Biology subjects

Wu, X.

Publications and source records attributed to Wu, X..

At least 397 records · Page 22Linked to original sources

bioRxiv2022

eEF2 improves dense connective tissue repair and healing outcome by regulating cellular death, autophagy, apoptosis, proliferation and migration

Outcomes following human dense connective tissue (DCT) repair are often variable and suboptimal, resulting in compromised function and development of chronic painful degenerative diseases. Moreover, biomarkers and mechanisms that guide good clinical outcomes after DCT injuries are mostly unknown. Here, we characterize the proteomic landscape of DCT repair following human tendon rupture and its association with long-term patient-reported outcome. Moreover, the regulatory mechanisms of relevant biomarkers were assessed partly by gene silencing experiments. A Mass-Spectrometry based proteomic approach quantified a large number (769) of proteins, including 51 differentially expressed proteins among 20 good versus 20 poor outcome patients. A novel biomarker, elongation factor-2 (eEF2) was identified as being strongly prognostic of the 1-year clinical outcome. Further bioinformatic and experimental investigation revealed that eEF2 positively regulated autophagy, cell proliferation and migration, as well as reduced cell death and apoptosis, leading to improved DCT repair and outcomes. Findings of eEF2 as novel prognostic biomarker could pave the way for new targeted treatments to improve healing outcomes after DCT injuries.

cell biology↗

bioRxiv2022

Mincle-GSDMD-mediated release of IL-1β containing small extracellular vesicles contributes to ethanol-induced liver injury

Background & AimsMacrophage inducible C-type lectin (Mincle) is expressed on Kupffer cells and senses ethanol-induced danger signals released from dying hepatocytes and promotes IL-1{beta} production. However, it remains unclear what and how ethanol-induced Mincle ligands activate downstream signaling events to mediate IL-1{beta} release and contribute to alcohol-associated liver disease (ALD). In this study, we investigated the association of circulating {beta}-glucosylceramide ({beta}-GluCer), an endogenous Mincle ligand, with severity of ALD and examined the mechanism by which {beta}-GluCer engages Mincle on Kupffer cells to release IL-1{beta} in the absence of cell death and exacerbates ALD. Approach and ResultsConcentrations of {beta}-GluCer were increased in serum of patients with severe AH and correlated with disease severity. Challenge of Kupffer cells with LPS and {beta}-GluCer induced formation of a Mincle and Gsdmd-dependent secretory complex containing chaperoned full-length GSDMD (Hsp90-CDC37-NEDD4) with polyubiquitinated pro-IL-1{beta} and components of the Casp8-NLRP3 inflammasome loaded as cargo in small extracellular vesicles (sEV). Gao-binge ethanol exposure to wild-type, but not Mincle-/- and Gsdmd-/-, mice increased release of IL-1{beta} containing sEVs from liver explant cultures. Myeloid-specific deletion of Gsdmd similarly decreased the formation of sEVs by liver explant cultures and protected mice from ethanol-induced liver injury. sEVs collected from ethanol-fed wild-type, but not Gsdmd-/-, mice promoted injury of cultured hepatocytes and, when injected into wild-type mice, aggravated Gao-binge ethanol-induced liver injury. Conclusion{beta}-GluCer functions as a DAMP activating Mincle-dependent GSDMD-mediated formation and release of IL-1{beta}-containing sEVs, which in turn exacerbate hepatocyte cell death and contribute to the pathogenesis of ALD.

immunology↗

bioRxiv2022

Resilient CD8+ T cells maintain a high cytotoxic capacity by balancing ROS via ME1 upregulation

Cytotoxic T lymphocytes (CTL) are indispensable in anti-tumor immunity. Although CTLs are prone to exhaustion in patients with advanced cancer, T cell resiliency explains the presence of tumor-reactive CTLs that are less exhausted, capable of cytolytic function, expansion, and rebound in response to immunotherapy to reject metastatic malignances. However, the features of resilient T cells have not been clearly defined. In this report, we demonstrate that peripheral CX3CR1+ CD8+ T cells with low mitochondrial membrane potential rebounded CTL function quickly after radiation therapy in patients with large tumor burden portraying their functional resiliency. Furthermore, CX3CR1+ CD8+ T cell with low, but not high, mitochondrial membrane potential are highly cytotoxic, accumulate less reactive oxygen species (ROS), and express more Malic enzyme 1 (ME1). ME1 overexpression increases ATP production in a glycolysisindependent manner while concurrently curtailing excessive ROS in activated CD8+ T cells; and expands CX3CR1+NKG7+ effector CD8+ T cells with enhanced cytotoxicity. Importantly, transfection of ME1 mRNA promotes tumoricidal activity in CD8+ T cells from patients with advanced cancers. Our study reveals a mechanism used by CTLs to balance excessive ROS via ME1 to maintain a metabolic and functional resiliency. Modification of ME1 expression in CTLs may be a novel method to improve the efficacy of cancer immunotherapy by preventing T cell exhaustion. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/517988v3_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@12e0f36org.highwire.dtl.DTLVardef@e8d412org.highwire.dtl.DTLVardef@1baf57eorg.highwire.dtl.DTLVardef@14b2b43_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICX3CR1+ and low Dy m identify functional resilient CD8+ T cells. C_LIO_LIResilient CD8+ T cells are highly cytotoxic and have less ROS. C_LIO_LIResilient CD8+ T cells express more ME1 that can balance extra ROS. C_LIO_LIME1 overexpression can promote CTL function of CD8+ T cells. C_LI

immunology↗

bioRxiv2022

The Neural Correlates of Arousal: The Ventral Posterolateral Nucleus-Global Transient Co-Activation

Arousal and awareness are two components of consciousness whose the neural mechanisms remain unclear. Spontaneous increases of global (brain-wide) blood-oxygenation-level-dependent (BOLD) signal has been found to be sensitive to changes in arousal. By contrasting BOLD datasets with altered arousal levels, we found that the activation of ventral posterolateral nucleus (VPL) decreased during transient increase in the global signal (top 17% data) in low arousal and awareness states (non-rapid eye movement sleep and anesthesia) as compared to wakefulness, and even in eye-closed (compared with eyes-open) in healthy awake-states, while this activation remained unchanged in patients with unresponsive wakefulness syndrome characterized by high arousal without awareness. These results demonstrate that co-activation of the VPL and global activity is critical to arousal, but not to awareness. One-Sentence SummaryThe VPL nucleus-global brain transient co-activation is related to physiological arousal but not to perceptual awareness.

neuroscience↗

bioRxiv2022

Mesenchymal stromal cells and alpha-1 antitrypsin have a strong synergy in modulating inflammation

Trauma, surgery, and infection can cause severe inflammation. Both dysregulated inflammation intensity and duration can lead to significant tissue injuries, organ dysfunction, mortality, and morbidity. Anti-inflammatory drugs such as steroids and immunosuppressants can dampen inflammation intensity, but they derail inflammation resolution, compromise normal immunity, and have significant adverse effects. The natural inflammation regulator mesenchymal stromal cells (MSCs) have high therapeutic potential because of their unique capabilities to mitigate inflammation intensity, enhance normal immunity, and accelerate inflammation resolution and tissue healing. Furthermore, clinical studies have shown that MSCs are safe and effective. However, they are not potent enough, alone, to completely resolve severe inflammation and injuries. One approach to boost the potency of MSCs is to combine them with synergistic agents. We hypothesized that alpha-1 antitrypsin (A1AT), a plasma protein used clinically and having an excellent safety profile, was a promising candidate for synergism. This investigation examined the efficacy and synergy of MSCs and A1AT to mitigate inflammation and to promote resolution, using in vitro cell cultures and a mouse acute lung injury and inflammation model. We found that the combination of MSCs and A1AT was much more effective than each component alone in i) modulating cytokine releases and inflammatory pathways, ii) inhibiting reactive oxygen species (ROS) and neutrophil extracellular traps (NETs) production by neutrophils, iii) enhancing phagocytosis and, iv) promoting inflammation resolution, tissue healing, and animal survival. Our results support the combined use of MSCs and A1AT for managing severe, acute inflammation.

bioengineering↗

bioRxiv2022

Deep-learning based bioactive therapeutic peptides generation and screening

Many bioactive peptides demonstrated therapeutic effects over-complicated diseases, such as antiviral, antibacterial, anticancer, etc. Similar to the generating de novo chemical compounds, with the accumulated bioactive peptides as a training set, it is possible to generate abundant potential bioactive peptides with deep learning. Such techniques would be significant for drug development since peptides are much easier and cheaper to synthesize than compounds. However, there are very few deep learning-based peptide generating models. Here, we have created an LSTM model (named LSTM_Pep) to generate de novo peptides and finetune learning to generate de novo peptides with certain potential therapeutic effects. Remarkably, the Antimicrobial Peptide Database has fully utilized in this work to generate various kinds of potential active de novo peptide. We proposed a pipeline for screening those generated peptides for a given target, and use Main protease of SARS-COV-2 as concept-of-proof example. Moreover, we have developed a deep learning-based protein-peptide prediction model (named DeepPep) for fast screening the generated peptides for the given targets. Together with the generating model, we have demonstrated iteratively finetune training, generating and screening peptides for higher predicted binding affinity peptides can be achieved. Our work sheds light on to the development of deep learning-based methods and pipelines to effectively generating and getting bioactive peptides with a specific therapeutic effect, and showcases how artificial intelligence can help discover de novo bioactive peptides that can bind to a particular target.

bioinformatics↗

bioRxiv2022

Fibronectin improves the impaired calcium signaling and myofilament activation in diabetic cardiomyocytes

Ventricular remodeling is one of the primary adaptive mechanisms in response to long-term mechanical overload in diabetes. In addition to cardiomyocyte hypertrophy, alterations in noncardiomyocyte compartments [e.g. extracellular matrix (ECM)] are an essential process in the remodeling of ventricle during diabetes. Integrins that link the ECM and intracellular cytoskeleton function as mechanotransducers to translate the mechanical force to intracellular signals. We hypothesize that mechanotransduction mechanisms are altered in diabetic cardiomyopathy mouse hearts. To test this hypothesis, force and intracellular calcium ([Ca2+]i) measurements on papillary muscle fibers were investigated in adult mouse cardiomyocytes from normal (non-db) and type 2 diabetic (db/db) mice. In addition, atomic force microscopy (AFM) was used to measure adhesion force between integrin receptors and ECM protein fibronectin (FN) by quantifying the unbinding force required to break FN-cardiomyocytes (integrin) bonds. In db/db mice, the peak active force decreased at 71% or 73% while the peak of [Ca2+]i decreased at 64% and 68% at 1 Hz or 2 Hz. In the presence of the FN (35 nM), active force was increased significantly by 40-50% in db/db mice. Furthermore, increased active force in the presence of FN was associated with 26-42% increase in [Ca2+]i at all giving stimulations of 1 Hz and 2 Hz in db/db mice, respectively. The increased effects on force and [Ca2+]i caused by FN were greater in ventricular muscles from db/db mice than from non-db mice. The unbinding force between FN (2.7 M) coated AFM probes and cardiomyocyte in db/db was 52% higher than non-db (58.3 {+/-} 0.3 pN vs 38.6 {+/-} 0.9 pN. p < 0.05). The binding probability of FN-cardiomyocytes, calculated as number of force curves with adhesion / number of total force curves sampled, was significantly reduced by 30% in db/db cardiomyocytes when compared to normal. In addition, the cell stiffness, representing changes in Ca2+ signaling and cytoskeletal reorganization, was 19% increase in db/db cardiomyocytes. The presented data indicate that dynamic changes of the mechanical properties of integrin-ECM interactions may contribute to impaired intracellular Ca2+ signaling and myofilament activation in the diabetic cardiomyopathy.

pathology↗

bioRxiv2022

Decoding the Variant-to-Function Relationship for LIPA, a Risk Locus for CAD

Translating human genomic discoveries into mechanistic insights requires linking genetic variations to candidate genes and their causal functional phenotypes. Genome-wide association studies have consistently identified LIPA as a risk locus for coronary artery disease (CAD), with previous expression quantitative trait loci (eQTL) analyses prioritizing LIPA as a candidate causal gene. However, functional studies elucidating the causal variants, regulatory mechanisms, target cell types, and their causal impact on atherosclerosis have been lacking. To address this gap, we applied functional genomics and experimental mouse models to establish the variant-to-function relationship at the LIPA locus. Our findings show that CAD risk alleles in the LIPA locus increase LIPA expression and enzyme activity specifically in monocytes/macrophages by enhancing PU.1 binding to an intronic enhancer region that interacts with the LIPA promoter. In myeloid Lipa-overexpressing mice, we observed larger atherosclerotic lesions accompanied by altered macrophage function, including increased macrophage accumulation due to enhanced monocyte recruitment, reduced neutral lipid accumulation, and upregulation of integrin and extracellular matrix pathways. Our work establishes a direct causal link between LIPA risk alleles and increased monocyte/macrophage LIPA that exacerbates atherosclerosis, bridging human functional genomic evidence to the mechanistic understanding of CAD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=58 SRC="FIGDIR/small/516293v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@11ce287org.highwire.dtl.DTLVardef@15c201aorg.highwire.dtl.DTLVardef@13f90c9org.highwire.dtl.DTLVardef@3aa3be_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2022

Cortico-Striatal Beta-Oscillations as a Marker of Learned Reward Value

Single neuron correlates of reward value have been observed in brain regions along the cortico-striatal pathway including ventral striatum, orbital, and medial prefrontal cortex. Brain imaging studies in humans further validate these findings and suggest that value is represented in a network of brain regions opposed to a particular area. Neural activity oscillates at periodic frequencies to coordinate long-range communication in widespread, dynamic networks. To explore how oscillatory dynamics across brain regions may represent reward value, we measured local field potentials of male Long-Evans rats during three distinct behavioral tasks, each probing a different aspect of reward processing. Our goal was to use a data-driven approach to identify a common electrophysiology property associated with reward value. We found that reward-locked oscillations at beta frequencies, in both single units and local field potentials, were markers of positive reward valence. More importantly, Reward-locked beta-oscillations scaled with expected reward value on specific trial types and in a behaviorally relevant way across tasks. Oscillatory signatures of reward processing were observed throughout the cortico-striatal network including electrodes placed in orbitofrontal cortex, anterior insula, medial prefrontal cortex, ventral striatum, and amygdala. These data suggests that beta-oscillations reflect learned reward value in a distributed network, and this may serve as a stable and robust bio-marker for future studies.

animal behavior and cognition↗

bioRxiv2022

Identifying Patients with Cognitive Motor Dissociation Using Resting-state Temporal Stability

BackgroundUsing task-dependent neuroimaging techniques, recent studies discovered a fraction of patients with disorders of consciousness (DOC) who had no command-following behaviors but showed a clear sign of awareness, which was defined as cognitive motor dissociation (CMD). Although many efforts were made to identify the CMD, existing task-dependent approaches might fail when patients had multiple cognitive function (e.g., attention, memory) impairments, and thus lead to false-negative findings. However, recent advances in resting-state fMRI (rs-fMRI) analysis allow investigation of the dynamic change of spontaneous brain activity, which might be a powerful tool to test the patients cognitive functions, while its capacity in identifying CMD was unclear. MethodsThe rs-fMRI study included 119 participants from three independent research sites. A sliding-window approach was used to investigate the dynamic functional connectivity of the brain in two aspects: the global and regional temporal stability, which measures how stable the brain functional architecture is across time. The temporal stability was compared in the first dataset (36/16 DOC/controls), and then a Support Vector Machine (SVM) classifier was built to discriminate DOC patients from controls. Furthermore, the generalizability of the SVM classifier was tested in the second independent dataset (35/21 DOC/controls). Finally, the SVM classifier was applied to the third independent dataset where patients underwent an rs-fMRI and brain-computer interface assessment (4/7 CMD/potential non-CMD), to test its performance in identifying CMD. ResultsOur results showed that the global and regional temporal stability were impaired in DOC patients, especially in regions from the cingulo-opercular task control, default mode, fronto-parietal task control, and salience network. Using the temporal stability as features, the SVM model not only showed a good performance in the first dataset (accuracy = 90 %), but a good generalizability in the second dataset (accuracy = 82 %). Most importantly, the SVM model generalized well in identifying CMD in the third dataset (accuracy = 91 %). ConclusionThe current findings suggested that rs-fMRI could be a potential tool to assist in diagnosing CMD. Furthermore, the temporal stability investigated in this study also contributed to a deeper understanding of the neural mechanism of the consciousness.

neuroscience↗

bioRxiv2022

Coupled functional physiological phenotyping and simulation model to infer the transpiration sensitivity traits and its implications for transpiration ideotype design

As agricultural drought becomes more frequent worldwide, it is essential to improve crop productivity whilst reducing the water consumption to achieve a sustainable production. Plant transpiration rate and water use efficiency (WUE) collectively determine the yield performance, yet it is challenging to balance the two in breeding programs due to still insufficient mechanistic understanding of the traits. Here we demonstrate the feasibility and effectiveness of calculating dynamic and momentary WUE by coupling WUE model and the state-of-the-art functional physiological phenotyping (FPP). We also present the method of quantifying genotype-specific traits reflecting sensitivity of transpiration to radiation (STr-Rad) and vapor pressure deficit (STr-VPD), under evolving developmental stage and water availability. Using these methods, we revealed the genotypic difference of STr-Rad and STr-VPD in three watermelon accessions, the dramatic change in each of them across the drought treatment phases, and the quantitative impacts of them on dynamic WUE patterns. Based on our results and computational simulations, a general principle for transpiration ideotype design is proposed, which highlights the benefits of lowering STr-VPD to increase WUE and increasing STr-Rad to offset the decline of Tr. FPP-enabled phenomic selection will help screen for elite crops lines with desired transpiration sensitivities.

physiology↗

bioRxiv2022

Ribosome-rescuer PELO catalyzes the oligomeric assembly of NLR family proteins via activating their ATPase

NOD-like receptors (NLRs) are pattern recognition receptors for diverse innate immune responses. Self-oligomerization after engagement with a ligand was a generally accepted model for the activation of each NLR. We report here that a catalyzer is required for the self-oligomerization. Protein pelota homolog (PELO, Dom34 in yeast), a well-known surveillance factor in translational quality control/ribosome rescue, interacts with all cytosolic NLRs and activates their ATPase. In the case of flagellin-initiated NLRC4 inflammasome activation, flagellin-bound NAIP5 recruits the first NLRC4 and then PELO is required for correctly assembling the rest of NLRC4s into the NLRC4 complex one by one by activating the NLRC4 ATPase. Stoichiometric and functional data revealed that PELO cannot be a structural constituent of NLRC4 inflammasome but a powerful catalyzer for its assembly. The catalytic role of PELO in the activation of cytosolic NLRs is unexpected and may break new ground for future studies of NLR family members.

immunology↗

bioRxiv2022

A SI3-sigma; arch stabilizes cyanobacteria transcription initiation complex

Multi-subunit RNA polymerases (RNAPs) associate with initiation factors ({sigma} in bacteria) to start transcription. The {sigma} factors are responsible for recognizing and unwinding promoter DNA in all bacterial RNAPs. Here, we report two cryo-EM structures of cyanobacterial transcription initiation complexes at near-atomic resolutions. The structures show that cyanobacterial RNAP forms an SI3-{sigma} arch interaction between domain 2 of {sigma}A ({sigma}2) and the sequence insertion 3 (SI3) in the mobile catalytic domain Trigger Loop (TL). The SI3-{sigma} arch facilitates transcription initiation from promoters of different classes through sealing the main cleft and thereby stabilizing RNAP-promoter DNA open complex. Disruption of the SI3-{sigma} arch disturbs cyanobacteria growth and stress response. Our study reports the structure of cyanobacterial RNAP and unique mechanism for its transcription initiation. Our data suggest functional plasticity of SI3 and provide foundation for further research into cyanobacteria and chloroplasts transcription.

biochemistry↗

bioRxiv2022

Understanding water conservation vs. profligation traits in vegetable legumes through a physio-transcriptomic-functional approach

Vegetable soybean and cowpea are related warm-season legumes showing contrasting leaf water use behaviors under similar root drought stresses, whose mechanisms are not well understood. Here we conducted an integrative phenomic-transcriptomic study on the two crops grown in a feedback irrigation system that enabled precise control of soil water contents. Continuous transpiration rate monitoring demonstrated that cowpea used water more conservatively under earlier soil drought stages, but tended to maintain higher transpiration under prolonged drought. Interestingly, we observed a soybean-specific transpiration rate increase accompanied by phase shift under moderate soil drought. Time-series transcriptomic analysis suggested a dehydration avoidance mechanism of cowpea at early soil drought stage, in which the VuHAI3 and VuTIP2;3 genes were suggested to be involved. Multifactorial gene clustering analysis revealed different responsiveness of genes to drought, time of day and their interactions between the two crops, which involved species-dependent regulation of the core clock genes. Gene network analysis identified two co-expression modules each associated with transpiration rate in cowpea and soybean, including a pair of negatively-correlated modules between species. Module hub genes, including the ABA-degrading gene GmCYP707A4 and the trehalose-phosphatase/synthase gene VuTPS9 were identified. Inter-modular network analysis revealed putative co-players of the hub genes. Transgenic analyses verified the role of VuTPS9 in regulating transpiration rate under osmotic stresses. These findings propose that species-specific transcriptomic reprograming in leaves of the two crops suffering similar soil drought was not only a result of the different drought resistance level, but a cause of it.

plant biology↗

bioRxiv2022

Highly synchronized cortical circuit dynamics mediate spontaneous pain

Cortical neural dynamics mediate information processing for the cerebral cortex, implicated in fundamental biological processes, such as vision and olfaction, in addition to neurological and psychiatric diseases. Spontaneous pain is a key feature of human neuropathic pain. Whether spontaneous pain pushes cortical network into an aberrant state, and if so, whether it can be brought back to a normal operating range to ameliorate pain are unknown. Using a clinically relevant mouse model of neuropathic pain with robust spontaneous pain-like behavior, we report that orofacial spontaneous pain activated a specific area within the primary somatosensory cortex (S1), displaying synchronized neural dynamics revealed by intravital two-photon calcium imaging. This synchronization was underpinned by local GABAergic interneuron hypoactivity. Pain-induced cortical synchronization could be attenuated by manipulating local S1 networks or clinically effective pain therapies. Specifically, both chemogenetic inhibition of pain-related c-Fos-expressing neurons, and selective activation of GABAergic interneurons, significantly attenuated S1 synchronization. Clinically effective pain therapies including carbamazepine and nerve root decompression could also dampen S1 synchronization. More importantly, restoring a normal range of neural dynamics, through attenuating pain-induced S1 synchronization, alleviated pain-like behavior. These results suggest spontaneous pain pushes S1 regional network into a synchronized state, whereas reversal of this synchronization alleviates pain.

neuroscience↗

bioRxiv2022

High-throughput TCRB enrichment sequencing of human cord blood exhibited a distinct fetal T cell repertoire in the third trimester of pregnancy

Study questionWhat are the molecular characteristics during the maturation process of the human fetal immune system in the third trimester of pregnancy? Summary answerBoth the diversity and length of complementarity determining region 3 (CDR3s) in the fetal TCRB repertoire were less than those of adult CDR3s, and the fetal CDR3 length increased with gestation weeks in late pregnancy. What is known alreadyThe adaptive immune system recognizes various pathogens based on a large repertoire of T-cell receptors (TCR repertoire), but the maturation dynamics of the fetal TCR repertoire in the third trimester are largely unknown. The CDR3is the most diversified segment in the T-cell receptor {beta} chain (TCRB) that binds and recognizes the antigen. Study design, size, and durationThis was a basic research to assess the composing characteristics of TCRBs in core blood and the dynamic pattern with fetal development in the third trimester of pregnancy. Participants/materials, setting methodsHigh-throughput TCRB-enrichment sequencing was utilized to characterize the TCRB repertoire of cord blood at 24~38 weeks of gestational age (WGA) with nonpreterm fetuses and to investigate their difference compared with that of adult peripheral blood. Main results and the role of chanceCompared to the adult control, the fetal TCRB repertoire had a 4.8-fold lower number of unique CDR3s, a comparable Shannon diversity index (p=0.7387), a lower mean top clone rate (p < 0.001) and a constrictive top 1000 unique clone rates. Although all kinds of TCRBV and TCRBJ genes present in adult CDR3s were identified in fetuses, nearly half of these fragments showed a significant difference in usage. Moreover, the fetal TCRB repertoire held a shorter CDR3 length, and the CDR3 length showed a progressive increase with fetal development. Jensen-Shannon (JS) divergences of TCRBV and TCRBJ gene usage in dizygotic twins were much lower than those in unrelated pairs. In the parental-fetal pair, JS divergence of TCRBV gene usage was not obviously different, while that of TCRBJ gene usage was only slightly lower. Limitations, reasons for cautionThe sample size is limited due to the limited accessibility to cord blood in late pregnancy with healthy nonpreterm fetuses. Wider implications of the findingsOur findings reveal the unique properties of fetal TCRB repertoires in the third trimester, fill the gap in our understanding of the maturation process of prenatal fatal immunity, and deepen our understanding of the immunologically relevant problems in neonates. Study funding/competing interest(s)This work was supported by the National Natural Science Foundation of China (82171661) and Tianjin Municipal Science and Technology Special Funds for Enterprise Development (NO. 14ZXLJSY00320). The authors declare that they have no competing interests.

genetics↗

bioRxiv2022

Analysis of Body-Fin Cooperative Propulsion Mechanism of Koi Carp Using Pose Estimation

Advances in modern deep learning-based computer vision perception techniques have revolutionized animal movement research methods. These techniques have also opened up new avenues for studying fish swimming. To that end, we have developed a visual perception system based on pose estimation to analyze fish swimming. Our system can quantify fish motion by 3D fish pose estimation and dynamically visualize the motion data of marked keypoints. Our experimental results show that our system can accurately extract the motion characteristics of fish swimming, which analyze how fish bodies and fins work together during different swimming states. This research provides an innovative idea for studying fish swimming, which can be valuable in designing, developing, and optimizing modern underwater robots, especially multi-fin co-driven bionic robotic fish. The code and dataset are available at https://github.com/wux024/AdamPosePlug. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/507033v6_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1b0ebfaorg.highwire.dtl.DTLVardef@547222org.highwire.dtl.DTLVardef@112addorg.highwire.dtl.DTLVardef@1153407_HPS_FORMAT_FIGEXP M_FIG C_FIG

animal behavior and cognition↗

bioRxiv2022

Identifying Pathogen and Allele Type Simultaneously (IPATS) in a single well using droplet digital PCR

A combined host biomarker and pathogen diagnosis provides insight into disease progression risk and contributes to appropriate clinical decision-making regarding prevention and treatment. In preventive veterinary medicine, such combined diagnosis could improve risk-based livestock herd management. We developed a single-well based test for combined diagnosis of bovine leukemia virus (BLV) and bovine MHC (BoLA)-DRB3 alleles. A fourplex droplet digital PCR method targeting the BLV pol gene, BLV-susceptible DRB3*016:01 allele, resistant DRB3*009:02 allele, and housekeeping RPP30 gene (IPATS-BLV) successfully measured the percentage of BLV-infected cells and determined allele types precisely. Furthermore, it discriminated homozygous from heterozygous carriers. Using this method to determine the impact of carrying these alleles on the BLV proviral load (PVL), we found DRB3*009:02-carrying cattle could suppress the PVL to a low or undetectable level, even with the presence of a susceptible allele. Although the population of DRB3*016:01-carrying cattle showed significantly higher PVLs when compared with cattle carrying other alleles, their individual PVLs were highly variable. Because of the simplicity and speed of this single-well assay, IPATS could be a suitable platform for the combined diagnosis of host biomarkers and pathogens in a wide range of other systems.

microbiology↗