bluuebunny/crossref_metadata_2025_split huggingface dataset:
VirB4- and VirD4-like ATPases, components of a putative type 4C secretion system in Clostridioides difficile
Authors: Sorokina Julya , Sokolova Irina , Rybolovlev Ivan , Shevlyagina Natalya , Troitskiy Vasiliy , Zhukhovitsky Vladimir , Belyi Yury 
Published: July 2021

AbstractThe type 4 secretion system (T4SS) represents a bacterial nanomachine capable of trans-cell wall transportation of proteins and DNA and which has attracted intense interest due to its roles in the pathogenesis of infectious diseases. During the current investigation we uncovered three distinct gene clusters in Clostridioides difficile strain 630 coding for proteins structurally related to components of the VirB4/D4 type 4C secretion system from Streptococcus suis strain 05ZYH33 and located within sequences of conjugative transposons (CTn). Phylogenic analysis shows that VirB4- and VirD4-like proteins of CTn4 locus, on one hand, and those of CTn2 and CTn5 loci, on the other hand, fit into separate clades, suggesting specific roles of identified secretion system variants in physiology of C. difficile. Our further study on VirB4- and VirD4-like products coded by CTn4 revealed that both proteins possess Mg2+-dependent ATPase activity, form oligomers (most probably, hexamers) in water solutions, and rely on potassium but not sodium ions for the highest catalytic rate. VirD4 binds nonspecifically to DNA and RNA. Its DNA binding activity strongly decreased with the W241A variant. Mutations in the nucleotide sequences coding for presumable Walker A and Walker B motifs decreased stability of the oligomers and significantly but not completely attenuated enzymatic activity of VirB4. In VirD4, substitutions of amino acid residues in the peptides reminiscent of Walker structural motifs resulted neither in attenuation of enzymatic activity of the protein nor influenced the oligomerization state of the ATPase.ImportanceC. difficile is a Gram-positive, anaerobic, spore-forming bacterium that causes life-threatening colitis in humans. Major virulence factors of the microorganism include toxins TcdA, TcdB and CDT. However, other bacterial products, including a type 4C secretion system, have been hypothesized to contribute to the pathogenesis of the infection and are considered as possible virulence factors of C. difficile. In the current paper we describe structural organization of putative T4SS machinery in C. difficile and characterize its VirB4- and VirD4-like components. Our studies, in addition to significance for basic science, can potentially aid development of anti-virulence drugs suitable for treatment of C. difficile infection.
Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacteriumBilophila wadsworthia
Authors: Burrichter Anna G. , Dörr Stefanie , Bergmann Paavo , Haiß Sebastian , Keller Anja , Fournier Corentin , Franchini Paolo , Isono Erika , Schleheck David 
Published: July 2021

AbstractBackgroundBilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves a glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethane sulfonate) into acetaldehyde and sulfite.ResultsWe demonstrate that taurine metabolism inB. wadsworthia3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential ironsulfur (FeS) cluster-containing shell protein identified by sequence analysis.ConclusionsWe characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiontB. wadsworthiaand on microbial H2S production in the human gut.
MetaFun: Unveiling Sex-based Differences in Multiple Transcriptomic Studies through Comprehensive Functional Meta-analysis
Authors: Malmierca-Merlo Pablo , Sánchez-Garcia Rubén , Grillo-Risco Rubén , Pérez-Díez Irene , Català-Senent José F. , Leon Santiago , Gómez-Martínez Helena , de la Iglesia-Vayá María , Hidalgo Marta R. , Garcia-Garcia Francisco 
Published: July 2021

AbstractWhile sex-based differences in various health scenarios have been thoroughly acknowledged in the literature, we lack a deep analysis of sex as a variable in this context. To fill this knowledge gap, we created MetaFun as an easy-to-use web-based tool to meta-analyze multiple transcriptomic datasets with a sex-based perspective to gain major statistical power and biological soundness. Furthermore, MetaFun can be used to perform case-control meta-analyses, allowing researchers with basic programming skills to access this methodology.Availability and implementationMetaFun is freely available athttp://bioinfo.cipf.es/metafunThe back end was implemented in R and Java, and the front end was developed using AngularContactfgarcia@cipf.es,mhidalgo@cipf.esSupplementary informationR code available athttps://gitlab.com/ubb-cipf/metafunr
Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection
Authors: Zhang Xiaodan , Hu Chuansheng , Huang Chen , Wei Ying , Li Xiaowei , Hu Miaomiao , Li Hua , Wu Ji , Czajkowsky Daniel M. , Guo Yan , Shao Zhifeng 
Published: July 2021

AbstractThe functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue. However, acquisition of comprehensive transcriptomes of spatially- and phenotypically-defined cells in situ remains challenging. Here we present a general and robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to acquire finely resolved spatial transcriptomes including isoforms with as few as tens of cells from snap-frozen or RNAlater-treated clinical tissues, circumventing the problem of significant RNA degradation during this time-consuming process. The efficacy of this approach is exemplified by the characterization of differences at the transcript isoform level between the mouse small intestine lacteal cells at the tip versus the main capillary body. With the extensive repertoire of specific antibodies that are presently available, our method provides a powerful means by which spatially resolved cellular states can now be delineated in situ with preserved tissues. Moreover, such high quality spatial transcriptomes defined by immunomarkers can be used to compare with the phenotypes derived from single-cell RNAseq of dissociated cells as well as applied to bead-based spatial transcriptomic approaches that require such information a priori for cell identification.
Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and related humans in the Netherlands
Authors: Lu Lu , Sikkema Reina S. , Velkers Francisca C. , Nieuwenhuijse David F. , Fischer Egil A.J. , Meijer Paola A. , Bouwmeester-Vincken Noortje , Rietveld Ariene , Wegdam-Blans Marjolijn C.A. , Tolsma Paulien , Koppelman Marco , Smit Lidwien A.M. , Hakze-van der Honing Renate W. , van der Poel Wim H. M. , van der Spek Arco N. , Spierenburg Marcel A. H. , Molenaar Robert Jan , de Rond Jan , Augustijn Marieke , Woolhouse Mark , Stegeman J. Arjan , Lycett Samantha , Oude Munnink Bas B. , Koopmans Marion P. G. 
Published: July 2021

AbstractIn the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and related humans on farms. High number of farm infections (68/126) in minks and farm related personnel (>50% of farms) were detected, with limited spread to the general human population. Three of five initial introductions of SARS-CoV-2 lead to subsequent spread between mink farms until November 2020. The largest cluster acquired a mutation in the receptor binding domain of the Spike protein (position 486), evolved faster and spread more widely and longer. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combing genetic information with epidemiological information at the animal-human interface.
Performance of large scale pooled CRISPR screens is dependent on Cas9 expression levels
Authors: Fernandes Neto João M. , Lieftink Cor , Jastrzebski Katarzyna , Krenning Lenno , Dias Matheus , Morris Ben , van der Ven Daimy , Heimans Hester , Medema René H. , Bernards René , Beijersbergen Roderick L. 
Published: July 2021

ABSTRACTBackgroundThe widespread application of CRISPR/Cas9 technology has yielded numerous findings in biomedical research in recent years, making it an invaluable tool for gene knockout and for high-throughput screening studies. In (low-throughput) gene knockout studies, editing efficiency is not a major concern because only a few edited clones are necessary for a successful assay. However, in large scale pooled screening studies, editing efficiency is a major concern because each sgRNA has to knockout its target gene in a large cell population in a short period of time. Therefore, a thorough understanding of the role that key factors play in determining CRISPR knockout efficiency is essential to improve the performance of pooled CRISPR screening.MethodsIn this study, cell lines with different expression levels of CAS9 were generated and used to determine gene-editing efficiency. Collections of sgRNAs targeting essential genes were used to study their depletion in the different cell line models.ResultsUsing cell lines with variable expression of Cas9, we confirmed that editing efficiency and speed are mostly dependent on the sgRNA sequence and Cas9 expression, respectively. Importantly, we show that the strategy employed for delivering sgRNAs and Cas9 to cells impacts the performance of high-throughput screens, which is improved in conditions with higher Cas9 expression.ConclusionsOur findings highlight the importance of optimizing Cas9 expression levels when performing gene editing experiments and provide guidance on the necessary decisions for implementing optimal pooled CRISPR screening strategies.
Disentangling environmental effects in microbial association networks
Authors: Deutschmann Ina Maria , Lima-Mendez Gipsi , Krabberød Anders K. , Raes Jeroen , Vallina Sergio M. , Faust Karoline , Logares Ramiro 
Published: July 2021

AbstractBackgroundEcological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the associations are environmentally-driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not.ResultsWe present EnDED (Environmentally-DrivenEdgeDetection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally-driven. The four approaches are Sign Pattern, Overlap, Interaction Information, and Data Processing Inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e. environmentally-driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally-driven edges—87% Sign Pattern and Overlap, 67% Interaction Information, and 44% Data Processing Inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally-driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally-driven, while individual methods predicted 24.8% (Data Processing Inequality), 25.7% (Interaction Information), and up to 84.6% (Sign Pattern as well as Overlap). The fraction of environmentally-driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors.ConclusionsTo reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally-driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses.
Binding Free energy Decomposition and Multiple Unbinding Paths of Buried Ligands in a PreQ1 Riboswitch
Authors: Hu Guodong , Zhou Huan-Xiang 
Published: July 2021

AbstractRiboswitches are naturally occurring RNA elements that control bacterial gene expression by binding to specific small molecules. They serve as important models for RNA-small molecule recognition and have also become a novel class of targets for developing antibiotics. Here, we carried out conventional and enhanced-sampling molecular dynamics (MD) simulations, totaling 141.5 μs, to characterize the determinants of binding free energies and unbinding paths for the cognate and synthetic ligands of a PreQ1 riboswitch. Binding free energy analysis showed that two triplets of nucleotides U6-C15-A29 and G5-G11-C16, contribute the most to the binding of the cognate ligands, by hydrogen bonding and by base stacking, respectively. Mg2+ ions are essential in stabilizing the binding pocket. For the synthetic ligands, the hydrogen-bonding contributions of the U6-C15-A29 triplet are significantly compromised, and the bound state resembles the apo state in several respects, including the disengagement of the C15-A14-A13 and A32-G33 base stacks. The bulkier synthetic ligands lead to significantly loosening of the binding pocket, including extrusion of the C15 nucleobase and a widening of the C15-C30 groove. Enhanced-sampling simulations further revealed that the cognate and synthetic ligands unbind in almost opposite directions. Our work offers new insight for designing riboswitch ligands.
Livestock as vectors of organic matter and nutrient loading in aquatic ecosystems in African savannas
Authors: Iteba Jacob O. , Hein Thomas , Singer Gabriel A. , Masese Frank O. 
Published: July 2021

AbstractPopulations of large wildlife have declined in many landscapes around the world, and have been replaced or displaced by livestock. The consequences of these changes on the transfer of organic matter (OM) and nutrients from terrestrial to aquatic ecosystems are not well understood. We used behavioural data, excretion and egestion rates and C: N: P stoichiometry of dung and urine of zebu cattle, to develop a metabolism-based estimate of loading rates of OM (dung), C, N and P into the Mara River, Kenya. We also directly measured the deposition of OM and urine by cattle into the river during watering. Per head, zebu cattle excrete and/or egest 25.6 g dry matter (DM, 99.6 g wet mass; metabolism) - 27.7 g DM (direct input) of OM, 16.0-21.8 g C, 5.9-9.6 g N, and 0.3-0.5 g P per day into the river. To replace loading rates OM of an individual hippopotamus by cattle, around 100 individuals will be needed, but much less for different elements. In parts of the investigated sub-catchments loading rates by cattle were equivalent to or higher than that of the hippopotamus. The patterns of increased suspended materials and nutrients as a result of livestock activity fit into historical findings on nutrients concentrations, dissolved organic carbon and other variables in agricultural and livestock areas in the Mara River basin. Changing these patterns of OM and nutrients transport and cycling are having significant effects on the structure and functioning of both terrestrial and aquatic ecosystems.
Entangling snakebite dynamics: the spatiotemporal role of rainfall on snake envenoming in Colombia
Authors: Bravo-Vega Carlos , Santos-Vega Mauricio , Cordovez Juan Manuel 
Published: July 2021

ABSTRACTThe role of climate forcing on the population dynamics of infectious diseases has typically been addressed via retrospective analyses of aggregated incidence records over whole political regions. A central question in epidemiology has been whether seasonal and interannual cycles are driven by climate variation, or instead generated by other factors such as poverty or underreporting. Here, we use process-based models to determine the role of rainfall in the dynamics of snakebite, which is one of the main neglected tropical diseases around the world. We combined space-time datasets of snakebite incidence and rainfall for Colombia in combination with stochastic epidemiological models and iterated filtering methods to show the response to rainfall forcing, specifically, modulating the encounter frequency with venomous snakes. We identified six zones with different rainfall patterns to demonstrate that the relationship between rainfall and snakebite incidence was heterogeneous. Rainfall only drives snakebite incidence in regions with marked dry seasons, where rainfall becomes the limiting resource. In addition, the encounter frequency also differs between regions, and it is higher in regions where Bothrops atrox can be found. Our results show how the heterogeneous spatial distribution of snakebite risk seasonality in the country may be related to important traits of venomous snakes’ natural history.SIGNIFICANCE STATEMENTThe association between seasonal climatic variables and diseases’ epidemiology has helped to understand disease burden under changing environments. For example, for several tropical zoonotic diseases rainfall has been identified as a critical covariate inducing incidence seasonality. Snakebite envenoming is a disease that affects mostly economically deprived populations, and the availability of treatment is scarce. However, the role of environmental factors on snakebite is still missing in the literature. We formulated an epidemiological model to quantify the role of rainfall on snakebite seasonality throughout Colombia. We found that rainfall has a significant effect on incidence in places with a marked dry season (Caribbean and Orinoco plains), but in areas without dry season (Amazonian basin and southwestern Colombia) incidence exhibits no seasonality. This study is the first epidemiological modeling approach to snakebite and underscores the importance of rainfall as the limiting resource in this system. Thus, it is important to consider the interaction between climate forcing and venomous snakes’ ecology as determinants of envenomation risk.
When Does Mutualism Offer a Competitive Advantage? A Game-Theoretic Analysis of Host-Host Competition in Mutualism
Authors: Halloway Abdel H. , Heath Katy D. , McNickle Gordon G. 
Published: July 2021

AbstractPlants due to their non-motile nature rely heavily on mutualistic interactions to obtain resources and carry out services. One key mutualism is the plant-microbial mutualism in which a plant trades away carbon to a microbial partner for nutrients like nitrogen and phosphorous. Plants show much variation in the use of this partnership from the individual level to entire lineages depending upon ecological, evolutionary, and environmental context. We sought to determine how this context dependency could result in the promotion, exclusion, or coexistence of the microbial mutualism by seeing if and when the partnership provided a competitive advantage to the plant. To that end, we created a simple 2 × 2 evolutionary game in which plants could either be a mutualist and pair with a microbe or a non-mutualist and forgo the partnership. This model included nutrients freely available to the plant, nutrients obtained only through mutualism with microbes, the cost of producing roots, the cost of trade with microbes, and the size of the local competitive neighborhood. Not surprisingly, we found that mutualism could offer a competitive advantage if its net benefit was positive. Coexistence between strategies is possible though due to competition between mutualists over the microbially obtained nutrient. In addition, the greater the size of the local competitive neighborhood, the greater the region of coexistence but only at the expense of mutualist fixation (non-mutualist fixation was unaffected). Our model, though simple, shows that plants can gain a competitive advantage from using a mutualism depending upon the context and points to basic experiments that can be done to verify the results.
Myonuclear maturation dynamics in aged and adult regenerating mouse skeletal muscle
Authors: Kurland Jesse V. , Van Deusen Ashleigh , Pawlikowski Brad , Hall Monica , Dalla Betta Nicole , Antwine Tiffany , Cutler Alicia C , Russell Alan , Allen Mary Ann , Dowell Robin , Olwin Bradley 
Published: July 2021

AbstractSkeletal muscle cells are multinucleated syncytial cells arising from cell fusion, yet despite sharing a common cytoplasm individual myonuclei express distinct transcriptional programs. Whether individual myonuclei acquire heterogenous transcriptional states via differences in their progenitors, during differentiation, or once their anatomical position is acquired, is not known. We performed transcriptome and pseudotime analysis of single myogenic nuclei from uninjured and post-injury murine skeletal muscle to assess when myonuclear heterogeneity is acquired. Two distinct progenitors contribute to myonuclei, one a non-myogenic fibroblast subtype, and skeletal muscle stem cells the other. Both progenitors enter a single pseudotime trajectory that bifurcates as myonuclei mature into two branches segregated by myosin isoform expression and metabolic profiles, suggesting transcriptional heterogeneity is acquired as myonuclei mature. In aged skeletal muscle myogenic progenitor expansion is perturbed and nuclei from aged muscle display distinct pseudotemporal kinetics compared to nuclei from young mice. In aged mice, the inferred myogenic differentiation trajectory is delayed, altering the distribution of myogenic nuclei in pseudotime, suggesting that altered transcriptional dynamics in nuclei in aged mice may drive age-associated muscle deficits and bias myonuclei towards acquiring oxidative metabolic profiles.