bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian Multidimensional Nominal Response Model for Observer Study of Radiologists
Authors: Nishio Mizuho , Kobayashi Daigo , Matsuo Hidetoshi , Urase Yasuyo , Nishioka Eiko , Murakami Takamichi
Published: August 2022

Purpose

This study proposes a Bayesian multidimensional nominal response model (MD-NRM) to statistically analyze the nominal response of multiclass classifications.

Materials and methods

First, for MD-NRM, we extended the conventional nominal response model to achieve stable convergence of the Bayesian nominal response model and utilized multidimensional ability parameters. We then applied MD-NRM to a 3-class classification problem, where radiologists visually evaluated chest X-ray images and selected their diagnosis from one of the three classes. The classification problem consisted of 150 cases, and each of the six radiologists selected their diagnosis based on a visual evaluation of the images. Consequently, 900 (= 150×6) nominal responses were obtained. In MD-NRM, we assumed that the responses were determined by the softmax function, the ability of radiologists, and the difficulty of images. In addition, we assumed that the multidimensional ability of one radiologist were represented by a 3×3 matrix. The latent parameters of the MD-NRM (ability parameters of radiologists and difficulty parameters of images) were estimated from the 900 responses. To implement Bayesian MD-NRM and estimate the latent parameters, a probabilistic programming language (Stan, version 2.21.0) was used.

Results

For all parameters, the Rhat values were less than 1.10. This indicates that the latent parameters of the MD-NRM converged successfully.

Conclusion

The results show that it is possible to estimate the latent parameters (ability and difficulty parameters) of the MD-NRM using Stan. Our code for the implementation of the MD-NRM is available as open source.

Short Abstract

To statistically analyze the nominal response of multiclass classifications, this study proposes a Bayesian multidimensional nominal response model (MD-NRM). With MD-NRM, it is possible to statistically analyze the nominal response of multiclass classifications obtained by radiologists.
Tracking patient clusters over time enables to extract all the information available in the medico-administrative databases
Authors: Lambert Judith , Leutenegger Anne-Louise , Jannot Anne-Sophie , Baudot Anaïs
Published: August 2022

Context

Identifying clusters (i.e., subgroups) of patients from the analysis of medico-administrative databases is particularly important to better understand disease heterogeneity. However, the complexity of these databases, in particular due to the presence of truncated longitudinal data, requires adaptation of clustering approaches.

Objective

We propose here cluster-tracking approaches to identify clusters of patients from longitudinal data contained in medico-administrative databases.

Material and Methods

We first cluster patients at each age using either the Markov Cluster algorithm (MCL) from patient networks or Kmeans from raw data. We then track the identified clusters over ages to construct cluster-trajectories. We compared our novel approaches with three longitudinal clustering approaches by calculating the silhouette score. As a use-case, we analyzed antithrombotic drugs prescribed from 2008 to 2018 contained in the Échantillon Généraliste des Bénéficiaires (EGB), a French national cohort.

Results

Our cluster-tracking approaches allowed us to identify several cluster-trajectories having clinical significance. Silhouette score comparison between the different approaches reveals that the best score is obtained for the cluster-tracking approaches.

Conclusion

The cluster-tracking approaches are a novel and efficient alternative to identify patient clusters from medico-administrative databases by taking into account their specificities.
Loss of tristetraprolin activates NF-κB induced phenotypic plasticity and primes transition to lethal prostate cancer
Authors: Morel Katherine L. , Hamid Anis A. , Falcón Beatriz G. , Nanda Jagpreet S. , Linder Simon , Bergman Andries M. , Poel Henk van der , Hofland Ingrid , Bekers Elise M. , Trostel Shana , Wilkinson Scott , Ku Anson T. , Burkhart Deborah L. , Kim Minhyung , Kim Jina , Plummer Jasmine T. , You Sungyong , Sowalsky Adam G. , Zwart Wilbert , Sweeney Christopher J. , Ellis Leigh
Published: August 2022

Phenotypic plasticity is a hallmark of cancer and increasingly realized as a mechanism of resistance in androgen indifferent prostate tumors. It is critical to identify mechanisms and actionable targets driving phenotypic plasticity. Here, we report that loss of tristetraprolin (TTP, geneZFP36), an RNA binding protein that regulates mRNA stability increases NF-κB activation and is associated with higher rates of aggressive disease and early recurrence in primary prostate cancer (PCa). We examined the clinical and biological impact ofZFP36loss combined withPTENloss, a known driver of PCa. Combined loss ofPTENandZFP36expression was associated with increased risk of recurrence in multiple independent primary PCa cohorts, and significantly reduced overall survival and time to progression following castration in genetically engineered mouse models.ZFP36loss alters the cell state that is driven byPTENloss, demonstrated by positive enrichment of gene sets including EMT, inflammation, TNFα/NF-κB, IL6-JAK/STAT3.ZFP36loss also induces enrichment of multiple gene sets involved in cell migration, chemotaxis, and proliferation. Use of the NF-κB inhibitor dimethylaminoparthenolide induced significant therapeutic responses in tumors withPTENandZFP36co-loss and reversed castration resistance. This work identifies a novel molecular mechanism driving phenotypic plasticity and castration resistance through loss ofZFP36expression, that can be reversed by inhibition of NF-κB activity.
High Resolution Kinetic Characterization and Dynamic Mathematical Modeling of the RIG-I Signaling Pathway and the Antiviral Responses
Authors: Burkart Sandy S. , Schweinoch Darius , Frankish Jamie , Sparn Carola , Wüst Sandra , Urban Christian , Piras Antonio , Pichlmair Andreas , Willemsen Joschka , Kaderali Lars , Binder Marco
Published: August 2022

The pattern recognition receptor RIG-I is essential for the recognition of viral dsRNA and the activation of a cell-autonomous antiviral response. Upon stimulation, RIG-I triggers a signaling cascade leading to the expression of cytokines, most prominently type I and III interferons (IFNs). IFNs are secreted and signal in an auto- and paracrine manner to trigger the expression of a large variety of IFN-stimulated genes, which in concert establish an antiviral state of the cell. While the topology of this pathway has been studied quite intensively, the dynamics, particularly of the RIG-I-mediated IFN induction, is much less understood. Here, we employed electroporation-based transfection to synchronously activate the RIG-I signaling pathway, enabling us to characterize the kinetics and dynamics of cell-intrinsic innate immune signaling to virus infections. By employing an A549 IFNAR1/IFNLR deficient cell line, we could analyze the difference between the primary RIG-I signaling phase and the secondary signaling phase downstream of the IFN receptors. We further used our quantitative data to set up and calibrate a comprehensive dynamic mathematical model of the RIG-I and IFN signaling pathways. This model accurately predicts the kinetics of signaling events downstream of dsRNA recognition by RIG-I as well as the feedback and signal amplification by secreted IFN and JAK/STAT signaling. We have furthermore investigated the impact of various viral immune antagonists on the signaling dynamics experimentally, and we utilized the here described modelling approach to simulate and in silico study these critical virus-host interactions. Our work provides a comprehensive insight into the signaling events occurring early upon virus infection and opens up new avenues to study and disentangle the complexity of the host-virus interface.
Microglia and astrocytes differentially endocytose exosomes facilitating alpha-Synuclein endolysosomal sorting
Authors: Pantazopoulou M. , Alexaki A. , Lamprokostopoulou A. , Delis A. , Coens A. , Melki R. , Pagakis S.N. , Stefanis L. , Vekrellis K.
Published: August 2022

Exosomes have emerged as key players in cell-to-cell communication in both physiological and pathological processes in the Central Nervous System (CNS). Thus far, the intracellular pathways involved in uptake and trafficking of exosomes within different cell types of the brain (microglia and astrocytes) are poorly understood. In our study, the endocytic processes and subcellular sorting of exosomes were investigated in primary glial cells, particularly linked with the exosome-associated α-synuclein (α-syn) transmission. Mouse microglia and astrocytic primary cultures were incubated with DiI-stained mouse brain-derived exosomes. The internalization and trafficking pathways were analysed in cells treated with pharmacological reagents that block the major endocytic pathways. Brain-derived exosomes were internalized by both glial cell types; however, uptake was more efficient in microglia than in astrocytes. Colocalization of exosomes with early and late endocytic markers (Rab5, Lamp1) indicated that exosomes are sorted to endolysosomes for subsequent processing. Treatment with Cytochalasin D, that blocks actin-dependent phagocytosis and/or macropinocytosis, inhibited exosome entry into glial cells, whereas treatment with inhibitors that strip off cholesterol from the plasma membrane, induced uptake, however differentially altered endosomal sorting. Exosome-associated fibrillar α-Syn was efficiently internalized and detected in Rab5- and Lamp1-positive compartments within microglia. Our study strongly suggests that exosomes enter glial cells through an actin network-dependent endocytic pathway and are sorted to endolysosomes for subsequent processing. Further, brain-derived exosomes are capable of mediating cell-to-glia transmission of pathological α-Syn that is also targeted to the endosomal pathway, suggesting a possible beneficial role in microglia-mediated clearance of toxic protein aggregates, present in numerous neurodegenerative diseases.
Antiretroviral treatment reveals a novel role for lysosomes in oligodendrocyte maturation
Authors: Festa Lindsay K. , Clyde Abigail E. , Long Caela C. , Roth Lindsay M. , Grinspan Judith B. , Jordan-Sciutto Kelly L.
Published: August 2022

White matter deficits are a common neuropathologic finding in neurologic disorders, including HIV-associated neurocognitive disorders (HAND). In HAND, the persistence of white matter alterations despite suppressive antiretroviral (ARV) therapy suggests that ARVs may be directly contributing to these impairments. Here, we report that a frontline ARV, bictegravir (BIC), significantly attenuates remyelination following cuprizone-mediated demyelination, a model that recapitulates acute demyelination, but has no impact on already formed mature myelin. Mechanistic studies in vitro revealed that treatment with BIC leads to significant decrease in mature oligodendrocytes accompanied by lysosomal de-acidification and impairment of lysosomal degradative capacity with no alterations in lysosomal membrane permeability or total lysosome number. Activation of the endolysosomal cation channel TRPML1 prevents both lysosomal de-acidification and impairment of oligodendrocyte differentiation by BIC. Lastly, we show that de-acidification of lysosomes by compounds that raise lysosomal pH is sufficient to prevent maturation of oligodendrocytes. Overall, this study has uncovered a critical role for lysosomal acidification in modulating oligodendrocyte function and has implications for neurologic diseases characterized by lysosomal dysfunction and white matter abnormalities.

Table of Contents

Main Points

The antiretroviral, bictegravir, inhibited remyelination through OPC differentiation blockade and had no effect on mature myelin

Bictegravir inhibits oligodendrocyte differentiation through de-acidification of lysosomes and this was prevented via activation of the lysosomal channel TRPML1

De-acidification of lysosomes by other drugs (e.g. bafilomycin A) is sufficient to inhibit oligodendrocyte maturation

Table of Contents Image
Diverse responses among wild banana species to vapour pressure deficit, a solution for drought tolerance breeding?
Authors: Eyland David , Gambart Clara , Swennen Rony , Carpentier Sebastien
Published: August 2022

1

The predicted rise in global temperature is not only affecting plant functioning directly, but is also increasing air vapour pressure deficit (VPD). The yield of banana is heavily affected by water deficit but so far breeding programs have never addressed the issue. A reduction in transpiration at high VPD has been suggested as a key drought tolerance breeding trait to avoid excessive water loss, hydraulic failure and to increase water use efficiency. In this study, stomatal and transpiration responses under increasing VPD at the leaf and whole-plant level of 8 wild banana (sub)species were evaluated, displaying significant differences in stomatal reactivity. Three different groups were identified under increasing VPD. M. acuminata spp. errans (group I), M. acuminata spp. zebrina (group II) and M. balbisiana (group II) showed the highest transpiration rate limitations to increasing VPD. In contrast to group I, group II only showed strong reductions at high VPD levels, limiting the cost of reduced photosynthesis and strongly increasing their water use efficiency. Group II genotypes thus show favourable responses for high water use efficiency in regions with high VPDs. This provides a basis for the identification of potential parent material within their wild populations for drought tolerance breeding.

Highlight

Wild banana species respond significantly different to water deficit caused by VPD increases and differ in the rate of stomatal reduction, revealing opportunities for drought tolerance breeding.
Culture of human nasal olfactory stem cells and their extracellular vesicles as advanced therapy medicinal products
Authors: Jaloux Charlotte , Bonnet Maxime , Vogtensperger Marie , Witters Marie , Veran Julie , Giraudo Laurent , Sabatier Florence , Michel Justin , Lacroix Romaric , Chareyre Corinne , Legré Regis , Guiraudie-Capraz Gaelle , Féron François
Published: August 2022

The olfactory ecto-mesenchymal stem cell (OE-MSC) are mesenchymal stem cells originating from the lamina propria of the nasal mucosa. They have neurogenic and immune-modulatory properties and showed therapeutic potential in animal models of spinal cord trauma, hearing loss, Parkinsons’s disease, amnesia, and peripheral nerve injury.

In this paper we designed a protocol that meet the requirements set by human health agencies to manufacture these stem cells for clinical applications.

Once purified, OE-MSCs can be usedper seor expanded in order to get the extracellular vesicles (EV) they secrete. A protocol for the extraction of these vesicles was validated and the EV from the OE-MSC were functionally tested on anin vitromodel.

Nasal mucosa biopsies from three donors were used to validate the manufacturing process of clinical grade OE-MSC. All stages were performed by expert staff of the cell therapy laboratory according to aseptic handling manipulations, requiring grade A laminar airflow. Enzymatic digestion provides more rapidly a high number of cells and is less likely to be contaminated. Foetal calf serum was replaced with human platelet lysate and allowed stronger cell proliferation, with the optimal percentage of platelet lysate being 10%. Cultivated OE-MSCs are sterile, highly proliferative (percentage of CFU-F progenitors was 15,5%) and their maintenance does not induce chromosomal rearrangement (karyotyping and chromosomal microarray analysis were normal). These cells express the usual phenotypic markers of OE-MSC. Purification of the EVs was performed with ultracentrifugation and size exclusion chromatography. Purified vesicles expressed the recognized markers of EVs (Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines) and promoted cell differentiation and neurite elongation in a model of neuroblastoma Neuro2a cell line.

We developed a safer and more efficient manufacturing process for clinical-grade olfactory stem cells, these cells can now be used in humans. A phase I clinical trial will begin soon.An efficient protocol for the purification of the OE-MSC EVs have been validated. These EVs exert neurogenic propertiesin vitro. More studies are needed to understand the exact mechanisms of action of these EVs and prove their efficacy and safety in animal models.
Ageing impairs protein leveraging in a sex-specific manner in Drosophila melanogaster
Authors: Rushby Helen J. , Andrews Zane B. , Piper Matthew D. W. , Mirth Christen K.
Published: August 2022

Modifying the relative proportions of macronutrients in an animal’s diet has noteworthy effects on its reproduction, lifelong health, and lifespan. Because of this, a wide range of animals carefully regulate their nutrient intake toward species and stage-specific targets. However, when animals are unable to reach their nutrient target from their existing food resources, they will compromise between overconsuming one nutrient and under-consuming the deficit nutrient. In this study, we used capillary feeding (CAFE) assays to understand the rules of compromise of adult fruit flies (Drosophila melanogaster) of different sex, mating status, and age when constrained to single diets. We found that young male and female D. melanogaster compromised by consuming more food on diets with low protein to carbohydrate (P:C) ratios compared to diets with high P:C ratios. Further, young male and female flies varied their carbohydrate intake significantly more than their protein intake, and female flies varied their carbohydrate intake significantly more than males. To test for effects of mating status on nutrient intake, we compared food intake of young mated and virgin females. We found that both virgin and mated females compromised by consuming more food on the low P:C diet compared to high P:C diets; however, mated females consumed more food than virgin females. As flies aged, they decreased their overall food intake and showed more modest alterations in their food intake across varying P:C diets. Further, mated females ceased to compromise for the protein deficit at a younger age than males. These findings provide new understanding about differences in protein leveraging behaviour across sexes, and how these behaviours change with age.

Highlights

Young fruit flies exhibit protein leveraging behaviour, varying their carbohydrate consumption more than protein

Young mated female flies vary their carbohydrate consumption significantly more than young males

Both virgin and mated female flies balance their nutrient intake similarly

As flies age, their ability to protein leverage declines, and this occurs faster in female flies
Connexin 43 Hemichannels Regulate Mitochondrial ATP Generation, Mobilization, and Mitochondrial Homeostasis against Oxidative Stress
Authors: Zhang Jingruo , Riquelme Manuel A. , Hua Rui , Acosta Francisca M. , Gu Sumin , Jiang Jean X.
Published: August 2022

Oxidative stress is a major risk factor that causes osteocyte cell death and bone loss. Prior studies primarily focus on the function of cell surface expressed Cx43 channels. Here, we reported a new role of mitochondrial Cx43 (mtCx43) and hemichannels (HCs) in modulating mitochondria homeostasis and function in bone osteocytes under oxidative stress. In osteocyte MLO-Y4 cells, the translocation of Cx43 to mitochondria was increased under H2O2-induced oxidative stress. H2O2increased the mtCx43 level accompanied by elevated mitochondrial Cx43 HC activity determined by dye uptake assay. Cx43 knockdown (KD) by CRISPR-Cas9 lentivirus system resulted in impairment of mitochondrial function, primarily manifested as decreased ATP production. Cx43 KD had reduced intracellular reactive oxidative species (ROS) levels and mitochondrial membrane potential. Additionally, live-cell imaging results demonstrated that the proton flux was dependent upon mtCx43 HCs because its activity was specifically inhibited by an antibody targeting Cx43 C-terminus. The co-localization and interaction of mtCx43 and ATP synthase subunit F (ATP5J2) were confirmed by fluorescence resonance energy transfer (FRET) and a protein pull-down assay. Together, our study suggests that mtCx43 hemichannels regulate mitochondrial ATP generation by mediating K+, H+, and ATP transfer across the mitochondrial inner membrane and the interaction with mitochondrial ATP synthase, leading to enhancing the protection capacity of osteocytes against oxidative insults.
Human endogenous retrovirus-R envelope is a host restriction factor against severe acute respiratory syndrome-coronavirus-2
Authors: Gupta Nidhi , Ansari Shabnam , Verma Rohit , Singh Oinam N , Yadav Mukesh Kumar , Binayke Akshay , Jakhar Kamini , Mani Shailendra , Awasthi Amit , Shalimar  , Nayak Baibaswata , Ranjith-Kumar C.T. , Surjit Milan
Published: August 2022

Coronavirus induced disease-19 (COVID-19), caused by the SARS-CoV-2 remains a major global health challenge. Human endogenous retroviruses (HERVs) represent retroviral elements that got integrated into the ancestral human genome. HERVs are important in development and diseases, including cancer, inflammation and viral infections. Here, we analyzed the expression of several HERVs in SARS-CoV-2 infected cells and observed increased activity of HERV-E, HERV-V, HERV-FRD, HERV-MER34, HERV-W and HERV-KHML2. In contrast, HERV-R-envelope was downregulated in cell-based models and COVID-19 patient PBMCs. HERV-R overexpression inhibited SARS-CoV-2 replication, suggesting its antiviral action. Further studies demonstrated the role of extracellular signal-regulated kinase (ERK) in regulating HERV-R antiviral activity. Cross-talk between the ERK and p38 MAPK controls HERV-R envelope synthesis, which in turn modulates the replication of SARS-CoV-2. These findings establish the importance of HERV-R envelope as a host restriction factor against SARS-CoV-2 and illustrate the advantage of integration and evolutionary maintenance of retroviral-elements in the human genome.
EDoF-Miniscope: pupil engineering for extended depth-of-field imaging in a fluorescence miniscope
Authors: Greene Joseph , Xue Yujia , Alido Jeffrey , Matlock Alex , Hu Guorong , Kiliç Kivilcim , Davison Ian , Tian Lei
Published: August 2022

Extended depth of field (EDoF) microscopy has emerged as a powerful solution to greatly increase the access into neuronal populations in table-top imaging platforms. Here, we present EDoF-Miniscope, which integrates an optimized thin and lightweight binary diffractive optical element (DOE) onto the gradient refractive index (GRIN) lens of a head-mounted fluorescence miniature microscope, i.e. “miniscope”. We achieve an alignment accuracy of 70 μm to allow a 2.8X depth-of-field extension between the twin foci. We optimize the phase profile across the whole back aperture through a genetic algorithm that considers the primary GRIN lens aberrations, optical property of the submersion media, and axial intensity loss from tissue scattering in a Fourier optics forward model. Compared to other computational miniscopes, our EDoF-Miniscope produces high-contrast signals that can be recovered by a simple algorithm and can successfully capture volumetrically distributed neuronal signals without significantly compromising the speed, signal-to-noise, signal-to-background, and maintain a comparable 0.9-μm lateral spatial resolution and the size and weight of the miniature platform. We demonstrate the robustness of EDoF-Miniscope against scattering by characterizing its performance in 5-μm and 10-μm beads embedded in scattering phantoms. We demonstrate that EDoF-Miniscope facilitates deeper interrogations of neuronal populations in a 100-μm thick mouse brain sample, as well as vessels in a mouse brain. Built from off-the-shelf components augmented by a customizable DOE, we expect that this low-cost EDoF-Miniscope may find utility in a wide range of neural recording applications.
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

The 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.

Importance

The 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

Spatial 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.

Teaser

Matrix-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

Minute 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

Background

Exposure 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.

Results

We 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.

Conclusion

Our 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

In 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

During 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

Introduction

Muscle 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.

Methodology

We 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).

Results

We 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.

Conclusions

We 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

The 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.
matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling
Authors: Davis Eric S. , Mu Wancen , Lee Stuart , Dozmorov Mikhail G. , Love Michael I. , Phanstiel Douglas H.
Published: August 2022

Deriving biological insights from genomic data commonly requires comparing attributes of selected genomic loci to a null set of loci. The selection of this null set is non trivial, as it requires careful consideration of potential covariates, a problem that is exacerbated by the non-uniform distribution of genomic features including genes, enhancers, and transcription factor binding sites. Propensity score-based covariate matching methods allow selection of null sets from a pool of possible items while controlling for multiple covariates; however, existing packages do not operate on genomic data classes and can be slow for large data sets making them difficult to integrate into genomic workflows. To address this, we developed matchRanges, a propensity score-based covariate matching method for the efficient and convenient generation of matched null ranges from a set of background ranges within the Bioconductor framework.
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

Single 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

The 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

Echinoderm 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.