Biology subjects

Zhou, T.

Publications and source records attributed to Zhou, T..

At least 127 records · Page 7Linked to original sources

bioRxiv2023

High-throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF

The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil to human lungs. The pulmonary extracellular matrix (ECM) is increasingly recognized as an independent bioactive entity by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key insoluble ECM proteins.

systems biology↗

bioRxiv2023

Social complexity affects cognitive abilities but not brain structure in a Poecilid fish

Complex cognitive performance is suggested to be the out-turn of complex social life, allowing individuals to achieve higher fitness through sophisticated "Machiavellian" strategies. Although there is ample support for this concept, especially when comparing species, most of the evidence is correlative. Here we provide an experimental investigation of how group size and composition may affect brain and cognitive development in the guppy (Poecilia reticulata). For six months, we reared sexually mature female guppies in one of three different social treatments: (i) three female guppies; (ii) three female guppies mixed with three female splash tetras (Copella arnoldi), a species that co-occurs with the guppy in the wild; and (iii) six female guppies. We then tested the guppies performance in inhibitory control, associative learning and reversal learning tasks to evaluate their self-control, operant conditioning and cognitive flexibility capabilities. Afterwards, we estimated their brain size and the size of major brain regions using X-ray imaging technology. We found that individuals in larger groups of six individuals, in both same and mixed species treatments, outperformed individuals from the smaller groups of three guppies in reversal learning, with no apparent differences in the inhibitory control and associative learning tasks. This is rare evidence of how living in larger social groups improves cognitive flexibility, supporting that social pressures play an important role in shaping individual cognitive development. Interestingly, social manipulation had no apparent effect on brain morphology, but relatively larger telencephalons were associated with better individual performance in reversal learning. This suggests alternative mechanisms beyond brain region size enabled greater cognitive flexibility in individuals from larger groups.

animal behavior and cognition↗

bioRxiv2023

Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells

The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

genomics↗

bioRxiv2023

High throughput functional profiling of genes at intraocular pressure loci reveals distinct networks for glaucoma

INTRODUCTIONPrimary open angle glaucoma (POAG) is a leading cause of blindness globally. Characterised by progressive retinal ganglion cell degeneration, the precise pathogenesis remains unknown. Genome-wide association studies (GWAS) have uncovered many genetic variants associated with elevated intraocular pressure (IOP), one of the key risk factors for POAG. This study sought to investigate the morphological and transcriptional consequences of perturbation of key genes at IOP loci in trabecular meshwork cell (TMC); the cellular regulators of IOP. We aimed to identify genetic and morphological variation that can be attributed to TMC dysfunction and raised IOP in POAG. METHODS62 genes across 55 loci were knocked-out in a primary human TMC line. Each knockout group, including five non-targeting control groups, underwent single-cell RNA-sequencing (scRNA-seq) for differentially-expressed gene (DEG) analysis. Multiplexed fluorescent staining of key organelles, was coupled with high-throughput microscopy for single-cell morphological analysis using CellProfiler image analysis. RESULTSAcross many of the individual gene knockouts scRNA-seq highlighted genes relating to matrix metalloproteinases and interferon-induced proteins. Our work has prioritised genes at four loci of interest to identify gene knockouts that may contribute to the pathogenesis of POAG, including ANGPTL2, LMX1B, CAV1, and KREMEN1. Three genetic networks of gene knockouts with similar transcriptomic profiles were identified (ABO / CAV1 / MYOC, ANGPT2 / PKHD1 / TNS1 / TXNRD2, and CAPZA1 / KALRN / LMO7 / PLEKHA7 / GNB1L / TEX41), suggesting a synergistic function in trabecular meshwork cell physiology. TEK knockout caused significant upregulation of nuclear granularity on morphological analysis, whilst knockout of TRIOBP, TMCO1 and PLEKHA7 increased granularity and intensity of actin and the cell-membrane. CONCLUSIONHigh throughput analysis of cellular structure and function through multiplex fluorescent single-cell analysis and scRNA-seq assays enabled the direct study of genetic perturbations at the single-cell resolution. This work provides a framework for investigating the role of genes in the pathogenesis of glaucoma and heterogenous diseases with a strong genetic basis.

genetics↗

bioRxiv2023

Grand Biological Universe: Genome space geometry unravels looking for a single metric is likely to be futile in evolution

Understanding the differences between genomic sequences of different lives is crucial for biological classification and phylogeny. Here, we downloaded all the reliable sequences of the seven kingdoms and determined the dimensions of the genome space embedded in the Euclidean space, along with the corresponding Natural Metrics. The concept of the Grand Biological Universe is further proposed. In the grand universe, the convex hulls formed by the universes of seven kingdoms are mutually disjoint, and the convex hulls formed by different biological groups within each kingdom are mutually disjoint. This study provides a novel geometric perspective for studying molecular biology and also offers an accurate way for large-scale sequence comparison in a real-time manner. Most importantly, this study shows that, due to the space-time distortion in the biological genome space similar to Einsteins theory, it is futile to look for a single metric to measure different biological universes, as previous studies have done.

evolutionary biology↗

bioRxiv2023

The Rapidly Evolving X-linked miR-506 Family Finetunes Spermatogenesis to Enhance Sperm Competition

Despite rapid evolution across eutherian mammals, the X-linked miR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (Slitrk2 and Fmr1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked miR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernable defects, but simultaneous ablation of five clusters containing nineteen members of the miR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked miR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the miR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis. Significance StatementThe X-linked miR-506 family has rapidly evolved in mammals, but their physiological significance remains elusive. Given their abundant and preferential expression in the testis and sperm, these X-linked miRNAs likely play a functional role in spermatogenesis and/or early embryonic development. However, the deletion of either individual miRNA genes or all of the five miRNA clusters encoding 38 mature miRNAs did not cause major fertility defects in mice. When these mutant males were subjected to conditions resembling polyandrous mating, the mutant sperm were much less competitive than the wild-type sperm, rendering the mutant males "functionally sub-fertile". Our data suggest that the miR-506 family of miRNAs regulates sperm competition and the reproductive fitness of the male.

developmental biology↗

bioRxiv2023

Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells

The mechanisms underlying the ability of embryonic stem cells (ESCs) to rapidly activate lineage-specific genes during differentiation remain largely unknown. Through multiple CRISPR-activation screens, we discovered human ESCs have pre-established transcriptionally competent chromatin regions (CCRs) that support lineage-specific gene expression at levels comparable to differentiated cells. CCRs reside in the same topological domains as their target genes. They lack typical enhancer-associated histone modifications but show enriched occupancy of pluripotent transcription factors, DNA demethylation factors, and histone deacetylases. TET1 and QSER1 protect CCRs from excessive DNA methylation, while HDAC1 family members prevent premature activation. This "push and pull" feature resembles bivalent domains at developmental gene promoters but involves distinct molecular mechanisms. Our study provides new insights into pluripotency regulation and cellular plasticity in development and disease. One sentence summaryWe report a class of distal regulatory regions distinct from enhancers that confer human embryonic stem cells with the competence to rapidly activate the expression of lineage-specific genes.

developmental biology↗

bioRxiv2023

CHPF boosts proliferation and invasion of clear cell renal cell carcinoma

BackgroundClear cell renal cell carcinoma (ccRCC) is a malignant tumor most commonly seen in the urinary system, featuring quick progression, invasive behavior, frequent recrudesce, and bad prognosis, whereas Chondroitin polymerizing factor (CHPF) is an essential glycosyl transferase of biosynthesis involved chondroitin sulphate. But the relationship between the two has not been fully understood so far. The present research will probe into the relationship between CHPF and ccRCC. MethodsExplore the CHPF expression level in renal ccRCC tissues through bioinformatics analysis of The Cancer Genome Atlas (TCGA) and the real-time quantitative polymerase chain reaction detection system (qPCR); acquire relevant clinical data from the TCGA data-base and use Kaplan-Meier survival analysis to verify the relevance of CHPF expression to the clinical prognosis of ccRCC patients; then, effectively silence CHPF in ccRCC 786-O cells by a lentivirus-mediated approach; next, observe the effects of CHPF on tumor cell proliferation, cell cycle progression, and apoptosis. ResultsIn ccRCC tissues, CHPF expression has been significantly upregulated; the higher expression, the shorter survival of ccRCC patients. CHPF downregulation in the 786-O cell can effectively hold back the proliferation, apoptosis and cycle of cancer cells. ConclusionBased on the above results, we arrive at a conclusion that CHPF expression contributes markedly to the development of human ccRCC cells. Therefore, CHPF may act as a potential prognostic marker of ccRCC and provide a new target for ccRCC treatment. Simple SummaryChondroitin polymerizing factor (CHPF) is an important glycosyltransferase involved in the biosynthesis of chondroitin sulfate, which is thought to have some pro-carcinogenic effects. However, the role and mechanism of CHPF in clear cell renal cell carcinoma (ccRCC) have not been reported. The aim of this study was to investigate the relationship between CHPF and ccRCC. In this study, we found that CHPF was highly expressed in ccRCC and knocking out CHPF can greatly inhibit the proliferation and cell cycle progression of ccRCC and accelerate its apoptosis, suggesting that CHPF can predict the prognosis of ccRCC and a potential target for treatment.

genetics↗

bioRxiv2023

Functional interrogation of twenty type 2 diabetesassociated genes using isogenic hESC-derived β-like cells

Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined {beta}-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-{beta} cells from each knockout line. Analyses of T2D GWAS signals overlapping with HNF4A-dependent ATAC peaks identified a specific SNP as a likely causal variant. In addition, we performed integrative association analyses and identified four genes (CP, RNASE1, PCSK1N and GSTA2) associated with insulin production, and two genes (TAGLN3 and DHRS2) associated with sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental hESC line, to identify a single likely functional variant at each of 23 T2D GWAS signals.

genetics↗

bioRxiv2023

LIPUS attenuates knee joint capsule fibrosis and athrogenic contracture through the TGF-β1/Smad signaling pathway

As one of main causes of athrogenic contracture, joint capsule fibrosis which is described as a condition with excessive deposition of collagen components and extracellular matrix (ECM) in joint capsule, is a response to long-time immobilization. The purpose of this study was to explore the effect and the underlying mechanism of low-intensity pulsed ultrasound (LIPUS) in treating knee joint capsule fibrosis. A rabbit model of knee joint capsule fibrosis induced by 6w-immobilization was employed in this study. The degree of knee joint capsule fibrosis was assessed by measurement of arthrogenic contracture and Masson-staining. Furthermore, malondialdehyde (MDA) and superoxide dismutase (SOD) were measured to assess the level of reactive oxygen species (ROS). Apart from these, the activation of TGF-{beta}1/Smad signaling pathway was determined through western blot analysis contained TGF-{beta}1, Smad2, p-Smad2, Smad3, p-Smad3 and Smad4, and immunohistochemical staining for p-Smad2/3 positive cells. After 6 wk-immobilization, the degree of arthrogenic contracture and the collagen density were increased. Moreover, the activity of MDA was upregulated and the content of SOD was downregulated. Correspondingly, the TGF-{beta}1/Smad signaling pathway was significantly activated. After 2 wk-LIPUS treatment, the degree of arthrogenic contracture and the collagen density were lower than 2 wk-remobilizaiton. Relatively, the activity of MDA was decresed and the content of SOD was increased compared with 2 wk-remobilizaiton. Importantly,the TGF-{beta}1/Smad signaling pathway was significantly inhibited compared with 2 wk-remobilizaiton. Our findings thus conclude that high level ROS and hyperactive TGF-{beta}1/Smad signaling pathway might be one of the causes of knee joint capsule fibrosis induced by immobilization and LIPUS attenuated the severity of immobilization-induced knee joint capsule fibrosis through inhibition of the production of ROS and the activation of TGF-{beta}1/Smad signaling pathway. Our findings might provide a theoretical basis for knee joint capsule fibrosis after immobilization and provide the potential therapeutic target.

molecular biology↗

bioRxiv2023

Generation of human cerebral organoids with a structured outer subventricular zone

Mammalian outer radial glia (oRG) emerge as cortical progenitor cells that directly support the development of an enlarged outer subventricular zone (oSVZ) and, in turn, the expansion of the neocortex. The in vitro generation of oRG is essential to model and investigate the underlying mechanisms of human neocortical development and expansion. By activating the STAT3 pathway using LIF, which is not produced in guided cortical organoids, we developed a cerebral organoid differentiation method from human pluripotent stem cells (hPSCs) that recapitulates the expansion of a progenitor pool into the oSVZ. The structured oSVZ is composed of progenitor cells expressing specific oRG markers such as GFAP, LIFR, HOPX, which closely matches human oRG in vivo. In this microenvironment, cortical neurons showed faster maturation with enhanced metabolic and functional activity. Incorporation of hPSC-derived brain vascular LIF- producing pericytes in cerebral organoids mimicked the effects of LIF treatment. These data indicate that the cellular complexity of the cortical microenvironment, including cell-types of the brain vasculature, favors the appearance of oRG and provides a platform to routinely study oRG in hPSC-derived brain organoids.

developmental biology↗

bioRxiv2023

A maize lipid droplet-associated protein is modulated by a virus to promote viral multiplication and infection

Pathogen infection induces massive reprogramming of host primary metabolism. Lipid and fatty acid metabolism is generally disrupted by pathogens and co-opted for their proliferation. Lipid droplets (LDs) that play important roles in regulating cellular lipid metabolism are utilized by a variety of pathogens in mammalian cells. However, the function of LDs during pathogenic infection in plants remains unknown. We show here that infection by rice black streaked dwarf virus (RBSDV) affects the lipid metabolism of maize, which causes elevated accumulation of C18 polyunsaturated fatty acids (PUFAs) leading to viral proliferation and symptom development. Overexpression of one of the two novel LD-associated proteins (LDAPs) of maize (ZmLDAP1 and ZmLDAP2) induces LD clustering. The core capsid protein P8 of RBSDV interacts with ZmLDAP2 and prevents its degradation through the ubiquitin-proteasome system mediated by a UBX domain-containing protein, PUX10. In addition, silencing of the ZmLDAP2 down-regulates expression of fatty acid desaturase genes in maize, leading to a decrease in C18 PUFAs levels and suppression of RBSDV accumulation. Our findings reveal that the plant virus recruits LDAP to regulate cellular fatty acid metabolism to promote viral multiplication and infection. These results expand the knowledge of the LD functions and viral infection mechanism in plants. One Sentence SummaryRice black streaked dwarf virus recruits a lipid droplet-associated protein to regulate cellular fatty acid metabolism for promoting viral multiplication and infection.

pathology↗

bioRxiv2023

Deep Learning-based Identification of Intraocular Pressure-Associated Genes Influencing Trabecular Meshwork Cell and Organelle Morphology

PURPOSEThe exact pathogenesis of primary open-angle glaucoma (POAG) is poorly understood. Genome-wide association studies (GWAS) have recently uncovered many loci associated with variation in intraocular pressure (IOP); a crucial risk factor for POAG. Artificial intelligence (AI) can be used to interrogate the effect of specific genetic knockouts on the morphology of trabecular meshwork cells (TMCs), the regulatory cells of IOP. METHODSSixty-two genes at fifty-five loci associated with IOP variation were knocked out in primary TMC lines. All cells underwent high-throughput microscopy imaging after being stained with a five-channel fluorescent cell staining protocol. A convolutional neural network (CNN) was trained to distinguish between gene knockout and normal control cell images. The area under the receiver operator curve (AUC) metric was used to quantify morphological variation in gene knockouts to identify potential pathological perturbations. RESULTSCells where RALGPS1 had been perturbed demonstrated the greatest morphological variation from normal TMCs (AUC 0.851, SD 0.030), followed by LTBP2 (AUC 0.846, SD 0.029) and BCAS3 (AUC 0.845, SD 0.020). Of seven multi-gene loci, five had statistically significant differences in AUC (p<0.05) between genes, allowing for pathological gene prioritisation. The mitochondrial channel most frequently showed the greatest degree of morphological variation (33.9% of cell lines). CONCLUSIONSWe demonstrate a robust method for functionally interrogating genome-wide association signals using high-throughput microscopy and AI. Genetic variations inducing marked morphological variation can be readily identified, allowing for the gene-based dissection of loci associated with complex traits.

genetics↗

bioRxiv2023

Real-Time Quantification of Cell Mechanics and Functions by Double Resonator Piezoelectric Cytometry -Theory and Study of Cellular Adhesion of HUVECs

Cell mechanics is closely associated with cellular structure and function. However, the inability to measure both cellular force and viscoelasticity of statistically significant number of cells noninvasively remains a challenge for quantitative characterizations of various cellular functions and practical applications. Here a double resonator piezoelectric cytometry (DRPC), using AT and BT cut quartz crystals of the same frequency and surface morphology is developed to simultaneously quantify the cells-generated forces ({Delta}S) and viscoelastic moduli (G', G'') of a population of isolated single cells or cells with different degrees of cell-cell interactions in a non-invasive and real time manner. DRPC captures the dynamic mechanical parameters {Delta}S and G', G'' during the adhesions of human umbilical vein endothelial cells (HUVECs) under different ligand densities of adhesion molecules fibronectin or Arg-Gly-Asp (RGD) modified on the gold surfaces of 9 MHz AT and BT cut quartz crystals, and different seeding densities of HUVECs. It is found that both the ligand density and cell seeding density affect the magnitudes of {Delta}S and G', G'' and their correlations are revealed for the first time by DRPC. The validity of DRPC is further verified by mechanical changes of the cells in response to treatments with cytoskeleton regulators.

biophysics↗

bioRxiv2023

The Effect of Electrical Resonance in Neurons upon the Instability of Electrical Nerve Stimulations

Repetitive electrical nerve stimulation can induce a long-lasting perturbation of the axons membrane potential, resulting in unstable stimulus-response relationships. Despite being observed in electrophysiology, the precise mechanisms underlying stimulus-induced instability is still an open question due to the lack of a proper theoretical model. This study proposes a new method based on a Circuit-Probability theory to reveal the interlinkages between the electrical resonance of neurons and the instability of neural response. Supported by in vivo investigations, this new model predicts several key characteristics of stimulus-induced instability and proposes a stimulation method to minimize the instability. This model provides a powerful tool to improve our understanding of the interaction between the external electric field and the complexity of the biophysical characteristics of axons.

neuroscience↗

bioRxiv2023

Chloroquine induces eryptosis in P. falciparum-infected red blood cells and the release of extracellular vesicles with a unique protein profile

Malaria is a vector-borne parasitic disease that affects millions worldwide. In order to reach the objective, set by the World Health Organization to decrease the cases by 2030, antimalarial drugs with novel modes of action are required. Previously, a novel mechanism of action of chloroquine (CQ) was reported involving features of programmed cell death in the parasite, mainly characterized by calcium efflux from the digestive vacuole (DV) permeabilization. Increased intracellular calcium induces the suicidal death of erythrocytes also known as eryptosis. This study aimed to identify the hallmarks of eryptosis due to calcium redistribution and the downstream cellular effects during CQ treatment in iRBCs. Plasmodium falciparum 3D7 at mid-late trophozoites were used for the antimalarial drug treatment. Our results revealed increased phosphatidylserine (PS) exposure, cell shrinkage and membrane blebbing, delineating an eryptotic phenotype in the host RBC. Interestingly, the blebs on the surface of the iRBCs released to the extracellular milieu become extracellular vesicles (EVs) which are essential for intercellular communication due to their cargo of proteins, nucleic acids, lipids and metabolites. The proteomic characterization displayed 2 highly enriched protein clusters in EVs from CQ-treated iRBCs, the proteasome and ribosome. We demonstrated that this unique protein cargo is not associated with the parasite growth rate. Additionally, we found that these particular EVs might activate IFN signaling pathways mediated by IL-6 in THP-1-derived macrophages. Our findings shed new insights into a novel drug-induced cell death mechanism that targets the parasite and specific components of the infected host RBC. IMPORTANCEOur previous studies have shown that chloroquine (CQ) treatment in iRBCs triggers Plasmodium falciparum digestive vacuole (DV) membrane permeabilization leading to calcium redistribution. Interestingly, increased intracellular calcium concentration is the main inducer of the suicidal death of red blood cells (RBCs) called eryptosis. The present study shed new insights into a novel CQ-induced cell death mechanism that targets the parasite and the infected host RBC by inducing key phenotypic hallmarks of eryptosis: PS exposure, cell shrinkage and membrane blebbing. Moreover, the proteomic characterization of the blebs released to the extracellular milieu also known as extracellular vesicles (EVs) revealed a cargo highly enriched in ribosomal proteins and proteasome subunits relevant for host-parasite interactions. These findings highlight CQs effect on calcium homeostasis disruption in infected red blood cells (iRBCs) with cellular and immunological consequences of great significance for malaria pathogenesis and potential clinical implications.

cell biology↗

bioRxiv2023

Relationships between competition sprint cycling power and endurance power are high across ALL durations and energetic pathways

This study investigates associations between power at several durations to show inter- relationships of power across a range of durations in sprint track cyclists. The currently-accepted hypothesis peak power holds a near perfect relationship with sprint performance, and thus a near 1:1 slope with power at sprint durations up to 30-s, is tested. The equally well-accepted and complementary hypothesis there is no strong association with power over longer durations is also tested. 56 data sets from 27 cyclists (21 male, 6 female) provided maximal power for durations from 1-s to 20-min. Peak power values are compared to assess strength of correlation (R2), and any relationship (slope) across every level. R2 between 15-s - 30-s power and durations from 1-s to 20-min remained high (R2 [≥] 0.83). Despite current assumptions around 1-s power, our data shows this relationship is stronger around competition durations, and 1-s power also still shared strong relationships with longer durations out to 20-min. Slopes for relationships shorter durations were closer to a 1:1 relationship than longer durations, but closer to long- duration slopes than to a 1:1 line. The present analyses contradicts both well-accepted hypotheses, and the concept of peak power being a primary metric for sprint cycling, based on very strong relationships to power from durations commonly associated with oxidative energetic pathways, as well as short durations. This study shows the importance and potential of training durations from 1-s to 20-min over a preparation period to improve competition sprint cycling performance.

physiology↗

bioRxiv2022

GeneSegNet: A deep learning framework for cell segmentation by integrating gene expression and imaging

When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphological features of cells. We developed a deep-learning-based method, GeneSegNet, that integrates both gene expression and imaging information to perform cell segmentation. GeneSegNet also employs a recursive training strategy to deal with noisy training labels. We show that GeneSegNet significantly improves cell segmentation performances over existing methods that either ignore gene expression information or underutilize imaging information.

bioinformatics↗