bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity and Structural Variability of Bacterial Microbial Communities in Rhizocompartments of Desert Leguminous Plants
Authors: Zhou Ziyuan , Ding Guodong , Yu Minghan , Gao Guanglei , Wang Genzhu 
Published: January 2020

ABSTRACTBy assessing diversity variations of bacterial communities under different rhizocompartment types (i.e., roots, rhizosphere soil, root zone soil, and inter-shrub bulk soil), we explore the structural variability of bacterial communities in different root microenvironments under desert leguminous plant shrubs. Results will enable the influence of niche differentiation of plant roots and root soil on the structural stability of bacterial communities under three desert leguminous plant shrubs to be examined. High-throughput 16S rRNA genome sequencing was used to characterize diversity and structural differences of bacterial microbes in the rhizocompartments of three xeric leguminous plants. Results from this study confirm previous findings relating to niche differentiation in rhizocompartments under related shrubs, and they demonstrate that diversity and structural composition of bacterial communities have significant hierarchical differences across four rhizocompartment types under leguminous plant shrubs. Desert leguminous plants had significant effects on the enrichment and filtration of specific bacterial microbiomes across different rhizocompartments (P<0.05). The core bacterial microbiomes causing structure and composition variability of bacterial communities across different niches of desert leguminous plants are also identified. By investigating the influence of niches on the structural variability of soil bacterial communities with the differentiation of rhizocompartments under desert leguminous plant shrubs, we provide data support for the identification of dominant bacteria and future preparation of inocula, and provide a foundation for further study of the host plants-microbial interactions.IMPORTANCEColonization by plant communities make valued contribution to sand-fixing in poor ecological desert environments, thereby reducing the effects of wind erosion in these areas. Our study revealed that specific core bacterial microbiomes in under-shrub soil microbial communities had a significant hierarchical enrichment effect among rhizocompartments, and were filtered into roots. The root endophyte microbiomes thus formed had low abundance and diversity, but their structural variability was the highest. In addition, our data also verified that the rhizocompartments of under desert leguminous plant shrubs had a significant differentiation effect for the core bacterial microbiomes enriched and filtered by host plants, and that each rhizocompartment represented a unique niche of bacterial communities. Understanding the interactions between xeric shrubs and soil microbial communities is a fundamental step for describing desert soil ecosystems, which in turn can offer a microbe-associated reference for evaluating the restoration of desert vegetation.
When enemies do not become friends: Experimental evolution of heat-stress adaptation in a vertically transmitted parasite
Authors: Dusi Eike , Krenek Sascha , Petzoldt Thomas , Kaltz Oliver , Berendonk Thomas U. 
Published: January 2020

AbstractStrict vertical (parent-to-offspring) transmission of symbionts may be associated with benevolence and mutualism, because host reproduction and symbiont transmission are linked. Nonetheless, many such symbionts do reduce host fitness costs and the factors driving their evolution are unclear. Using microcosm populations ofCaedibacter taeniospiralis, a vertically transmitted bacterial symbiont of the protozoanParamecium tetraurelia, we investigated evolutionary change under permissive conditions (26°C) and under heat stress (32°C), over 150 host generations. We found evidence for symbiont adaptation to heat stress, involving increased infection persistence and, consequently, higher rates of vertical transmission. For certain genetic backgrounds, heat-stress adaptation was associated with higher proliferation of infected lines at 26°C, suggesting cost-free evolution of super-generalists. Despite a general decrease in symbiont virulence relative to ancestral strains, infected evolved lines still showed substantial reductions (>20%) in population growth. There was no sign of a temperature-specific reduction in virulence or protection of the host against heat stress. Our results show that obligately vertically transmitted symbionts can still qualify as ‘parasites’ and evolve adaptations that do not help their hosts. Long-term infection persistence might require additional mechanisms, such as the symbiont-mediated ’killer trait’ in this system, allowing the selective elimination of uninfected individuals in the population.
Plasmid diversity among genetically relatedKlebsiella pneumoniae blaKPC-2andblaKPC-3isolates collected in the Dutch national surveillance
Authors: Hendrickx Antoni P.A. , Landman Fabian , de Haan Angela , Borst Dyogo , Witteveen Sandra , van Santen Marga , van der Heide Han , Schouls Leo M. ,   the Dutch CPE surveillance Study Group
Published: January 2020

AbstractCarbapenemase-producingKlebsiella pneumoniaeemerged over the past decades as an important pathogen causing morbidity and mortality in hospitalized patients. For infection prevention and control, it is important to track the spread of bacterial strains in humans including the plasmids they contain. However, little is known concerning the plasmid repertoire amongK. pneumoniaestrains. Therefore, the major aim was to recapitulate the size, contents and diversity of the plasmids of genetically relatedK. pneumoniaestrains harboring the beta-lactamase geneblaKPC-2orblaKPC-3to determine their dissemination in the Netherlands and the former Dutch Caribbean islands from 2014-2019. Next-generation sequencing was combined with long-read third-generation sequencing to reconstruct 18 plasmids ofK. pneumoniae. wgMLST revealed five genetic clusters (termed KpnClusters) comprised ofK. pneumoniae blaKPC-2isolates and four clusters consisted ofblaKPC-3isolates. Each cluster was characterized by a distinct resistome and plasmidome. KpnCluster-019blaKPC-2isolates were found both in the Netherlands and the Caribbean islands.K. pneumoniae blaKPC-3isolates were found in the collection of the Netherlands. The 18 plasmids were mostly unrelated and varied betweenK. pneumoniae blaKPC-2andblaKPC-3clusters. However, the large and medium sized plasmids contained a variety of antibiotic resistance genes, transposons, insertion sequence elements, conjugal transfer systems, cation transport systems, toxin/antitoxin systems, and prophage-related sequence elements. The small plasmids carried genes implicated in virulence. Thus, implementing long-read plasmid sequencing analysis forK. pneumoniaesurveillance provided important insights in the success and understanding of transmission of a KpnCluster-019blaKPC-2strain between the Netherlands and the Caribbean.ImportanceCarbapenemase-producingKlebsiella pneumoniaehas spread globally and is of great concern for debilitated patients.K.pneumoniaeis notorious for spreading antimicrobial resistance genes by plasmids amongEnterobacterales. Combining short and long read sequencing enables reconstruction of plasmids containing antibiotic resistance genes, conjugation machinery, transposons, toxins and/or virulence determinants and thereby enhancing international pathogen surveillance.
Genome Sequences ofBurkholderia thailandensis strains E421, E426, and DW503
Authors: Mageeney Catherine M. , Sinha Anupama , Williams Kelly P. , Branda Steven S. 
Published: January 2020

AbstractWe present the draft genome sequences of threeBurkholderia thailandensisstrains: E421, E426, and DW503. E421 consists of 90 contigs of 6,639,935bp and 67.73% GC content. E426 consists of 106 contigs of 6,587,853bp and 67.73% GC content. DW503 consists of 102 contigs of 6,458,767bp and 67.64% GC content.
Swine ANP32A supports avian influenza virus polymerase
Authors: Peacock Thomas P. , Swann Olivia C. , Staller Ecco , Leung P. Brian , Goldhill Daniel H. , Zhou Hongbo , Long Jason S. , Barclay Wendy S. 
Published: January 2020

AbstractAvian influenza viruses occasionally infect and adapt to mammals, including humans. Swine are often described as ‘mixing vessels’, being susceptible to both avian and human origin viruses, which allows the emergence of novel reassortants, such as the precursor to the 2009 H1N1 pandemic. ANP32 proteins are host factors that act as influenza virus polymerase cofactors. In this study we describe how swine ANP32A, uniquely among the mammalian ANP32 proteins tested, supports some, albeit limited, activity of avian origin influenza virus polymerases. We further show that after the swine-origin influenza virus emerged in humans and caused the 2009 pandemic it evolved polymerase gene mutations that enabled it to more efficiently use human ANP32 proteins. We map the super pro-viral activity of swine ANP32A to a pair of amino acids, 106 and 156, in the LRR and central domains and show these mutations enhance binding to influenza virus trimeric polymerase. These findings help elucidate the molecular basis for the ‘mixing vessel’ trait of swine and further our understanding of the evolution and ecology of viruses in this host.
A Fob1 independent role for the Smc5/6 complex in the rDNA that modulates lifespan
Authors: Moradi-Fard Sarah , Mojumdar Aditya , Chan Megan , Harkness Troy A. A. , Cobb Jennifer A. 
Published: January 2020

SUMMARYThe ribosomal DNA (rDNA) inSaccharomyces cerevisiaeis in one tandem repeat array on Chromosome XII. Two spacer regions within each repetitive element, callednon-transcribedspacer1(NTS1) and NTS2, are important in nucleolar organization. Smc5/6 localizes to both NTS1 and NTS2 and is involved in the regulation of Sir2 and Cohibin binding at NTS1, whereas Fob1 and Sir2 are required for optimal binding of the complex to NTS1 and NTS2, respectively. We demonstrate that Smc5/6 functions in chromatin silencing at NTS1 independently of its role in homologous recombination (HR) when forks pause at the replication fork barrier (RFB). In contrast, when the complex does not localize to the rDNA innse3-1 mutants, the shortened lifespan correlates with NTS2 homeostasis independently ofFOB1status. Our data identify the importance of Smc5/6 integrity in NTS2 transcriptional silencing and repeat tethering, which in turn underscores rDNA stability and replicative lifespan.HighlightsSmc5/6 is important for transcriptional silencing in the rDNA.Smc5/6 tethers the rDNA array to the periphery.Transcriptional silencing of ncRNA at NTS1 and NTS2 is differentially regulated.Smc5/6 has a role in rDNA maintenance independent of HR processing at the RFB.Fob1-independent disruption of Smc5/6 at NTS2 leads to lifespan reduction.
Transcriptional analysis supports the expression of human snRNA variants and reveals U2 snRNA homeostasis by an abundant U2 variant
Authors: Kosmyna Brian , Gupta Varun , Query Charles 
Published: January 2020

SUMMARYAlthough expansion of snRNA genes in the human genome and sequence variation in expressed transcripts were both identified long ago, no study has comprehensively analyzed which genes are transcriptionally active. Here, we use comprehensive bioinformatic analysis to differentiate between similar or identical genomic loci to determine that 49 snRNA genes are actively transcribed. This greatly expands on previous observation of sequence variation within snRNA transcripts. Further analysis of U2 snRNA variants reveals sequence variation maintains conserved secondary structures, yet sensitizes these U2 snRNAs to modulation of assembly factors. Homeostasis of total U2 snRNA level is maintained by altering the ratio of canonical and an abundant U2 snRNA variant. Both canonical and variant snRNA promoters respond to MYC and appear differentially sensitive to increased MYC levels. Thus, we identify transcribed snRNA variants and the sequence variation within, and propose mechanisms of transcriptional and post-transcriptional regulation of snRNA levels and pre-mRNA splicing.HIGHLIGHTSChIP-seq of active promoters identifies uncharacterized snRNA genesTranscribed repetitive snRNA genes are distinguished from falsely-mapped snRNA lociU2 snRNA variants are sensitive to modulations in snRNP assemblyWidely expressed U2 snRNA variants provide homeostasis for total U2 snRNP levels
Cell to cell communication is an early event in glioblastoma
Authors: Portela Marta , Mitchell Teresa , Casas-Tintó Sergio 
Published: January 2020

SummaryGlioblastoma (GB) is the most aggressive and lethal tumour of the central nervous system (CNS). GB cells proliferate rapidly and display a network of ultra-long tumour microtubes (TMs) that mediate cell to cell communication. GB TMs infiltrate into the brain, enwrap neurons and facilitate the depletion of Wingless (Wg)/WNT from the neighbouring neurons. GB cells establish a positive feedback loop including Wg signalling upregulation that activates the JNK pathway and matrix metalloproteases (MMPs), in turn, these signals promote TMs infiltration, GB progression and neuronal synapse loss and degeneration. Thus, cellular and molecular signals other than primary mutations emerge as central players of GB. Here we describe the temporal organization of the events that occur in GB. We define the progressive activation of JNK pathway signalling mediated by Grindelwald (Grnd) receptor, is caused by the ligand Eiger (Egr)/TNFα produced by the healthy tissue. We propose that cellular interactions of GB with the rest of the brain is an early event that precedes GB proliferation and expansion. We conclude that non-autonomous signals facilitate GB progression and contribute to the complexity and versatility of these incurable tumours.
PAKC: A novel Panel of HLA class I Antigen presentation machinery Knockout Cells from the same genetic origin
Authors: de Waard Antonius A. , Verkerk Tamara , Jongsma Marlieke L.M. , Hoefakker Kelly , Sethumadhavan Sunesh , Gerke Carolin , Bliss Sophie , Janssen George M.C. , de Ru Arnoud H. , Claas Frans H.J. , Mulder Arend , Tampé Robert , van Veelen Peter A. , Halenius Anne , Spaapen Robbert M. 
Published: January 2020

AbstractWith the emergence of immunotherapies, the understanding of functional HLA class I antigen presentation to T cells is more relevant than ever. Current knowledge on antigen presentation is based on decades of research in a wide variety of cell types with varying antigen presentation machinery (APM) expression patterns, proteomes and HLA haplotypes. This diversity complicates the establishment of individual APM contributions to antigen generation, selection and presentation. Therefore, we generated a novel Panel of APM Knockout Cell lines (PAKC) from the same genetic origin. After CRISPR/Cas9 genome-editing of ten individual APM components in a human cell line, we derived clonal cell lines and confirmed their knockout status and phenotype. We then show how PAKC will accelerate research on the functional interplay between APM components and their role in antigen generation and presentation. This will lead to improved understanding of peptide-specific T cell responses in infection, cancer and autoimmunity.Key pointsWe generated a panel of cell lines to study HLA class I antigen presentationWe show how this will spark research in infection, tumor biology and autoimmunity
Differential effects of aquaporin-4 channel inhibition on BOLD fMRI and Diffusion fMRI responses in rat visual cortex
Authors: Komaki Yuji , Debacker Clément , Djemai Boucif , Ciobanu Luisa , Tsurugizawa Tomokazu , Le Bihan Denis 
Published: January 2020

AbstractThe contribution of astrocytes to the BOLD fMRI and DfMRI responses in visual cortex of mice following visual stimulation were investigated an aquaporin 4 (AQP4) channel blocker, TGN-020, acting as an astrocyte function perturbator. Under TGN-020 injection the amplitude of the BOLD fMRI response became significantly higher. In contrast no significant changes in the DfMRI responses and the electrophysiological responses were observed. Those results further confirm the implications of astrocytes in the neurovascular coupling mechanism underlying BOLD fMRI, while DfMRI relies on other, not astrocyte-mediated mechanisms.
SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription
Authors: Bergenholtz Seth , Yang Xiaoyu , Maliskova Lenka , Yun Li , Shen Yin 
Published: January 2020

AbstractAccurate RNA quantification at the single-cell level is critical for understanding the dynamics of gene expression and regulation across space and time. Single molecule FISH (smFISH), such as RNAscope, provides spatial and quantitative measurements of individual transcripts, therefore, can be used to explore differential gene expression among a heterogeneous cell population if combined with cell identify information. However, such analysis is not straightforward, and existing image analysis pipelines cannot integrate both RNA transcripts and cellular staining information to automatically output cell type-specific gene expression. We developed an efficient and customizable analysis method, Single-Molecule Automatic RNA Transcription Quantification (SMART-Q), to enable the analysis of gene transcripts in a cell type-specific manner. SMART-Q efficiently infers cell identity information from multiplexed immuno-staining and quantifies cell type-specific transcripts using a 3D Gaussian fitting algorithm. Furthermore, we have optimized SMART-Q for user experiences, such as flexible parameters specification, batch data outputs, and visualization of analysis results. SMART-Q meets the demands for efficient quantification of single-molecule RNA and can be widely used for cell type-specific RNA transcript analysis.
Comparison of Anorectal Function Measured using Wearable Digital Manometry and a High Resolution Manometry System
Authors: Attari Ali , Chey William D. , Baker Jason R. , Ashton-Miller James A. 
Published: January 2020

AbstractThere is a need for a lower cost manometry system for assessing anorectal function in primary and secondary care settings. We developed an index finger-based system (termed “digital manometry”) and tested it in healthy volunteers, patients with chronic constipation, and fecal incontinence. Anorectal pressures were measured in 16 participants with the digital manometry system and a 23-channel high-resolution anorectal manometry system. The results were compared using a Bland-Altman analysis at rest as well as during maximum squeeze and simulated defecation maneuvers. Myoelectric activity of the puborectalis muscle was also quantified simultaneously using the digital manometry system. The limits of agreement between the two methods were −7.1 ± 25.7 mmHg for anal sphincter resting pressure, 0.4 ± 23.0 mmHg for the anal sphincter pressure change during simulated defecation, −37.6 ± 50.9 mmHg for rectal pressure changes during simulated defecation, and −20.6 ± 172.6 mmHg for anal sphincter pressure during the maximum squeeze maneuver. The change in the puborectalis myoelectric activity was proportional to the anal sphincter pressure increment during a maximum squeeze maneuver (slope = 0.6, R2= 0.4). Digital manometry provided a similar evaluation of anorectal pressures and puborectalis myoelectric activity at an order of magnitude less cost than high-resolution manometry, and with a similar level of patient comfort. Digital Manometry provides a simple, inexpensive, point of service means of assessing anorectal function in patients with chronic constipation and fecal incontinence.
Information processing in biological molecular machines
Authors: Kurzynski M. , Chelminiak P. 
Published: January 2020

ABSTRACTBiological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics of conformational transitions which often manifests in fluctuating rates of the catalyzed processes and the presence of short-term memory resulting from the preference of certain conformations. For arbitrarily complex stochastic dynamics of protein machines, we proved the generalized fluctuation theorem predicting the possibility of reducing free energy dissipation at the expense of creating some information stored in memory. That this may be the case has been shown by interpreting results of computer simulations for a complex model network of stochastic transitions. The subject of the analysis was the time course of the catalyzed processes expressed by sequences of jumps at random moments of time. Since similar signals can be registered in the observation of real systems, all theses of the paper are open to experimental verification.STATEMENT OF SIGNIFICANCEThe transient utilization of memory for storing information turns out to be crucial for the movement of protein motors and the reason for most protein machines to operate as dimers or higher organized assemblies. From a broader physical point of view, the division of free energy into the operation and organization energies is worth emphasizing. Information can be assigned a physical meaning of a change in the value of both these functions of state.
Structural insights into the insecticidal Vip3A toxin ofBacillus thuringiensis
Authors: Jiang Kun , Zhang Yan , Chen Zhe , Wu Dalei , Cai Jun , Gao Xiang 
Published: January 2020

AbstractThe vegetative insecticidal proteins (Vips) secreted byBacillus thuringiensisare regarded as the new generation of insecticidal toxins because they have different insecticidal properties compared with commonly applied insecticidal crystal proteins (Cry toxins). Vip3A toxin, representing the vast majority of Vips, has been used commercially in transgenic crops and bio-insecticides. However, the lack of both structural information of Vip3A and a clear understanding of its insecticidal mechanism at the molecular level, limits its further development and broader application. Here we present the first crystal structure of the Vip3A toxin in an activated form. Since all members of this insecticidal protein family are highly conserved, the structure of Vip3A provides unique insight into the general domain architecture and protein fold of the Vip3 family of insecticidal toxins. Our structural analysis reveals a four-domain organization, featuring a potential membrane insertion region, a receptor binding domain, and two glycan binding domains of activated Vip3A. We further identify the specific glycan moieties recognized by Vip3A through a glycan array screen. Taken together, these findings provide insights into the mode of action of Vip3 family of insecticidal toxins, and will boost the development of Vip3 into more efficient bio-insecticides.