Biology subjects

Zhang, D.

Publications and source records attributed to Zhang, D..

At least 307 records · Page 17Linked to original sources

bioRxiv2022

Mechanoreceptor signal convergence and transformation in the dorsal horn flexibly shape a diversity of outputs to the brain

The encoding of touch in the spinal cord dorsal horn (DH) and its influence on tactile representations in the brain are poorly understood. Using a range of mechanical stimuli applied to the skin, large scale in vivo electrophysiological recordings, and genetic manipulations, here we show that neurons in the mouse spinal cord DH receive convergent inputs from both low- and high-threshold mechanoreceptor subtypes and exhibit one of six functionally distinct mechanical response profiles. Genetic disruption of DH feedforward or feedback inhibitory motifs, comprised of interneurons with distinct mechanical response profiles, revealed an extensively interconnected DH network that enables dynamic, flexible tuning of postsynaptic dorsal column (PSDC) output neurons and dictates how neurons in primary somatosensory cortex respond to touch. Thus, mechanoreceptor subtype convergence and nonlinear transformations at the earliest stage of the somatosensory hierarchy shape how touch of the skin is represented in the brain.

neuroscience↗

bioRxiv2022

Identification of key molecules and biological processes in TCF21 treated tumor pericytes

Colorectal cancer has become a major public health problem in the US. Transcription factor 21 (TCF21) is reported to be silenced in colorectal cancer tissues. However, the mechanism of TCF21 in tumor pericytes is still unclear. In our study, we aim to identify the key biological processes and signaling pathways by analyzing the RNA-seq data. The GSE200064 was produced by the Illumina NovaSeq 6000 (Homo sapiens). The KEGG and GO analyses showed that MAPK signaling pathway and complement/coagulation cascades are the major changed signaling pathways in the progression of tumor pericytes with overexpression of TCF21. Moreover, we identified several interactive molecules including VEGFA, MMP2, CCL2, COL3A1, COL1A2, CXCL12, ELN, PDGFRB, VWF, and APOE. These findings may benefit the study of colorectal cancer treatment.

bioinformatics↗

bioRxiv2022

A transcriptional complex of FtMYB102 and FtbHLH4 coordinately regulates the accumulation of rutin in Fagopyrum tataricum

Tartary buckwheat is rich in flavonoids, which not only play an important role in plant-environment interaction, but are also beneficial to human health. Rutin is a therapeutic flavonol which is massively accumulated in Tartary buckwheat. It has been demonstrated that transcription factors control rutin biosynthesis. However, the transcriptional regulatory network of rutin is not fully clear. In this study, through transcriptome and target metabolomics, we validated the role of FtMYB102 and FtbHLH4 TFs at the different developmental stages of Tartary buckwheat. The elevated accumulation of rutin in the sprout appears to be closely associated with the expression of FtMYB102 and FtHLH4. Yeast two-hybrid, transient luciferase activity and co-immunoprecipitation demonstrated that FtMYB102 and FtbHLH4 can interact and form a transcriptional complex. Moreover, yeast one-hybrid showed that both FtMYB102 and FtbHLH4 directly bind to the promoter of chalcone isomerase (CHI), and they can coordinately induce CHI expression as shown by transient luciferase activity assay. Finally, we transferred the FtMYB102 and FtbHLH4 into the hairy roots of Tartary buckwheat and found that they both can promote the accumulation of rutin. Our results indicate that FtMYB102 and FtbHLH4 can form a transcriptional complex by inducing CHI expression to coordinately promote the accumulation of rutin.

plant biology↗

bioRxiv2022

MEIG1/PACRG associated and non-associated functions of axonemal dynein light intermediate polypeptide 1 (DNALI1) in mammalian spermatogenesis

Axonemal dynein light intermediate polypeptide 1 (DNALI1) was originally cloned from Chlamydomonas reinhardtii in an effort to find motor proteins essential for flagellar motility. Here we report that DNALI1 is a binding partner of parkin co-regulated gene 1 (PACRG), which forms a complex with meiosis expressed gene 1 (MEIG1) in the manchette, a transient and unique structure only present in the elongating spermatids and required for normal spermiogenesis of the male germ cell differentiation process. DNALI1 recruits the PACRG protein in transfected CHO cells, and also stabilizes PACRG in bacteria and transfected mammalian cells. The untagged DNALI1 could also be co-purified with His-tagged PACRG in the gel filtration assay. Immunofluorescence staining on isolated male germ cells revealed that DNALI1 was present in the manchette of elongating spermatids, and colocalized with PACRG in this structure. In Pacrg mutant mice, localization of DNALI1 in the manchette was not changed, suggesting that DNALI1 and PACRG form a complex in the manchette, with DNALI1 being an upstream molecule. Mice deficiency in DNALI1 specifically in male germ cells showed dramatically reduced sperm numbers and were infertile. In addition, majority of the sperm exhibited abnormal morphology including misshapen heads, bent tails and enlarged midpiece, discontinuous accessory structure, and loss of sperm individualization, emphasizing the importance of DNALI1 in sperm development. Examination of testis histology revealed impaired spermiogenesis in the conditional Dnali1 knockout mice. Electron microscopy revealed disrupted ultrastructure in sperm of the Dnali1 mutant mice. Testicular levels of MEIG1, PACRG and SPAG16L proteins were not changed in the Dnali1 mutant mice. However, MEIG1 and SPAG16L were no longer present in the manchette in the absence of DNALI1. These findings demonstrate that DNALI1 is involved in the connection of the MEIG1/PACRG complex to carry cargo proteins along the manchette microtubules for sperm flagella formation. Given that Dnali1 mutant mice showed impaired sperm individualization that was not observed in the MEIG1 nor PACRG-deficient mice, DNALI1 might fulfill other functions beyond its role associated with the MEIG1/PACRG complex. Thus, DNALI1 plays multiple roles in sperm cell differentiation and function. Summary statementAxonemal dynein light intermediate polypeptide 1 (DNALI1) is required for sperm formation and male fertility. It associates with the MEIG1/PACRG complex in the manchette and is involved in a cargo transport system. In addition, it might be related to IFT and sperm individualization.

cell biology↗

bioRxiv2022

Genomic analyses identify significant biological processes in DDX21-mediated colorectal cancer cells

Colorectal cancer is the third most common cancer in the US. There has been an incline in the number of young patients with colorectal cancer due to unclear reasons at this point in time. Currently, DEAD-box RNA helicase protein DDX21 is identified as a prognosis marker for early-stage colorectal cancer. However, the mechanism of DDX21 mediated-colorectal cancer is still unknown. Here, our objective is to determine the key molecules and signaling by analyzing the RNA-seq data. The GSE184726 was created by the Illumina NovaSeq 6000 (Homo sapiens). The KEGG and GO analyses indicated Neuroactive ligand-receptor interaction and Ras signaling pathway were the key signaling pathways during the knockdown of DDX21 in colorectal cancer. Moreover, we identified several interactive genes including PTPRC, FN1, ITGAM, RAD51, TRAF6, CCNB1, FOXP3, CCNA2, HIST2H2AC, and HSPA5. Our study may provide new insights into the treatment of colorectal cancer.

bioinformatics↗

bioRxiv2022

Downregulating PTBP1 fails to convert astrocytes into hippocampal neurons and to alleviate symptoms in Alzheimer's mouse models

Conversion of astroglia into functional neurons has been considered as a promising therapeutic strategy for neurodegenerative diseases. Recent studies reported that downregulation of the RNA binding protein, PTBP1, converts astrocytes into neurons in situ in multiple mouse brain regions, consequently improving pathological phenotypes associated with Parkinsons disease, RGC loss, and aging. Here, we demonstrate that PTBP1 downregulation using antisense oligonucleotides or an astrocyte specific AAV-mediated shRNA system fails to convert hippocampal astrocytes into neurons in WT, and {beta}-amyloid (5xFAD) and tau (PS19) Alzheimers disease (AD) mouse models, and fails to reverse synaptic/cognitive deficits and AD-associated pathology. Similarly, PTBP1 downregulation cannot convert astrocytes into neurons in the striatum and substantia nigra. Together, our study suggests that cell fate conversion strategy for neurodegenerative disease therapy through manipulating one single gene, such as PTBP1, warrants more rigorous scrutiny.

neuroscience↗

bioRxiv2022

Opposite polarity programs regulate asymmetric subsidiary cell divisions in grasses

Grass stomata recruit lateral subsidiary cells (SCs), which are key to the unique stomatal morphology and the efficient plant-atmosphere gas exchange in grasses. Subsidiary mother cells (SMCs) strongly polarise before an asymmetric division forms a SC. Yet apart from a proximal polarity module that includes PANGLOSS1 (PAN1) and guides nuclear migration, little is known regarding the developmental processes that form SCs. Using the genetic model grass Brachypodium distachyon, we identified BdPOLAR, which forms a novel, distal polarity domain in SMCs that is reciprocal to the proximal PAN1 domain. Both polarity domains are required for the formative SC division yet exhibit distinct roles in regulating pre-mitotic nuclear migration and SMC division plane orientation, respectively. Nonetheless, the domains are linked as the proximal domain controls polarisation of the distal domain. In summary, we identified two opposing polarity domains that coordinate the SC division, a process crucial for grass stomatal physiology.

plant biology↗

bioRxiv2022

Global and gene-specific translational regulation in Escherichia coli across different conditions

How well mRNA transcript levels represent protein abundances has been a controversial issue. Particularly across different environments, correlations between mRNA and protein exhibit remarkable variability from gene to gene. Translational regulation is likely to be one of the key factors contributing to mismatches between mRNA level and protein abundance in bacteria. Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. By quantifying the mRNA-RTE correlation both across genes and across conditions, we uncovered a diversity of gene-specific translational regulations, cooperating with transcriptional regulations, in response to carbon (C), nitrogen (N), and phosphate (P) limitations. Intriguingly, we found that many genes regulating translation are themselves subject to translational regulation, suggesting possible feedbacks. Furthermore, a random forest model suggests that codon usage partially predicts a genes cross-condition variability in translation efficiency; such cross-condition variability tends to be an inherent quality of a gene, independent of the specific nutrient limitations. These findings broaden the understanding of translational regulation under different environments, and provide novel strategies for the control of translation in synthetic biology.

genomics↗

bioRxiv2022

Dynamics and Energetics of Bottlenose Dolphins (Tursiops truncatus) Fluke-and-Glide Gait

Intermittent locomotion composed of periods of active flapping/stroking followed by inactive gliding has been observed with species that inhabit both aerial and marine environments. However, studies on the energetic benefits of a fluke-and-glide (FG) gait during horizontal locomotion are limited for dolphins. This work presents a physics-based model of FG gait and analysis of the associated costs of transport of bottlenose dolphins (Tursiops truncatus). New estimates of gliding drag coefficients for the model were estimated experimentally from free-swimming bottlenose dolphins. The data-driven approach used kinematic measurement from 84 hours of biologging tag data collected from 3 animals to estimate the coefficients. A set of 532 qualified gliding events were automatically extracted for gliding drag coefficient estimation, and an additional 783 FG bouts were parameterized and used to inform the model-based dynamic analysis. Experimental results indicate that FG gait was preferred at speeds around 2.2 - 2.7 m/s. Observed FG bouts had an average duty factor of 0.45 and gliding duration of 5 sec. The average associated metabolic cost of transport (COT) and mechanical cost of transport (MECOT) of FG gait are 2.53 and 0.35 J {middle dot} m-1 {middle dot} kg-1 at the preferred speeds. This corresponded to an 18.9% and 27.1% reduction in cost when compared to modeled continuous fluking gait at the same reference speed. Average thrust was positively correlated with fluking frequency and amplitude as animals accelerated during the FG bouts. While fluking frequency and amplitude were negatively correlated for a given thrust range. These results support the supposition that FG gait enhances the horizontal swimming efficiency of bottlenose dolphins and provides new dynamical insights into the gait of these animals.

animal behavior and cognition↗

bioRxiv2022

Commercial ChIP-Seq library preparation kits performed differently for different classes of protein targets

BackgroundChIP-Seq is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of input DNA levels. ResultsIn this study, we evaluated the performance of four ChIP-Seq library preparation protocols [NEB NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo (now PerkinElmer) NEXTflex] on three target proteins, chosen to represent the three typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3) and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments. ConclusionsOur results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries. For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice as it performed well for each of the three targets we tested across a wide array of input DNA levels.

bioinformatics↗

bioRxiv2022

Trophoblast and blood vessel organoid cultures recapitulate the role of WNT2B in promoting intravillous vascularization in human intrauterine and ectopic pregnancy

Tubal ectopic pregnancy (TEP), a pregnancy complication caused by aberrant implantation in fallopian tubes, accounts for 9-13% pregnancy-related deaths. The lack of models for human TEP hampers the understanding of its pathological mechanisms. Here, we employed multiple models to investigate the crosstalk between human trophoblast development and intravillous vascularization. We found that the severity of TEP, the size of placental villi, and the depth of trophoblast invasion are correlated with the extent of intravillous vascularization. We identified a key pro-angiogenic factor secreted by trophoblasts, WNT2B, that promotes villous vasculogenesis, angiogenesis, and vascular network expansion. In an organoid coculture model consisting of trophoblast organoids and blood vessel organoids, knockdown of WNT2B in trophoblast organoids compromises their pro-angiogenic effect on the development of blood vessel organoids. These organoid-based models reveal an important role for WNT-mediated angiogenesis in pregnancies and could be employed to investigate the commutations between trophoblasts and endothelial/endothelial progenitor cells.

cell biology↗

bioRxiv2022

Highly Parallelized, Multicolor Optogenetic Recordings of Cellular Activity for Therapeutic Discovery Applications in Ion Channels and Disease-associated Excitable Cells

Optogenetic assays provide a flexible, scalable and information rich approach to probe compound effects for ion channel drug targets in both heterologous expression systems and associated disease relevant cell types. Despite the potential utility and growing adoption of optogenetics, there remains a critical need for compatible platform technologies with the speed, sensitivity, and throughput to enable their application to broader drug screening applications. To address this challenge, we developed the Swarm, a custom designed optical instrument for highly parallelized, multicolor measurements in excitable cells, simultaneously recording changes in voltage and calcium activities at high temporal resolution under optical stimulation. The compact design featuring high power LEDs, large numerical aperture optics, and fast photodiode detection enables all-optical individual well readout of 24-wells simultaneously from multi-well plates while maintaining sufficient temporal resolution to probe millisecond response dynamics. The Swarm delivers variable intensity blue-light optogenetic stimulation to enable membrane depolarization and red or lime-light excitation to enable fluorescence detection of the resulting changes in membrane potential or calcium levels, respectively. The Swarm can screen ~10,000 wells / day in 384-well format, probing complex pharmacological interactions via a wide array of stimulation protocols. To evaluate the Swarm screening system, we optimized a series of heterologous optogenetic spiking HEK293 cell assays for several voltage-gated sodium channel subtypes including Nav1.2, Nav1.5, and Nav1.7. The Swarm was able to record pseudo-action potentials stably across all 24 objectives and provided pharmacological characterization of diverse sodium channel blockers. We performed a Nav1.7 screen of 200,000 small molecules in a 384-well plate format with all 560 plates reaching a Z[≥]0.5. As a demonstration of the versatility of the Swarm, we also developed an assay measuring cardiac action potential and calcium waveform properties simultaneously under paced conditions using human induced pluripotent stem (iPS) cell-derived cardiomyocytes as an additional counter screen for cardiac toxicity. In summary, the Swarm is a novel high-throughput all-optical system capable of collecting information-dense data from optogenetic assays in both heterologous and iPS cell-derived models, which can be leveraged to drive diverse therapeutic discovery programs for nervous system disorders and other disease areas involving excitable cells.

bioengineering↗

bioRxiv2022

TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource

Immunotherapy is a promising cancer treatment method, but only a few patients benefit from it. Developing new immunotherapy strategies and effective biomarkers of response and resistance is urgent. Recent high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources in these regards. However, these resources are not well organized and systematic analysis is difficult. Here, we present TIGER, a tumor immunotherapy gene expression resource, which contains bulk transcriptome data of 1508 tumor samples with immunotherapy clinical outcome and 11,057 tumor/normal samples without immunotherapy clinical outcome, as well as single-cell transcriptome data of 2,116,945 immune cells of 655 samples. TIGER provides many useful modules to analyze the collected data and user-provided data. Using the resource in TIGER, we identified a tumor enriched subset of CD4+ T cells. Melanoma patients with higher signature score of this subset have significantly better response and survival under immunotherapy. We believe that TIGER will be helpful for understanding anti-tumor immunity mechanisms and discovering effective biomarkers. TIGER is freely accessible at http://tiger.canceromics.org/.

bioinformatics↗

bioRxiv2022

Identification of YAB11-NGAL1 controlling leaf serrations through enhanced genome-wide association studies of Populus

Leaf margins are complex plant morphological features and contribute to the diversity of leaf shapes which effect on plant structure, yield and adaptation. Although several regulators of leaf margins have been identified, the genetic basis of natural variation therein has not been fully elucidated. We first profiled two distinct types (serration and smooth) of leaf morphology using the persistent homology mathematical framework (PHMF) in poplar. Combined genome-wide association studies (GWAS) and expression quantitative trait nucleotide (eQTN) mapping to create a module of leaf morphology controlling using data from Populus tomentosa and P. simonii association population, respectively. Natural variation of leaf margins is associated with transcript abundances of YABBY11 (YAB11) in poplar. In P. tomentosa, PtoYAB11 carries premature stop codon (PtoYAB11PSC) resulting in lost its positive regulation in PtoNGAL-1, PtoRBCL, PtoATPA, PtoATPE, and PtoPSBB. Overexpression of PtoYAB11PSC serrated leaf margin, enlarged leaves, promoted photosynthesis and increased biomass. Overexpression of PsiYAB11 in P. tomentosa could rescue leaf margin serration and increase stomatal density and light damage repair ability. In poplar, YAB11-NGAL1is sensitive to environmental conditions and play positive regulator of leaf margin serration. It might be important regulator which bridge environment signaling to leaf morphological plasticity.

plant biology↗

bioRxiv2022

ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2

MotivationThe advent of long-read sequencing technologies has increased demand for the visualisation and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use. Availability and implementationggtranscript is available at https://github.com/dzhang32/ggtranscript, DOI: https://doi.org/10.5281/zenodo.6374061

bioinformatics↗

bioRxiv2022

Inter-brain coupling reflects disciplinary differences in real-world classroom learning

Classroom is the primary site for learning. One important feature of classroom learning is its organization into different disciplines. While disciplinary differences could substantially influence students learning processes, little is known about the neural mechanism underlying successful disciplinary learning. In the present study, wearable EEG devices were used to record a group of high school students during their classes of a soft (Chinese) and a hard (Math) discipline throughout one semester. The students with higher learning outcomes in Chinese were found to have better inter-brain neural couplings with their excellent peers, whereas the students with higher Math outcomes were found to have better couplings with the class average. Moreover, the inter-brain couplings showed distinct dominant frequencies for the two disciplines. Our results illustrate disciplinary differences in successful learning from an inter-brain perspective and suggest the neural activities of excellent peers and class average as exemplars for soft and hard disciplines. TeaserSuccessful classroom learning is associated with distinct inter-brain coupling patterns for soft and hard disciplines

neuroscience↗

bioRxiv2022

Novel Murine models of Mania and Depression

Neuropathological mechanisms triggering manic syndrome or manic episodes in bipolar disorder remain poorly characterised, as the research progress is severely limited by the paucity of appropriate animal models. Here we developed a novel manic mice model by combining a series of chronic unpredictable rhythm disturbances (CURD), which include disruption of circadian rhythm, sleep deprivation, exposure to cone light, with subsequent interference of followed spotlight, stroboscopic illumination, high temperature stress, noise disturbance and foot shock. To validate this novel manic model, we used multiple behavioural and cell biology approaches comparing the CURD-model with healthy controls and depressed mice. The depression model was created by an exposure to an improved chronic unpredictable mild stress, which we defined as chronic unpredictable mild restraint (CUMR). A novel manic mice model induced by environmental stressors and free from genetic or pharmacological interventions will benefit research into pathological mechanisms of mania.

animal behavior and cognition↗

bioRxiv2022

Cryo-EM structures reveal the activation and substrate recognition mechanism of human enteropeptidase

The enteropeptidase (EP) initiates the intestinal digestion by proteolytic processing of trypsinogen, generating catalytic active trypsin. The dysfunction of EP will cause a series of pancreatic diseases, the most severe of which is acute necrotizing pancreatitis. However, the molecular mechanism of EP activation and substrate recognition remain elusive due to the lack of structural information, hampering the structure-based research of EP and even further EP-targeted drug design. Here we report cryo-EM structures of human EP in multiple states, covering the functional cycle spanning from inactive to active state and eventually to the substrate binding state, with the inactive core region reached an atomic 2.7-[A]-resolution. The heavy chain of EP exhibits a clamping configuration with the CUB2 domain serving for substrate recognition. The N-terminus of light chain induces the surface loop remodeling from inactive to active conformation, resulting in a highly dynamic and active EP. Then the heavy chain performs like a hinge to ensure the flexibility of light chain for substrate recruitment and subsequent cleavage. Our study provides structural insights of EP remodeling and heavy chain dynamics while performing enzymatic function, facilitating our understanding of the pathogenies of EP-related pancreatitis and the EP-targeted treatment of pancreatitis.

cell biology↗