bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics ofStreptococcus oralisidentifies large scale homologous recombination and a genetic variant associated with infection
Authors: Joyce Luke R. , Youngblom Madison A. , Cormaty Harshini , Gartstein Evelyn , Barber Katie E. , Akins Ronda L. , Pepperell Caitlin S. , Palmer Kelli L. 
Published: August 2022

AbstractThe viridans group streptococci (VGS) are a large consortium of commensal streptococci that colonize the human body. Many species within this group are opportunistic pathogens causing bacteremia and infective endocarditis (IE), yet little is known about why some strains cause invasive disease. Identification of virulence determinants is complicated by the difficulty of distinguishing between the closely related species of this group. Here, we analyzed genomic data from VGS isolated from patient blood cultures with invasive infections and from oral swabs of healthy volunteers and determined the best performing methods for species identification. Using whole-genome sequence data, we characterized the population structure of a diverse sample ofStreptococcus oralisisolates and found evidence of frequent recombination. We used multiple genome-wide association study tools to identify candidate determinants of invasiveness. These tools gave consistent results, leading to the discovery of a single synonymous single nucleotide polymorphism (SNP) that was significantly associated with invasiveness. This SNP is within a previously undescribed gene that is conserved across the majority of VGS species. Using growth in the presence of human serum and a simulated infective endocarditis vegetation model, we were unable to identify a phenotype for the enriched allele in laboratory assays, suggesting a phenotype may be specific to natural infection. These data highlight the power of analyzing natural populations for gaining insight into pathogenicity, particularly for organisms with complex population structures like the VGS.ImportanceThe viridians group streptococci (VGS) are a large collection of closely related commensal streptococci, with many being opportunistic pathogens causing invasive diseases such as bacteremia and infective endocarditis. Little is known about virulence determinants in these species, and there is a distinct lack of genomic information available for the VGS. In this study, we collected VGS isolates from invasive infections and healthy volunteers and performed whole genome sequencing for a suite of downstream analyses. We focused on a diverse sample ofStreptococcus oralisgenomes and identified high rates of recombination in the population as well as a single genome variant highly enriched in invasive isolates. The variant lies within a previously uncharacterized gene,nrdM, which shares homology with the anaerobic ribonucleoside triphosphate reductase,nrdD, and is highly conserved among VGS. This work increases our knowledge of VGS genomics and indicates that differences in virulence potential amongS. oralisisolates is, at least in part, genetically determined.
Matrix-seq: An adjustable-resolution spatial transcriptomics via microfluidic matrix-based barcoding
Authors: Zhao Haifeng , Tian Geng , Hu Aihua 
Published: August 2022

AbstractSpatial transcriptomics technology complements the spatial information lost in single-cell RNA sequencing, which enables visualization and quantitative analysis of transcriptomics of cells in tissue sections. Although this technology is a promising tool to study complex biological processes, its popularization is limited by cumbersome barcoding steps. We presented a microfluidics-based barcoding strategy called Matrix-seq, which gets rid of both precision instruments and the in situ indexing. The deterministic barcoding matrix is fabricated by the crossflow of Barcode-X and Barcode-Y. The overlapping areas (spot) formed deterministic barcoding primers (Barcode-X-Y) via the ligation reaction. Matrices with different spot size (ranging from 10 to 50 μm), which was decided by the width of microchannels, were fabricated and then applied to a mouse main olfactory bulb section and a mouse brain section. While maintaining high performance and resolution, this technology greatly reduces the technical threshold and cost of spatial barcoding. As a result, Matrix-seq can be rapidly applied in various fields including developmental biology, neuroscience and clinical pathology.TeaserMatrix-seq provides an orthogonal microchannel-based barcoding strategy for adjustable-resolution spatial transcriptomics.
Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii
Authors: Schultz Dylan L , Selberherr Evelyne , Stouthamer Corinne M , Doremus Matthew R , Kelly Suzanne E , Hunter Martha S , Schmitz-Esser Stephan 
Published: August 2022

AbstractMinute parasitoid wasps in the genus Encarsia are commonly used as biological pest control agents of whiteflies and armored scale insects in greenhouses or in the field. They are also a key host of the bacterial endosymbiont Cardinium hertigii which can cause a suite of reproductive manipulation phenotypes, including parthenogenesis, feminization, and cytoplasmic incompatibility; the last being most thoroughly studied in Encarsia suzannae. Despite their biological and economic importance, there are currently no published Encarsia genomes and only one public transcriptome. In this study, we applied a mapping-and-removal approach to eliminate known contaminants from previously-obtained Illumina sequencing data. We generated de novo transcriptome assemblies for both female and male E. suzannae which contain 45,986 and 54,762 final coding sequences, respectively. Benchmarking Single-Copy Orthologs (BUSCO) results indicate both assemblies are highly complete. Preliminary analyses revealed the presence of homologs of sex-determination genes characterized in other insects and putative venom proteins. These transcriptomes will be valuable tools to better understand the biology of Encarsia wasps and their evolutionary relatives. Furthermore, the separate male and female assemblies will be particularly useful references for studies involving insects of only one sex.
Acute IL-6 exposure triggers canonical IL-6R signalling in hiPSC microglia, but not neural progenitor cells
Authors: Couch Amalie C. M. , Solomon Shiden , Marrocu Alessia , Duarte Rodrigo , Sun Yiqing , Sichlinger Laura , Matuleviciute Rugile , Dutan Polit Lucia , Hanger Bjørn , Kordasti Shahram , Srivastava Deepak P. , Vernon Anthony C. 
Published: August 2022

AbstractBackgroundExposure to elevated interleukin (IL)-6 levels in utero is consistently associated with increased risk for psychiatric disorders with a putative neurodevelopmental origin, such as schizophrenia (SZ) and autism spectrum condition (ASC). Although rodent models provide causal evidence for this association, we lack a detailed understanding of the cellular and molecular mechanisms in human model systems. To close this gap, we characterised the response of hiPSC-derived microglia-like cells (MGL) and neural progenitor cells (NPCs) to IL-6 in monoculture.ResultsWe observed that human forebrain NPCs did not respond to acute IL-6 exposure in monoculture at both a protein and transcript level due to the absence of IL-6Ra expression and sIL-6Ra secretion. By contrast, acute IL-6 exposure resulted in STAT3 phosphorylation and increased IL-6, JMJD3 and IL-10 expression in MGL, confirming activation of canonical IL-6R signalling. Bulk RNAseq identified 156 upregulated genes (FDR <0.05) in MGL following acute IL-6 exposure, including IRF8, REL, HSPA1A/B and OXTR, which significantly overlapped with an upregulated gene set from post-mortem brain tissue from individuals with schizophrenia. Acute IL-6 stimulation significantly increased MGL motility suggestive of a gain of surveillance function, consistent with gene ontology pathways highlighted from the RNAseq data. Finally, MGLs displayed elevated CCL1, CXCL1, MIP-1A/B, IL-8, IL-13, IL-16, IL-18, MIF and Serpin-E1 secretion post 3h and 24h IL-6 exposure.ConclusionOur data provide evidence for cell specific effects of acute IL-6 exposure in a human model system and strongly suggest microglia-NPC co-culture models are required to study how IL-6 influences human cortical neural progenitor cell development in vitro.
Persistent effects of acute trauma on Pavlovian-to-instrumental transfer
Authors: Derman Rifka C. , Lattal K. Matthew 
Published: August 2022

AbstractIn humans, an acutely traumatic experience can lead to post-traumatic stress disorder (PTSD), which is often characterized by changes in anxiety and motivation months after trauma. There are few demonstrations of the persistent motivational effects of an acute stressor in rodent approaches to PTSD. In two experiments, we evaluated the persistent effects of a battery of footshocks in one context on appetitive Pavlovian conditioning, instrumental learning, and Pavlovian-to-instrumental transfer (PIT) in a different context. A battery of footshocks before appetitive training caused deficits in single-outcome PIT in male Long Evans rats. The same battery of footshocks after appetitive training, but before testing had little effect on single-outcome PIT, but there were some qualitative deficits. Although males showed more generalized fear from the aversive to the appetitive context compared to females, there were no effects of shock on sensory-specific PIT in male or female rats. In general females showed less evidence for sensory-specific PIT compared to males, who showed robust sensory-specific PIT, with clear extinction and spontaneous recovery of the sensory-specific PIT effect across test sessions. These findings show that (a) an acute trauma can have persistent effects on general motivational processes and (b) sensory-specific PIT is a useful approach for exploring sex differences in strategies for instrumental learning. We discuss implications for current approaches to stress and motivation in preclinical and clinical studies.
Toll-like receptor 4 signaling in osteoblasts is required for load-induced bone formation in mice
Authors: Rajpar Ibtesam , Kumar Gaurav , Fortina Paolo , Tomlinson Ryan E. 
Published: August 2022

ABSTRACTDuring skeletal development, expression of nerve growth factor (NGF) leads to the survival of afferent sensory nerves that express neurotrophic tyrosine kinase receptor type 1 (TrkA), the high affinity receptor for NGF. In adulthood, NGF is expressed by mature osteoblasts following mechanical loading and signals through TrkA receptors in resident sensory nerves to support load-induced bone formation. However, the regulation of NGF in osteoblasts following loading is not well understood. In this study, we sought to determine whether osteoblastic expression of toll-like receptor 4 (TLR4), a key receptor in the NF-κB signaling pathway, is required to initiate NGF-TrkA signaling to support skeletal adaptation following mechanical loading. First, we observed that NF-κB inhibition reduces NGF expression induced by axial forelimb compression. Moreover, we observed that TLR4+ periosteal cells are increased after mechanical loading. Therefore, we generated a novel mouse model in whichTlr4is selectively removed from the mature osteoblast lineage. AlthoughTlr4conditional knockout mice have normal skeletal mass and strength in adulthood, the loss of TLR4 signaling results in significant reductions in periosteal lamellar bone formation following axial forelimb compression. Furthermore, we demonstrated that the upregulation ofNgffollowing application of fluid shear stress to calvarial osteoblasts is significantly reduced by NF-κB and TLR4 inhibitors. Finally, RNA sequencing demonstrated that the deficits in load-induced bone formation in CKO mice can be attributed to dysregulated inflammatory signaling. In total, our study reveals a novel role for TLR4 in skeletal adaptation to mechanical loading in bone, which may enable new therapeutic strategies for diseases of low bone mass and provide new targets for musculoskeletal pain relief.
Internal calibration for opportunistic computed tomography muscle density analysis
Authors: Smith Ainsley C.J. , Tse Justin J. , Waungana Tadiwa H. , Bott Kirsten N. , Kuczynski Michael T. , Michalski Andrew S. , Boyd Steven K. , Manske Sarah L. 
Published: August 2022

AbstractIntroductionMuscle weakness can lead to reduced physical function and quality of life. Computed tomography (CT) can be used to assess muscle health through measures of muscle cross-sectional area and density loss associated with fat infiltration. However, there are limited opportunities to measure muscle density in clinically acquired CT scans because a density calibration phantom, allowing for the conversion of CT Hounsfield units into density, is typically not included within the field-of-view. For bone density analysis, internal density calibration methods use regions of interest within the scan field-of-view to derive the relationship between Hounsfield units and bone density, but these methods have yet to be adapted for muscle density analysis. The objective of this study was to design and validate a CT internal calibration method for muscle density analysis.MethodologyWe CT scanned 10 bovine muscle samples using two scan protocols and five scan positions within the scanner bore. The scans were calibrated using internal calibration and a reference phantom. We tested combinations of internal calibration regions of interest (e.g., air, blood, bone, muscle, adipose).ResultsWe found that the internal calibration method using two regions of interest, air and adipose or blood, yielded accurate muscle density values (< 1% error) when compared with the reference phantom. The muscle density values derived from the internal and reference phantom calibration methods were highly correlated (R2 > 0.99). The coefficient of variation for muscle density across two scan protocols and five scan positions was significantly lower for internal calibration (mean = 0.33%) than for Hounsfield units (mean = 6.52%). There was no difference between coefficient of variation for the internal calibration and reference phantom methods.ConclusionsWe have developed an internal calibration method to produce accurate and reliable muscle density measures from opportunistic computed tomography images without the need for calibration phantoms.
Dynamics and mechanisms of ERK activation after different protocols that induce long-term facilitation in Aplysia
Authors: Zhang Yili , Liu Rong-Yu , Smolen Paul , Cleary Leonard J. , Byrne John H. 
Published: August 2022

AbstractThe mitogen-activated protein kinase (MAPK) isoform extracellular signal–regulated kinase (ERK) is a key kinase involved in the induction of long-term synaptic facilitation (LTF) of the Aplysia sensorimotor synapse. Therefore, elucidating the dynamics of ERK activation after LTF-inducing protocols is critical for understanding the mechanisms underlying neuronal and synaptic plasticity. ERK activation has rich dynamic features. After a single stimulus, activation peaks 45-minute later and declines rapidly, but after two stimuli spaced 45 min apart, activation persists (Kopec et al. 2015). However, little is known about possible changes in ERK activation for periods beyond 3 h. Given its key role in long-term learning, understanding the dynamics of ERK at 3 h and beyond might provide insights into new protocols that could enhance memory retention. Three different protocols that induce LTF were used to probe the dynamics of ERK activation. The first, termed the Standard protocol, consists of five 5-min pulses of serotonin (5-HT) with regular interstimulus intervals (ISIs) of 20 min. The second, termed the Enhanced protocol, consists of five pulses of 5-HT with irregular ISIs identified with the use of computer simulations. This protocol induces greater and longer-lasting LTF than the Standard protocol. A third protocol, termed the two-pulse protocol, consists of just two 5-min pulses of 5-HT with an ISI of 45 min. Immunofluorescence revealed complex patterns of ERK activation up to 24 h after 5-HT treatment. The Standard and two-pulse protocols led to an immediate increase in active, phosphorylated ERK (pERK), which decayed within 5 h post treatment. A second wave of increased pERK was detected at 18 h post treatment. This late phase was blocked by RpcAMP (an inhibitor of protein kinase A), and by TrkB Fc and TGF-β RII F antagonists. The latter two are chimeras that act via receptor sequestration. These results suggest that complex interactions among kinase pathways and growth factor cascades contribute to the late increase of ERK activity after different LTF-inducing protocols. Interestingly, ERK activity returned to basal levels 24 h after the Standard or two-pulse protocol, but remained elevated 24 h after the Enhanced protocol. This finding may help explain, in part, why the Enhanced protocol is superior to the Standard protocol in inducing long-lasting LTF.
SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C data
Authors: Lee Lindsay , Yu Miao , Li Xiaoqi , Zhu Chenxu , Zhang Yanxiao , Yu Hongyu , Ren Bing , Li Yun , Hu Ming 
Published: August 2022

AbstractSingle cell Hi-C (scHi-C) has been used to map genome organization in complex tissues. However, computational tools to detect dynamic chromatin contacts from scHi-C datasets in development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a computational pipeline to identify differential chromatin contacts (DCCs) between two scHi-C datasets. Compared to methods designed for bulk Hi-C data, SnapHiC-D detects DCCs with high sensitivity and accuracy. We used SnapHiC-D to identify celltype-specific chromatin contacts at 10 kilobase resolution in mouse hippocampal and human prefrontal cortical tissues, and demonstrated that DCCs detected in the cortical and hippocampal cell types are generally correlated with cell-type-specific gene expression patterns and epigenomic features.
F-actin-rich territories coordinate apoptosome assembly and caspase activation during intrinsic apoptosis
Authors: King Virginia L , Campellone Kenneth G 
Published: August 2022

ABSTRACTThe actin cytoskeleton is a ubiquitous participant in cellular functions that maintain viability, but how it controls programmed cell death processes is not well understood. Here we show that in response to DNA damage, human cells form juxtanuclear F-actin-rich territories that coordinate the organized progression of apoptosome assembly to caspase activation. These cytoskeletal compartments are created by the actin nucleation factors JMY, WHAMM, and the Arp2/3 complex, and they exclude proteins that inhibit JMY and WHAMM activity. Within the territories, JMY localization overlaps with punctate structures containing the core apoptosome components cytochrome c and Apaf-1. The F-actin-rich areas also encompass initiator caspase-9 and clusters of a cleaved form of executioner caspase-3, while restricting accessibility of the caspase inhibitor XIAP. The clustering and potency of caspase-3 activation are positively regulated by the amount of actin polymerized by JMY and WHAMM. These results indicate that JMY-mediated actin reorganization functions in apoptotic signaling by coupling the biogenesis of apoptosomes to the localized processing of caspases.
Live imaging of echinoderm embryos to illuminate evo-devo
Authors: Barone Vanessa , Lyons Deirdre C. 
Published: August 2022

AbstractEchinoderm embryos have been model systems for cell and developmental biology for over 150 years, in good part because of their optical clarity. Discoveries that shaped our understanding of fertilization, cell division and cell differentiation were only possible because of the transparency of sea urchin eggs and embryos, which allowed direct observations of intracellular structures. More recently, live imaging of sea urchin embryos, coupled with fluorescence microscopy, has proven pivotal to uncovering mechanisms of epithelial to mesenchymal transition, cell migration and gastrulation. However, live imaging has mainly been performed on sea urchin embryos, while echinoderms include numerous experimentally tractable species that present interesting variation in key aspects of morphogenesis, including differences in embryo compaction and mechanisms of blastula formation. The study of such variation would allow us not only to understand how tissues are formed in echinoderms, but also to identify which changes in cell shape, cell-matrix and cell-cell contact formation are more likely to result in evolution of new embryonic shapes.Here we argue that adapting live imaging techniques to more echinoderm species will be fundamental to exploit such an evolutionary approach to the study of morphogenesis, as it will allow measuring differences in dynamic cellular behaviors - such as changes in cell shape and cell adhesion - between species. We briefly review existing methods for live imaging of echinoderm embryos and describe in detail how we adapted those methods to allow long-term live imaging of several species, namely the sea urchin Lytechinus pictus and the sea stars Patiria miniata and Patiriella regularis. We outline procedures to successfully label, mount and image early embryos for 10-16 hours, from cleavage stages to early blastula. We show that data obtained with these methods allows 3D segmentation and tracking of individual cells over time, the first step to analyze how cell shape and cell contact differ among species.The methods presented here can be easily adopted by most cell and developmental biology laboratories and adapted to successfully image early embryos of additional species, therefore broadening our understanding of the evolution of morphogenesis.
Chemoenzymatic Synthesis of Genetically-Encoded Multivalent Liquid N-glycan Arrays
Authors: Lin Chih-Lan , Sojitra Mirat , Carpenter Eric J. , Hayhoe Ellen Susanah , Sarkar Susmita , Volker Elizabeth Anne , Atrazhev Alexei , Lowary Todd L. , Macauley Matthew S. , Derda Ratmir 
Published: August 2022

AbstractA hallmark of cellular glycosylation is its chemical complexity and heterogeneity, which can be challenging to capture synthetically. Using chemoenzymatic synthesis on M13 phage, we produce a genetically-encoded liquid glycan array (LiGA) of biantennary complex type N-glycans. Ligation of azido-functionalized sialylglycosyl-asparagine derived from egg yolk to phage functionalized with 50–1000 copies of dibenzocyclooctyne produced divergent intermediate that can be trimmed by glycosidases and extended by glycosyltransferases to yield a library of phages with different N-glycans. Post-reaction analysis by MALDI-TOF MS provided a rigorous approach to confirm N-glycan structure and density, both of which were encoded in the bacteriophage DNA. The binding of this N-glycan LiGA by ten lectins, including CD22 or DC-SIGN expressed on live cells, uncovered an optimal structure/density combination for recognition. Injection of the LiGA into mice identified glycoconjugates with structures and avidity necessary for enrichment in specific organs. This work provides an unprecedented quantitative evaluation of the interaction of complex N-glycans with GBPs in vitro and in vivo.