through our results we aim to develop tools which provide greater precision in obesity-related movement analysis. Such tools could also help address the disparities in rates of obesity associated with different ethnic or socioeconomic background.
Unravelling Key Interactions and the Mechanism of Demethylation during hAGT mediated DNA Repair via Simulations
Authors: G Shruti T , Siddiqui Shakir Ali , Dubey Kshatresh Dutta 
Published: July 2022

AbstractAlkylating agents possess the biggest threat to the genomic integrity of cell by damaging DNA bases through regular alkylation. Such damages are repaired by several automated machinery inside cell. O6-alkylguanine-DNA alkyltransferase (AGT) is such an enzyme which performs the direct repair of an alkylated guanine base by transferring the alkyl group to a Cysteine residue. In the present study using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of damaged base as a three step in thermodynamically feasible and irreversible manner. Our calculations show that the final products forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.
Tenotomy-induced muscle atrophy is sex-specific and independent of NFκB
Authors: Meyer Gretchen A. , Thomopoulos Stavros , Abu-Amer Yousef , Shen Karen C. 
Published: July 2022

AbstractThe nuclear factor-κB (NFκB) pathway is a major thoroughfare for skeletal muscle atrophy and is driven by diverse stimuli. Targeted inhibition of NFκB through its canonical mediator IKKβ effectively mitigates loss of muscle mass across many conditions, from denervation to unloading to cancer. In this study, we used gain- and loss-of-function mouse models to examine the role of NFκB in muscle atrophy following rotator cuff tenotomy – a model of chronic rotator cuff tear. IKKβ was knocked down or constitutively activated in muscle-specific inducible transgenic mice to elicit a 2-fold gain or loss of NFκB signaling. Surprisingly, neither knockdown of IKKβ nor overexpression of caIKKβ significantly altered the loss of muscle mass following tenotomy. This finding was consistent across measures of architectural adaptation (fiber cross-sectional area, fiber length, fiber number), tissue pathology (fibrosis and fatty infiltration) and intracellular signaling (ubiquitin-proteasome, autophagy). Intriguingly, late-stage tenotomy-induced atrophy was exacerbated in male mice compared to female mice. This sex specificity was driven by ongoing decreases in fiber cross-sectional area, which paralleled the accumulation of large autophagic vesicles in male, but not female muscle. These findings suggest that tenotomy-induced atrophy is not dependent on NFκB and instead may be regulated by autophagy in a sex-specific manner.
RET enhancer haplotype-dependent remodeling of the human fetal gut development program
Authors: Chatterjee Sumantra , Fries Lauren E. , Yaacov Or , Hu Nan , Berk-Rauch Hanna E. , Chakravarti Aravinda 
Published: July 2022

AbstractHirschsprung disease (HSCR) is associated with deficiency of the receptor tyrosine kinase RET, resulting in loss of cells of the enteric nervous system (ENS) during fetal gut development. The major contribution to HSCR risk is from common sequence variants in RET enhancers with additional risk from rare coding variants in many genes. Here, we demonstrate that these RET enhancer variants specifically alter the human fetal gut development program through significant decreases in gene expression of RET, members of the RET-EDNRB gene regulatory network (GRN), other HSCR genes, and an altered transcriptome with 2,382 differentially expressed genes with diverse neuronal and mesenchymal functions. A parsimonious hypothesis for these results is that beyond RET’s direct effect on its GRN, it also has a major role in enteric neural crest derived cell (ENCDC) precursor proliferation, its deficiency reducing ENCDCs with relative expansion of non-ENCDC cells. Thus, genes reducing RET proliferative activity can potentially cause HSCR. One such class is the 23 RET-dependent transcription factors enriched in early gut development. We show that their knockdown in human neuroblastoma SK-N-SH cells reduces RET and/or EDNRB gene expression, expanding the RET-EDNRB GRN. The human embryos we studied had major remodeling of the gut transcriptional but were unlikely to have had HSCR: thus, genetic changes in addition to those in RET are required for a significant enough reduction in ENCDCs to cause aganglionosis.
Genomics of viruses infecting green and purple sulfur bacteria in two euxinic lakes
Authors: Hesketh-Best P. J. , Bosco-Santos A. , Garcia S. L. , Werne J. P. , Gilhooly W. P. , Silveira C. B. 
Published: July 2022

AbstractViral infections of marine bacteria modulate the rates of primary production and the cycling of organic and inorganic matter in the world’s oceans. Here, we investigated the hypothesis that viral infections influence the ecology of purple and green sulfur bacteria (PSB and GSB) in anoxic and sulfidic (euxinic) lakes, modern analogs of early Earth oceans. Over 200 high and medium quality viral contigs were identified in long-read metagenomes from the sediments and water column of Lime Blue and Poison Lake, respectively. We compared these sequences with 94 predicted prophages identified in the complete genomes of PSB (n = 213) and GSB (n = 33). Viral genomes carrying psbA, encoding the small subunit of photosystem II protein, were present in all three datasets (sediment, water column, and complete genomes). The ubiquity of these genes suggests that PSB and GSB viruses interfere with the light reactions of sulfur-oxidizing autotrophs in a process similar to viral modulation of photosynthesis in Cyanobacteria. Viruses predicted to infect PSB and GSB also encoded auxiliary metabolic genes involved in reductive sulfur assimilation as cysteine, a pathway not yet described in these sulfur bacteria, as well as genes involved in pigment production (crtF) and carbon fixation (CP12, zwf, PGD). These observations highlight the potential for viral modulation of metabolic markers used as proxies to interpret biogeochemical processes in early Earth oceans.
ArtiaX: An Electron Tomography Toolbox for the Interactive Handling of Sub-Tomograms in UCSF ChimeraX
Authors: Ermel Utz H. , Arghittu Serena M. , Frangakis Achilleas S. 
Published: July 2022

AbstractCryo-electron tomography analysis involves the selection of macromolecular complexes to be used for subsequent sub-tomogram averaging and structure determination. Here, we describe a plugin developed for UCSF ChimeraX that allows for the display, selection, and editing of particles within tomograms. Positions and orientations of selected particles can be manually set, modified and inspected in real-time, both on screen and in virtual reality, and exported to various file formats. The plugin allows for the parallel visualization of particles stored in several meta data lists, in the context of any 3D image that can be opened with UCSF ChimeraX. The particles are rendered in user-defined colors or using colormaps, such that individual classes or groups of particles, cross-correlation coefficients or other types of information can be highlighted to the user. The implemented functions are fast, reliable and intuitive, exploring the broad range of features in UCSF ChimeraX. They allow for a fluent human-machine interaction, which enables an effective understanding of the sub-tomogram processing pipeline, even for non-specialist users.
Novel leaf-root coordination driven by leaf water storage tissues in mangroves
Authors: Cao Jingjing , Yang Qingpei , Chen Jing , Lu Mingzhen , Ren Weizheng , Xiong Yanmei , Pei Yuxin , Kong Deliang 
Published: July 2022

AbstractInteractions among root and leaf traits (in particular, leaf hydraulic and leaf economics traits) are fundamental in generating diverse strategies in land plants, yet it remains a knowledge gap in mangrove plants that experiences saline stress distinct from most other vascular plants. Here, we tested the trait relationships in mangrove plants and compared them with typical land plants (non-mangrove). Consistent with non-mangrove plants, leaf hydraulic and economics traits were decoupled in mangrove plants. However, mangrove leaf economics traits correlated strongly with root hydraulic traits, which are normally decoupled in non-mangrove plants. Moreover, we observed a unique scaling relationship between leaf dry mass per area and root hydraulic traits in mangroves. The novel coordination between leaves and roots arises from the wide-presence of leaf water storage tissues in mangroves, and this potentially represents a new paradigm with which we look into the ecology, physiology and evolution of this important vegetation.
PROTEIN CODING VARIATION IN OUTBRED LABORATORY MOUSE STOCKS PROVIDES A MOLECULAR BASIS FOR DISTINCT RESEARCH APPLICATIONS
Authors: Cornes Belinda , Paisie Carolyn , Swanzey Emily , Schile Andrew , Brackett Kelly , Reinholdt Laura , Srivastava Anuj 
Published: July 2022

ABSTRACTOutbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice for biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that ensures research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined the novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for on-going genetic quality control. We also compared these data to protein coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. That individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability.
The genetics of immune and infection phenotypes in wild mice, Mus musculus domesticus
Authors: Cheynel Louise , Lazarou Luke , Riley Eleanor M. , Viney Mark 
Published: July 2022

AbstractWild animals are under constant threat from a wide range of micro- and macroparasites in their environment. Animals make immune responses against parasites, and these are important in affecting the dynamics of parasite populations. Individual animals vary in their anti-parasite immune responses. Genetic polymorphism of immune-related loci contributes to inter-individual differences in immune responses, but most of what we know in this regard comes from studies of humans or laboratory animals; there are very few such studies of wild animals naturally infected with parasites. Here we have investigated the effect of polymorphism in immune-related loci (the MHC, and genes coding for cytokines and Toll-like receptors) on a wide range of immune and infection phenotypes in UK wild house mice, Mus musculus domesticus. We found strong effects of polymorphisms in various MHC and cytokine coding loci on both immune measures (antibody concentration and cytokine production) and on infection phenotypes (infection with mites, worms and viruses). Our study provides a comprehensive view of how polymorphism of immune-related loci affects immune and infection phenotypes in naturally infected wild rodent populations.
Biofilm competency of Desulfovibrio vulgaris Hildenborough facilitates colonization in the gut and represses adenoma development in a rat model of colon cancer
Authors: Busi Susheel Bhanu , De León Kara B. , Montonye Dan R. , Wall Judy D. , Landgraf James Amos- 
Published: July 2022

AbstractHuman epidemiological and animal model studies have shown that the presence of colon cancer is associated with certain microbiota. Previous human colon cancer case-control reports and our preclinical model studies identify several bacterial taxa correlating with the suppression of tumor growth. This includes a sulfate-reducing bacteria from the genus Desulfovibrio, which correlates with fewer tumors and decreased phenotype penetrance as early as 1 month of age in rats. However, other studies have shown that Desulfovibrio spp. are decreased in relative abundance in healthy patient controls. To address this disparity we treated PIRC rats, a model of human familial colon cancer that harbored a complex gut microbiota, with biofilm-forming and biofilm-deficient strains of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH). We found that the biofilm-forming DvH strain could stably colonize the rat colon, with the bacteria detected even at 3.5 months post treatment. The biofilm-deficient DvH mutant only transiently colonized the rat colon and was no longer detected in fecal samples one-week post treatment. The colonic adenoma burden at four months of age was significantly reduced in rats colonized with the biofilm- forming DvH compared to those treated with the biofilm-deficient DvH. We found a differential shift in the endogenous gut microbiota (GM) structure over time, with a notable increase in known mucin degraders in the buffer-treated control and biofilm-deficient DvH treated groups. These latter groups of rats also showed a higher level of expression of MUC2 in the colon, which encodes for the sulfonated mucin 2 expressed primarily in the gut and trachea. We also detected more dissolved sulfide in the feces from rats treated with either buffer or biofilm-deficient DvH compared to rats colonized with the biofilm-competent DvH. We found that the in vitro biofilm- forming capacity of DvH enabled in vivo engraftment of this bacterium within a complex GM population, altering the bacterial composition, and significantly reducing tumor burden in PIRC rats.
Conformation and structural dynamics of the Xist lncRNA A-repeats
Authors: Jones Alisha N. , Gabel Frank , Bohn Stefan , Wolfe Gregory , Sattler Michael 
Published: July 2022

ABSTRACTLncRNAs are emerging to play crucial roles in the regulation of many essential cellular processes and have been linked to human disease, but a detailed understanding of their structure and how this relates to underlying molecular mechanisms is still limited. The structure that a lncRNA adopts can interconvert between multiple conformations. However, characterizing the structure and dynamics is challenging given their large size. Here, we present an integrated approach, combining biochemical and biophysical techniques to investigate the core structural elements and conformational dynamics of the A-repeats of the lncRNA Xist. We combine chemical RNA structure probing, SAXS, NMR-spectroscopy and cryo-EM to comprehensively describe the conformational landscape of the Xist A-repeats. We show that under native-like conditions, the A-repeats are modular, comprising building blocks made from stable AUCG tetraloop hairpins and inter-repeat dimers separated by flexible uracil-rich regions. The structural core of the A-repeats involves dimerization of sequential repeats to form two subdomains, comprising repeats 1-4 and 5-8. The overall topology of the A-repeats is dynamic, with structural variability linked to the uracil-rich linker regions. Our results rationalize context and buffer-dependent structural variations of the Xist lncRNA. The integrative approach presented here establishes a general pipeline for investigating lncRNA structure and dynamics.GRAPHICAL ABSTRACT
Microtubule severing enzymes oligomerization and allostery: a tale of two domains
Authors: Macke Amanda C. , Kelly Maria S. , Varikoti Rohith Anand , Mullen Sarah , Groves Daniel , Forbes Clare , Dima Ruxandra I. 
Published: July 2022

AbstractSevering proteins are nanomachines from the AAA+ (ATPases associated with various cellular activities) superfamily whose function is to remodel the largest cellular filaments, microtubules. The standard AAA+ machines adopt hexameric ring structures for functional reasons, while being primarily monomeric in the absence of the nucleotide. Both major severing proteins, katanin and spastin, are believed to follow this trend. However, studies proposed that they populate lower-order oligomers in the presence of co-factors, which are functionally relevant. Our simulations show that the preferred oligomeric assembly is dependent on the binding partners, and on the type of severing protein. Essential dynamics analysis predicts that the stability of an oligomer is dependent on the strength of the interface between the helical bundle domain (HBD) of a monomer and the convex face of the nucleotide binding domain (NBD) of a neighboring monomer. Hot spots analysis found that the region consisting of the HBD tip and the C-terminal (CT) helix is the only common element between the allosteric networks responding to nucleotide, substrate, and inter-monomer binding. Clustering analysis indicates the existence of multiple pathways for the transition between the secondary structure of the HBD tip in monomers and the structure(s) it adopts in oligomers.