bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Host-Harbored Metabolic Susceptibility of Coronavirus Enables Broad-Spectrum Targeting
Authors: Fang Huan , Wang Yonglun , Liu Lu , Cheng Kunlun , Li Pei , Tan Ya , Hao Xingjie , Mei Miao , Xu Xinxuan , Yao Yuanhang , Zan Fuwen , Wu Linzhi , Zhu Yuangang , Xu Bolin , Huang Dong , Wang Chaolong , Tan Xu , Qian Zhaohui , Chen Xiao-Wei 
Published: December 2022

AbstractHost-based antivirals could offer broad-spectrum therapeutics and prophylactics against the constantly-mutating viruses including the currently-ravaging coronavirus, yet must target cellular vulnerabilities of viruses without grossly endangering the host. Here we show that the master lipid regulator SREBP1 couples the phospholipid scramblase TMEM41B to constitute a host “metabolism-to-manufacture” cascade that maximizes membrane supplies to support coronaviral genome replication, harboring biosynthetic enzymes including Lipin1 as druggable viral-specific-essential (VSE) host genes. Moreover, pharmacological inhibition of Lipin1, by a moonlight function of the widely-prescribed beta-blocker Propranolol, metabolically uncouples the SREBP1-TMEM41B cascade and consequently exhibits broad-spectrum antiviral effects against coronaviruses, Zika virus, and Dengue virus. The data implicate a metabolism-based antiviral strategy that is well tolerated by the host, and a potential broad-spectrum medication against current and future coronavirus diseases.
Whole-Genome Sequencing and Variant Discovery ofCitrus reticulata‘Kinnow’ from Pakistan
Authors: Jabeen Sadia , Saif Rashid , Haq Rukhama , Hayat Akbar , Naz Shagufta 
Published: December 2022

AbstractCitrus is a source of many nutritional and medicinal advantages, which is cultivated worldwide with major citrus groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all of its major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars such as Feutral’s Early, Dancy, Honey and Kinnow. The present study was designed to understand the genetic architecture of this unique variety ofCitrus reticulata -’Kinnow’. The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seededness, juice content, thickness of peel and its shelf-life. A total of 139,436,350 raw sequence reads using Illumina platform were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, a total of 3,503,033 SNPs, 176,949 MNPs, 323,287 INS and 333,083 DEL were identified using GATK4 variant calling pipeline againstCitrus clementinaas a reference genome. Further, g:Profiler bioinformatics tool was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1,009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts involved in cellular components inCitrus reticulata. In a nutshell, 18,153 high-impact variants and 216 genic-variants found in the current study which may be used for marker assisted breeding programs of ‘Kinnow’ to identify this particular variety among others and to propagate its valued traits to improve the contemporary citrus varieties as well.Graphical Abstract
The impact of sex and physical activity on the local immune response to muscle pain
Authors: Lesnak Joseph B. , Hayashi Kazuhiro , Plumb Ashley N. , Janowski Adam J. , Chimenti Michael S. , Sluka Kathleen A. 
Published: December 2022

AbstractInduction of muscle pain triggers a local immune response to produce pain and this mechanism may be sex and activity level dependent. The purpose of this study was to measure the immune system response in the muscle following induction of pain in sedentary and physically active mice. Muscle pain was produced via an activity-induced pain model using acidic saline combined with fatiguing muscle contractions. Prior to induction of muscle pain, mice (C57/BL6) were sedentary or physically active (24hr access to running wheel) for 8 weeks. The ipsilateral gastrocnemius was harvested 24hr after induction of muscle pain for RNA sequencing or flow cytometry. RNA sequencing revealed activation of several immune pathways in both sexes after induction of muscle pain, and these pathways were attenuated in physically active females. Uniquely in females, the antigen processing and presentation pathway with MHC II signaling was activated after induction of muscle pain; activation of this pathway was blocked by physical activity. Blockade of MHC II attenuated development of muscle hyperalgesia exclusively in females. Induction of muscle pain increased the number of macrophages and T-cells in the muscle in both sexes, measured by flow cytometry. In both sexes, the phenotype of macrophages shifted toward a pro-inflammatory state after induction of muscle pain in sedentary mice (M1+M1/2) but toward an anti-inflammatory state in physically active mice (M2+M0). Thus, induction of muscle pain activates the immune system with sex-specific differences in the transcriptome while physical activity attenuates immune response in females and alters macrophage phenotype in both sexes.
AutoGater: A Weakly Supervised Neural Network Model to Gate Cells in Flow Cytometric Analyses
Authors: Eslami Mohammed , Moseley Robert C. , Eramian Hamed , Bryce Daniel , Haase Steven B. 
Published: December 2022

AbstractFlow cytometry is a useful and efficient method for the rapid characterization of a cell population based on the optical and fluorescence properties of individual cells. Ideally, the cell population would consist of only healthy viable cells as dead cells can confound the analysis. Thus, separating out healthy cells from dying and dead cells, and any potential debris, is an important first step in analysis of flow cytometry data. While gating of debris can be conducted using measured optical properties, identifying dead and dying cells often requires utilizing fluorescent stains (e.g. Sytox, a nucleic acid stain that stains cells with compromised cell membranes) to identify cells that should be excluded from downstream analyses. These stains prolong the experimental preparation process and use a flow cytometer’s fluorescence channels that could otherwise be used to measure additional fluorescent markers within the cells (e.g. reporter proteins). Here we outline a stain-free method for identifying viable cells for downstream processing by gating cells that are dying or dead. AutoGater is a weakly supervised deep learning model that can separate healthy populations from unhealthy and dead populations using only light-scatter channels. In addition, AutoGater harmonizes different measurements of dead cells such as Sytox and CFUs.
An Integrated Approach to the Characterization of Immune Repertoires Using AIMS: An Automated Immune Molecule Separator
Authors: Boughter Christopher T. , Meier-Schellersheim Martin 
Published: December 2022

AbstractThe adaptive immune system employs an array of receptors designed to respond with high specificity to pathogens or molecular aberrations faced by the host organism. Binding of these receptors to molecular fragments - collectively referred to as antigens - initiates immune responses. These antigenic targets are recognized in their native state on the surfaces of pathogens by antibodies, whereas T cell receptors (TCR) recognize processed antigens as short peptides, presented on major histocompatibility complex (MHC) molecules. Recent research has led to a wealth of immune repertoire data that are key to interrogating the nature of these molecular interactions. However, existing tools for the analysis of these large datasets typically focus on molecular sets of a single type, forcing researchers to separately analyze strongly coupled sequences of interacting molecules. Here, we introduce a software package for the integrated analysis of immune repertoire data, capable of identifying distinct biophysical differences in isolated TCR, MHC, peptide, antibody, and antigen sequence data. This integrated analytical approach allows for direct comparisons across immune repertoire subsets and provides a starting point for the identification of key interaction hotspots in complementary receptor-antigen pairs. The software (AIMS - Automated Immune Molecule Separator) is freely available as an open access package in GUI or command-line form.
Micronutrient Optimization Using Design of Experiments Approach in Tissue Engineered Articular Cartilage for Production of Type II Collagen
Authors: Cruz Maria A. , Gonzalez Yamilet , Vélez Toro Javier A. , Karimzadeh Makan , Rubbo Anthony , Morris Lauren , Medam Ramapaada , Splawn Taylor , Archer Marilyn , Fernandes Russell J. , Dennis James E. , Kean Thomas J. 
Published: December 2022

ABSTRACTTissue Engineering of cartilage has been hampered by the inability of engineered tissue to express native levels of type II collagenin vitro. Inadequate levels of type II collagen are, in part, due to a failure to recapitulate the physiological environment in culture. In this study, we engineered primary rabbit chondrocytes to express a secreted reporter,GaussiaLuciferase, driven by the type II collagen promoter, and applied a Design of Experiments approach to assess chondrogenic differentiation in micronutrient-supplemented medium. Using a Response Surface Model, 240 combinations of micronutrients absent in standard chondrogenic differentiation medium, were screened and assessed for type II collagen expression. Five conditions predicted to produce the greatest Luciferase expression were selected for further study. Validation of these conditions in 3D aggregates identified an optimal condition for type II collagen expression. Engineered cartilage grown in this condition, showed a 170% increase in type II collagen expression (Day 22 Luminescence) and in Young’s tensile modulus compared to engineered cartilage in basal media alone. Collagen cross-linking analysis confirmed formation of type II-type : II collagen and type II-type : IX collagen cross-linked heteropolymeric fibrils, characteristic of mature native cartilage. Combining a Design of Experiments approach and secreted reporter cells in 3D aggregate culture enabled a high-throughput platform that can be used to identify more optimal physiological culture parameters for chondrogenesis.
Expression of mRNA encoding two gain-of-functioncyfip2variants associated with DEE65 results in spontaneous seizures inXenopus laevistadpoles
Authors: Panthi Sandesh , Szyszka Paul , Beck Caroline W. 
Published: December 2022

ABSTRACTDevelopmental and epileptic encephalopathies (DEE) are a genetically diverse group of disorders with similar early clinical presentations. DEE65 is caused byde novo, non-synonymous, gain-of-function mutations in CYFIP2. It presents in early infancy as hypotonia, epileptic spasms and global developmental delay. While modelling loss-of-function mutations can be done using knockdown or knockout techniques to reduce the amount of functional protein, modelling gain-of-function mutations requires different approaches. Here, we show that transient ectopic expression of the Arg87Cys pathogenic variant ofcyfip2mRNA inXenopus laevistadpoles resulted in increased seizure-related behaviours such as rapid darting and swimming in circles. In contrast, expression of a second pathological variant, Tyr108Cys, did not alter tadpole behaviour. Expression of either pathogenic variant resulted in spontaneous epileptic activity in the brain. For both variants, neuronal hyperactivity was reduced by treating the tadpole with 5 mM of the anti-seizure drug valproate (VPA). mRNA overexpression of gain-of-function variants inX. laevistadpoles may be useful both for understanding the aetiology of DEE and for pre-clinical drug testing.
MAPK/ERK Activation in Macrophages PromotesLeishmaniaInternalization and Pathogenesis
Authors: Barrie Umaru , Floyd Katherine , Datta Arani , Wetzel Dawn M. 
Published: December 2022

ABSTRACTThe obligate intracellular protozoan parasiteLeishmaniabinds several host cell receptors to trigger its uptake by phagocytic cells, ultimately resulting in visceral or cutaneous leishmaniasis. AfterLeishmaniaengages receptors on macrophages and other phagocytes, a series of signaling pathways in the host cell are activated during its internalization, which are critical for establishment and persistence ofLeishmaniainfection. Thus, preventingLeishmaniainternalization by phagocytes could be a novel therapeutic strategy for leishmaniasis. However, the host cellular machinery that mediates promastigote and amastigote uptake is not well understood. Here, using small molecule inhibitors of Mitogen-activated protein kinases/Extracellular signal regulated kinases (MAPK/ERK), we demonstrate that ERK1/2 mediatesLeishmania amazonensisuptake and (to a lesser extent) phagocytosis of beads by macrophages. We find that inhibition of MEK1/2 or ERK1/2 leads to inefficient amastigote uptake by macrophages. Moreover, using inhibitors and primary macrophages lacking spleen tyrosine kinase (SYK) or Abl family kinases, we show that SYK and Abl family kinases mediate Raf, MEK, and ERK1/2 activity and are necessary for efficient uptake. Finally, we demonstrate that trametinib, a MEK1/2 inhibitor used clinically to treat certain cancers, significantly reduces disease severity and parasite burden inLeishmania-infected mice, even if it is started significantly after lesions develop. Our results show that maximalLeishmaniainfection requires MAPK/ERK and highlight the potential for MAPK/ERK-mediated signaling pathways to be novel therapeutic targets for leishmaniasis.Lay summaryLeishmaniais a single-celled parasite that causes skin ulcers or a disseminated disease in humans. Our goal is to identify new drugs to treatLeishmaniainfection.Leishmaniamust live inside human immune cells to cause disease. IfLeishmaniais not able to enter human immune cells, it dies. Our studies demonstrate howLeishmaniainfection permits a set of proteins called MAP kinases to pass signals from one protein to the next within mammalian immune cells. The resulting signals allowLeishmaniato enter into these immune cells and survive within its host. Importantly, trametinib, a drug that prevents these signals from MAP kinases, decreases the development of skin ulcers when it is given to mice that are infected withLeishmania. Our findings suggest that leishmaniasis could be treated with drugs that act on kinases found in humans rather than the parasites themselves.One sentence summaryAn Abl2-SYK-Raf-MEK-ERK pathway facilitatesLeishmaniauptake by phagocytic cells and promotes disease severity inLeishmania-infected mice.
A mechanical wave travels along a genetic guide to drive the formation of an epithelial furrow
Authors: Popkova Anna , Pagnotta Sophie , Rauzi Matteo 
Published: December 2022

ABSTRACTEpithelial furrowing is a morphogenetic process that is pivotal during embryo gastrulation, neurulation and the shaping of the animal body. A furrow often results from a fold that propagates along a line. How fold formation and propagation are initiated, driven and controlled is still poorly understood. To shed new light on this fundamental morphogenetic process, we study the formation of the cephalic furrow: a fold that runs along the dorsal-ventral axis of the embryo during earlyDrosophilagastrulation and the developmental role of which is still unknown. Here, we provide evidence of its function and show that the cephalic furrow is initiated by two groups of cells located on the left and right lateral sides of the embryo. These cellular clusters work as a pacemaker triggering a bi-directional morphogenetic wave powered by actomyosin contractions and sustained byde novomedial apex-to-apex cell adhesion. The Cartesian position of the pacemakers is under the cross-control of the embryo anterior-posterior and dorsal-ventral gene patterning systems. Thus, furrow initiation and propagation are driven by a mechanical trigger wave that travels under the control of a multidimensional genetic guide.
SARM1 detection in oligodendrocytes but not Schwann cells thoughsarm1/Sarm1deletion does not perturb CNS nor PNS myelination in zebrafish and mice
Authors: Fazal Shaline V. , Mutschler Clara , Chen Civia Z. , Turmaine Mark , Chen Chiung-Ya , Hsueh Yi-Ping , Loreto Andrea , Casillas-Bajo Angeles , Cabedo Hugo , Franklin Robin J.M. , Barker Roger A. , Monk Kelly R. , Steventon Benjamin J. , Coleman Michael P. , Gomez-Sanchez Jose A. , Arthur-Farraj Peter 
Published: December 2022

AbstractSARM1 is a central regulator of programmed axon death and is required to initiate axon self-destruction after traumatic and toxic insults to the nervous system. Abnormal activation of this axon degeneration pathway is increasingly recognized as a contributor to human neurological disease and SARM1 knockdown or inhibition has become an attractive therapeutic strategy to preserve axon loss in a variety of disorders of the peripheral and central nervous system. Despite this, it remains unknown whetherSarm1/SARM1 is present in myelinating glia and whether it plays a role in myelination in the PNS or CNS. It is important to answer these questions to understand whether future therapies inhibiting SARM1 function may have unintended deleterious impacts on myelination. Here we show thatSarm1mRNA is present in oligodendrocytes in zebrafish but only detectable at low levels in Schwann cells in both zebrafish and mice. We find SARM1 protein is readily detectable in murine oligodendrocytesin vitro and in vivoand activation of endogenous SARM1 in oligodendrocytes induces cell death. In contrast, SARM1 protein is not detectable in Schwann cells and satellite glia in the adult murine nervous system. Cultured Schwann cells contain negligible functional SARM1 and are insensitive to specific SARM1 activators. Using zebrafish and mouseSarm1mutants, we show that SARM1 is not required for initiation of myelination nor myelin sheath maintenance by oligodendrocytes and Schwann cells. Thus, strategies to inhibit SARM1 function in the nervous system to treat neurological disease are unlikely to perturb myelination in humans.Main PointsSARM1 protein is detectable in oligodendrocytes but not in Schwann cellsOligodendrocytes but not Schwann cells die in response to endogenous SARM1 activationCNS nor PNS myelination, in zebrafish and mice, is hindered by loss ofsarm1/Sarm1
FiNuTyper: an automated deep learning-based platform for simultaneous fiber and nucleus type analysis in human skeletal muscle
Authors: Lundquist August , Lázár Enikő , Han Nan Sophia , Emanuelsson Eric B , Reitzner Stefan M , Chapman Mark A , Alkass Kanar , Druid Henrik , Petri Susanne , Sundberg Carl Johan , Bergmann Olaf 
Published: December 2022

SummaryWhile manual quantification is still considered the gold standard for skeletal muscle histological analysis, it is time-consuming and prone to investigator bias. We assembled an automated image analysis pipeline, FiNuTyper (Fiber and Nucleus Typer), from recently developed deep learning-based image segmentation methods, optimized for unbiased evaluation of fresh and postmortem human skeletal muscle. We validated and utilized SERCA1 and SERCA2 as type-specific myonucleus and myofiber markers. Parameters including myonuclei per fiber, myonuclear domain, central myonuclei per fiber, and grouped myofiber ratio were determined in a fiber type-specific manner, revealing a large degree of gender- and muscle-related heterogeneity. Our platform was also tested on pathological muscle tissue (ALS) and adapted for the detection of other resident cell types (leukocytes, satellite cells, capillary endothelium). In summary, we present an automated image analysis tool for the simultaneous quantification of myofiber and myonuclear types, to characterize the composition of healthy and diseased human skeletal muscle.HighlightsA deep learning-based automated platform for skeletal muscle microscopic analysisHigh-fidelity identification and characterization of myonuclei and myofibersValidation of SERCA1 and SERCA2 as markers for myofiber and myonuclear subtypesCharacterization of healthy and pathological human skeletal muscle tissue featuresAdaptations provided for studies on other resident cell types like satellite cellseTOC BlurbAn automated platform for unbiased analysis of skeletal muscle immunohistochemical images, focusing on type-specific myofiber-myonucleus relationships, facilitating high-throughput studies of healthy and diseased tissues.
Different hemispheric lateralization for periodicity and formant structure of vowels in the auditory cortex and its changes between childhood and adulthood
Authors: Orekhova E.V. , Fadeev K.A. , Goiaeva D.E. , Obukhova T.S. , Ovsiannikova T.M. , Prokofyev A.O. , Stroganova T.A. 
Published: December 2022

AbstractThe spectral formant structure and periodicity pitch are the major features that determine the identity of vowels and the characteristics of the speaker. However, very little is known about how the processing of these features in the auditory cortex changes during development. To address this question, we independently manipulated the periodicity and formant structure of vowels while measuring auditory cortex responses using MEG in children aged 7-12 years and adults. We analyzed the sustained negative shift of source current associated with these vowel properties, which was present in the auditory cortex in both age groups despite differences in the transient components of the auditory response. In adults, the sustained activation associated with formant structure was lateralized to the left hemisphere early in the auditory processing stream requiring neither attention nor semantic mapping. This lateralization was not yet established in children, in whom the right hemisphere contribution to formant processing was strong and decreased during or after puberty. In contrast to the formant structure, periodicity was associated with a greater response in the right hemisphere in both children and adults. These findings suggest that left-lateralization for the automatic processing of vowel formant structure emerges relatively late in ontogenesis and pose a serious challenge to current theories of hemispheric specialization for speech processing.
Disruption of the nuclear localization signal in RBM20 is causative in dilated cardiomyopathy
Authors: Zhang Yanghai , Gregorich Zachery R. , Wang Yujuan , Braz Camila Urbano , Zhang Jibin , Liu Yang , Liu Peiheng , Aori Nanyumuzi , Hacker Timothy A. , Granzier Henk , Guo Wei 
Published: December 2022

ABSTRACTHuman patients carrying genetic mutations in RNA binding motif 20 (RBM20) develop a clinically aggressive dilated cardiomyopathy (DCM). RBM20 is a splicing factor with two canonical domains, an RNA recognition motif (RRM) and an arginine-serine rich (RS) domain. RRM loss-of-function disrupts the splicing of RBM20 target transcripts and leads to systolic dysfunction without overt DCM, while mutations in the RS domain precipitate DCM. We show that mice lacking the RS domain (Rbm20ΔRS) manifest DCM with mis-splicing of RBM20 target transcripts. We found that RBM20 is mis-localized inRbm20ΔRSmice but not in mice lacking the RRM, which are also deficient in RBM20 splicing. We determine that the RS domain, not other domains including the RRM, is critical for RBM20 nuclear import and define the core nuclear localization signal (NLS) within this domain. Mutation analysis of phosphorylation sites within the RS domain indicate that phosphorylation is dispensable for RBM20 nuclear import. Collectively, our findings establish disruption of the NLS in RBM20 as a causative mechanism in DCM through nucleocytoplasmic transport.