Biology subjects

Cai, W.

Publications and source records attributed to Cai, W..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Improving functional recovery after severe spinal cord injury by a noninvasive dual functional approach of neuroprotection and neuromodulation

Despite tremendous unmet medical needs, there is no effective pharmacological treatment to promote functional recovery after spinal cord injury (SCI). Although multiple pathological events have been implicated in SCI, the development of a noninvasive pharmacological approach to simultaneously target the different mechanisms involved in SCI remains a formidable challenge. In this study, we report the development of a noninvasive nanodrug delivery system that consists of ROS-responsive amphiphilic copolymers and an encapsulated neurotransmitter-conjugated KCC2 agonist. We show that upon intravenous administration, the nanodrugs were able to enter the injured spinal cord due to blood spinal cord barrier disruption and ROS-responsive disassembly. Remarkably, once in the injured spinal cord, these nanodrugs exhibited dual functions: scavenging ROS accumulated in the lesion to protect spared connections and increasing neuronal excitability in the injured spinal cord through targeted delivery of the KCC2 agonist to inhibitory neurons. Thus, the noninvasive treatment led to significant functional recovery in the rats with contusive SCI. Together, these findings provide a much-needed translational pharmacological approach for treating severe SCI.

neuroscience↗

bioRxiv2022

The 24-chain core-shell nanostructure of wood cellulose microfibrils in seed plants

Wood cellulose microfibrils (CMFs) are the most abundant organic substance on earth, but their nanostructures are poorly understood. There are controversies regarding the glucan chain number (N) of CMFs during initial synthesis and whether they become fused afterwards. Here, we combined small-angle X-ray scattering (SAXS), solid-state nuclear magnetic resonance (ssNMR) and X-ray diffraction (XRD) analyses to resolve these controversies. We successfully developed SAXS measurement methods for the cross-section aspect ratio and area of the crystalline-ordered CMF core, which showed higher density than the semi-disordered shell. The 1:1 aspect ratio suggested that CMFs remain mostly segregated, not fused. The area measurement revealed the chain number in the core zone (Ncore). The ratio of ordered cellulose over total cellulose, termed Roc, was determined by ssNMR. Using the formula N = Ncore / Roc, we found that the majority of wood CMFs contain 24 chains, conserved between gymnosperm and angiosperm trees. The average wood CMF has a crystalline-ordered core of [~]2.2 nm diameter and a semi-disordered shell of [~]0.5 nm thickness. In naturally and artificially aged wood, we only observed CMF aggregation (contact without crystalline continuity) but not fusion (forming conjoined crystalline unit). This further argued against the existence of partially fused CMFs in new wood, overturning the recently proposed 18-chain fusion hypothesis. Our findings are important for advancing wood structural knowledge and more efficient utilization of wood resources in sustainable bio-economies.

plant biology↗

bioRxiv2021

Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer specific driver

Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (1) co-expression network analyses focusing on correlations between genes; (2) linear regressions (usually regularized) to select multiple genes jointly. Both suffer from the problem of stability: a slight change of parameterization or dataset could lead to dramatic alternations of outcomes. Here, we propose Stabilized Core gene and Pathway Election, or SCOPE, a tool integrating bootstrapped LASSO and co-expression analysis, leading to robust outcomes insensitive to variations in data. By applying SCOPE to six cancer expression datasets (BRCA, COAD, KIRC, LUAD, PRAD and THCA) in The Cancer Genome Atlas, we identified core genes capturing interaction effects in crucial pan-cancer pathways related to genome instability and DNA damage response. Moreover, we highlighted the pivotal role of CD63 as an oncogenic driver and a potential therapeutic target in kidney cancer. SCOPE enables stabilized investigations towards complex interactions using transcriptome data. Availabilityhttps://github.com/QingrunZhangLab/SCOPE

bioinformatics↗

bioRxiv2021

Autologous mitochondria transport via transzonal filopodia rejuvenates aged oocytes by UC-MSCs derived granulosa cells-oocyte aggregation

Mitochondria transfer can rescue oocyte aging-related infertility. However, heterologous techniques are suspended due to heteroplasmy. Regarding autologous approaches, the donor source and manipulating procedures require further optimization. Here we propose a strategy using umbilical cord mesenchymal stem cells (UC-MSCs) as mitochondria donor cells and employing intercellular mitochondria transport as the transfer method. We cryopreserved UC-MSCs of the female pup. When the female aged, its UC-MSCs were induced into granulosa cells (iGCs). The zona-weakened GV oocytes were aggregated with autologous iGCs into iGC-oocyte complexes. After cultivation in GDF9-containing media, mitochondria migrated from iGCs into the GV oocyte via transzonal filopodia. The maturation rate, quality, and developmental potential of these oocytes were substantially increased. Furthermore, the birth rate after embryo transfer has been improved. This approach utilized noninvasive procedures to collect mitochondria donor cells and optimized mitochondria transfer manipulations, so may represent a promising advance towards the improvement of aging-related infertility.

developmental biology↗

bioRxiv2021

Using causality and correlation analysis to decipher microbial interactions in activated sludge

Network theory is widely used to understand microbial interactions in activated sludge and numerous other artificial and natural environments. However, when using correlation-based methods, it is not possible to identify the directionality of interactions within microbiota. Based on the classic Granger test of sequencing-based time-series data, a new Microbial Causal Correlation Network (MCCN) was constructed with distributed ecological interaction on the directed, associated links. As a result of applying MCCN to a time series of activated sludge data, we found that the hub species OTU56, classified as belonging the genus Nitrospira, was responsible for completing nitrification in activated sludge, and mainly interacted with Proteobacteria and Bacteroidetes in the form of amensal and commensal relationships, respectively. Phylogenetic tree suggested a mutualistic relationship between Nitrospira and denitrifiers. Zoogloea displayed the highest ncf value within the classified OTUs of the MCCN, indicating that it could be a foundation for activated sludge through forming the characteristic cell aggregate matrices into which other organisms embed during floc formation. Overall, the introduction of causality analysis greatly expands the ability of a network to shed a light on understanding the interactions between members of a microbial community.

bioinformatics↗

bioRxiv2021

Reg4 defenses the intestine against Salmonella infection via binding the flagellin

Salmonella Typhimurium is gram-negative flagellated bacteria that can cause food-borne gastroenteritis and diarrhea in humans and animals. The regenerating islet-derived family member 4 (Reg4) is overexpressed in the gastrointestinal tract during intestinal inflammation. However, the role of Reg4 in the intestinal inflammation induced by Salmonella Typhimurium is largely unknown. In this study, we reported for the first time that Reg4 has bactericidal activity against intestinal infection caused by Salmonella Typhimurium. In vivo, Reg4 could reduce the colonization of Salmonella Typhimurium and attenuate intestinal inflammation in the Salmonella Typhimurium-infected model. Additionally, the mice with the epithelial cell specific deletion of Reg4 (Reg4{Delta}IEC) exhibited more severe intestinal inflammation and more colonization of Salmonella Typhimurium. However, the administration of Reg4 could reverse these negative impacts. In vitro, Reg4 protein was showed to inhibit the growth of Salmonella Typhimurium. We further investigate the function motif of Reg4 and find that the "HDPQK" motif in Reg4 is essential to its bactericidal activity. Reg4 exerted the bactericidal effect by binding to the flagellin of Salmonella Typhimurium and suppressing its motility, adhesion, and invasion to the intestinal epithelia. In conclusion, our findings identify Reg4 as a novel antimicrobial peptide against infection by Salmonella Typhimurium and explore its possible mechanism, which may be of great significance for developing novel agents against flagellated micro pathogens.

microbiology↗

bioRxiv2021

Presynaptic HCN channels constrain GABAergic synaptic transmission in pyramidal cells of the medial prefrontal cortex

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are widely expressed in neurons in the central nervous system. It has been documented that HCN channels regulate the intrinsic excitability of pyramidal cells in the medial prefrontal cortex (mPFC) of rats. Here, we report that HCN channels limited GABAergic transmission onto pyramidal cells in the mPFC. Pharmacological block of HCN channels resulted in a significant increase in the frequency of both spontaneous and miniature inhibitory postsynaptic currents (IPSCs) in mPFC pyramidal cells. Such facilitation effect on mIPSCs required presynaptic Ca2+ influx and reversed by high-dose cAMP. Such facilitation did not exist in the presence of the T-type Ca2+ channel selective blockers. Immunofluorescence staining revealed that HCN channels expressed in presynaptic GABAergic terminals, as well as in both soma and neurite of parvalbumin-expressing (PV-expressing) basket cells in the mPFC. The present results indicate that HCN channels in GABAergic interneurons, most likely PV-expressing basket cells, constrain inhibitory control over layer 5-6 pyramidal cells through restricting presynaptic Ca2+ entry.

neuroscience↗

bioRxiv2021

Total Biosynthesis of Triacsin Featuring an N-hydroxytriazene Pharmacophore

Triacsins are an intriguing class of specialized metabolites possessing a conserved N-hydroxytriazene moiety not found in any other known natural products. Triacsins are notable as potent acyl-CoA synthetase inhibitors in lipid metabolism, yet their biosynthesis has remained elusive. Through extensive mutagenesis and biochemical studies, we here report all enzymes required to construct and install the N-hydroxytriazene pharmacophore of triacsins. Two distinct ATP-dependent enzymes were revealed to catalyze the two consecutive N-N bond formation reactions, including a glycine-utilizing hydrazine-forming enzyme, Tri28, and a nitrous acid-utilizing N-nitrosating enzyme, Tri17. This study paves the way for future mechanistic interrogation and biocatalytic application of enzymes for N-N bond formation.

biochemistry↗

bioRxiv2021

Machine-Perception Nanosensor Platform to Detect Cancer Biomarkers

Conventional molecular recognition elements, such as antibodies, present issues for the development of biomolecular assays for use in point-of-care devices, implantable/wearables, and under-resourced settings. Additionally, antibody development and use, especially for highly multiplexed applications, can be slow and costly. We developed a perception-based platform based on an optical nanosensor array that leverages machine learning algorithms to detect multiple protein biomarkers in biofluids. We demonstrated this platform in gynecologic cancers, which are often diagnosed at advanced stages, leading to low survival rates. We investigated the platform for detection in uterine lavage samples, which are enriched with cancer biomarkers compared to blood. We found that the method enables the simultaneous detection of multiple biomarkers in patient samples, with F1-scores of ~0.95 in uterine lavage samples from cancer patients. This work demonstrates the potential of perception-based systems for the development of multiplexed sensors of disease biomarkers without the need for specific molecular recognition elements.

bioengineering↗

bioRxiv2021

Climate-induced forest dieback drives compositional change in insect communities that is concentrated amongst rare species

Marked decline in insect species richness, abundance and biomass have recently been quantified in Europe. We metabarcoded 224 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging have an impact on flying insects (ca. 3000 insect species) in silver fir Pyrenean forests. We found no evidence that climate-induced forest dieback impacted species richness of flying insects but revealed compositional turnover patterns consistent with those seen during natural forest succession, given that the key covariates explaining compositional variation were canopy openness versus microhabitat diversity and deadwood amount at local and landscape scales, respectively. Importantly, most change was driven by rare species. In contrast, observed levels of salvage logging did not explain change in species richness or composition. Hence, although forest dieback appears to cause changes in species assemblages mimicking natural forest succession, it also increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.

ecology↗

bioRxiv2021

A bacterial "shield and sword": A previously uncharacterized two-component system protects uropathogenic Escherichia coli from host-derived oxidative insults and promotes hemolysin-mediated host cell pyroptosis

Uropathogenic Escherichia coli (UPEC) deploys an array of virulence factors to successfully establish urinary tract infections. Coordinated expression of these various virulence factors is critical for UPECs overall fitness in the host. Two-component signaling systems (TCSs) are a major mechanism by which bacteria sense environmental cues and initiate adaptive responses. Here, we report a previously uncharacterized TCS encoded on a pathogenicity island in UPEC that directly activates the expression of a putative methionine sulfoxide reductase system (C3566/C3567) and a pore-forming -hemolysin in response to host-derived hydrogen peroxide (H2O2) exposure. The TCS increases UPEC resistance to H2O2 in vitro and survival in macrophages in tissue culture via C3566/C3567. Additionally, the TCS mediates -hemolysin-induced renal epithelial cell and macrophage death via a pyroptosis pathway. Taken together, our data suggest a paradigm in which this signal transduction system coordinates both bacterial pathogen defensive and offensive traits in the presence of host-derived signals.

microbiology↗

bioRxiv2021

Phagocytic 'teeth' and myosin-II 'jaw' power target constriction during phagocytosis

Phagocytosis requires rapid actin reorganization and spatially controlled force generation to ingest targets ranging from pathogens to apoptotic cells. How actomyosin activity directs membrane extensions to engulf such diverse targets remains unclear. Here, we combine lattice light-sheet microscopy (LLSM) with microparticle traction force microscopy (MP-TFM) to quantify actin dynamics and subcellular forces during macrophage phagocytosis. We show that spatially localized forces leading to target constriction are prominent during phagocytosis of antibody-opsonized targets. This constriction is largely mediated by Arp2/3-mediated assembly of discrete actin protrusions containing myosin 1e and 1f ("teeth") that are interconnected in a ring-like organization. Contractile myosin-II activity contributes to late-stage phagocytic force generation and progression, suggesting a specific role in phagocytic cup closure. Observations of partial target eating attempts and sudden target release via a popping mechanism suggest that constriction may be critical for resolving complex in vivo target encounters. Overall, our findings suggest a phagocytic cup-shaping mechanism that is distinct from cytoskeletal remodeling in 2D cell motility and may contribute to mechanosensing and phagocytic plasticity.

cell biology↗

bioRxiv2021

Identifying long non-coding RNAs and characterizing their functional roles in swine mammary gland from colostrogenesis to lactogenesis

Long non-coding RNAs (lncRNAs) play important regulatory roles in milk biological processes. While, little is known about the identification and function of swine lncRNAs in response to mammary gland development. Here, we identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition using the published RNA-seq data. The expression pattern of these DE lncRNAs was examined, and most of lncRNAs expressions were strongly changed from Day -2 to Day +1. Functional annotation revealed that the DE lncRNAs were mainly involved in the mammary gland developing, lactation developing, milk composition metabolism and colostrum function. By performing the weighted gene co-expression network analysis (WGCNA), we identified 7 out of 12 lncRNA-mRNA modules, including 35 lncRNAs and 319 mRNAs, which were highly associated with the mammary gland at Day -14, Day -2 and Day +1. Integrated analysis of the DE lncRNAs expression pattern examination, targets prediction, function annotation and WGCNA suggested that 18 lncRNAs (such as, XLOC_020627, ENSSSCG00000051193, XLOC_025150, ENSSSCG00000042618, XLOC_963181, ENSSSCG00000051701, XLOC_018030, and XLOC_025146) and their 20 target genes (such as, ACTN4, ADCY1, CSN3, SMO, CSN2, PRKAG2, FIBCD1, and GALNT7), were considered as the promising candidates for swine parturition and colostrum occurrence processes. Our research provided the insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.

genetics↗

bioRxiv2021

Environment-Dependent Switch between Two Immune Systems against Ralstonia solanacearum Infections in Pepper

O_LIAlthough plant diseases generally cause more severe symptoms under conditions of high temperature and high humidity(HTHH), how plant respond to pathogen attack under this condition remains elusive. C_LIO_LIAs an example, we herein comparatively studied pepper(Capsicum annuum) immunity against Ralstonia solanacearum under HTHH and ambient temperature by approaches of reverse genetics. We found that pepper respond to R.solanacearum infection by activating salicylic-acid- and jasmonic-acid-mediated immunity at ambient temperature. Under HTHH, However, it no longer activates JA-mediated immunity and activates only transient SA signaling at the early stage of R.solanacearum infection, but instead induces cytokinin mediated immunity. C_LIO_LIThese two immune systems are positively regulated by CaWRKY40 via binding the WT-box and a novel W-box like (WL) box, respectively, in an environment-dependent manner: CaWRKY40 is activated upon R. solanacearum infection under HTHH, thereby upregulating ISOPENTENYLTRANSFERASE5(IPT5). The resulting cytokinin then works synergistically with CaWRKY40 in activating a subset of glutathione S-transferase genes via chromatin activation and WL-box binding, but prevent CaWRKY40 from activating ISOCHORISMATE SYNTHASE1 (ICS1) or SA-/JA-dependent pathogenesis-related genes by chromatin inactivation or by blocking WT-box binding. C_LIO_LIThese results highlight the specific pepper immune response to R. solanacearum infection under HTHH and its synergistic activation by CaWRKY40 and cytokinins. C_LI

plant biology↗

bioRxiv2020

A comprehensive catalogue of regulatory variants in the cattle transcriptome

Characterization of genetic regulatory variants acting on the transcriptome of livestock is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here, we build a cattle Genotype-Tissue Expression atlas (cattle GTEx, http://cgtex.roslin.ed.ac.uk/) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 11,642 RNA-Seq datasets. We describe the landscape of the transcriptome across over 100 tissues and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 24 major tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association study (TWAS) and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.

genomics↗

bioRxiv2020

Activated Expression of Master Regulator MYB31 and of Capsaicinoid Biosynthesis Genes Results in Capsaicinoid Biosynthesis and Accumulation in the Pericarp of the Extremely Pungent Capsicum chinense

Capsaicinoids confer pungency in Capsicum fruits, and the capsaicinoid content varies greatly among the five domesticated Capsicum species. Although it is generally recognized that capsaicinoid biosynthesis occurs exclusively in the placenta, few studies have focused on capsaicinoid biosynthesis gene (CBG) expression in the pericarp. Therefore, the transcriptional regulation mechanisms of capsaicinoid biosynthesis in the pericarp remain elusive. Here, the capsaicinoid contents of 32 accessions from five domesticated Capsicum species were analyzed. The results showed that the capsaicinoid contents of C. chinense accessions are significantly higher than those of the other four Capsicum species due to the increased accumulation of capsaicinoids, especially in the pericarp. Compared to that in accessions with low pericarp capsaicinoid content, the expression of the master regulator MYB31 is significantly upregulated in the pericarp in C. chinense accessions, which leads to high levels of CBG expression. Moreover, in fruits of the extremely pungent Trinidad Moruga Scorpion (C. chinense) and low-pungency 59 inbred line (C. annuum) at different developmental stages, the capsaicinoid accumulation patterns were consistent with the MYB31 and CBG expression levels in the pericarp. Taken together, our results provide novel insights into the molecular mechanism arising from the expression of a master regulator in the pericarp that results in exceedingly hot peppers. The genetic resources identified in this study could be used as genetic resources for the genetic improvement of pepper pungency.

plant biology↗

bioRxiv2020

Spatially expandable fiber-based probes as a multifunctional deep brain interface

Understanding the cytoarchitecture and wiring of the brain requires improved methods to record and stimulate large groups of neurons with cellular specificity. This requires miniaturized neural interfaces that integrate into brain tissue without altering its properties. Existing neural interface technologies have been shown to provide high-resolution electrophysiological recording with high signal-to-noise ratio. However, with single implantation, the physical properties of these devices limit their access to one, small brain region. To overcome this limitation, we developed a platform that provides three-dimensional coverage of brain tissue through multisite multifunctional fiber-based neural probes guided in a helical scaffold. Chronic recordings from the spatially expandable fiber probes demonstrate the ability of these fiber probes capturing brain activities with a single-unit resolution for long observation times. Furthermore, using Thy1-ChR2-YFP mice we demonstrate the application of our probes in simultaneous recording and optical/chemical modulation of brain activities across distant regions. Similarly, varying electrographic brain activities from different brain regions were detected by our customizable probes in a mouse model of epilepsy, suggesting the potential of using these probes for the investigation of brain disorders such as epilepsy. Ultimately, this technique enables three-dimensional manipulation and mapping of brain activities across distant regions in the deep brain with minimal tissue damage, which can bring new insights for deciphering complex brain functions and dynamics in the near future.

bioengineering↗

bioRxiv2020

Discovery and biosynthesis of clostyrylpyrones from the obligate an-aerobe Clostridium roseum

Anaerobic bacteria are a promising new source for natural product discovery. Examination of extracts from the obligate anaerobe Clostridium roseum led to discovery of a new family of natural products, the clostyrylpyrones. The polyketide synthase-based biosynthetic mechanism of clostyrylpyrones is further proposed based on bioinformatic, gene knockout, biochemical analysis and heterologous expression studies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/245514v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1f24265org.highwire.dtl.DTLVardef@1e51bd7org.highwire.dtl.DTLVardef@86c761org.highwire.dtl.DTLVardef@8bd052_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗