Biology subjects

Liao, M.

Publications and source records attributed to Liao, M..

48 records · Page 3Linked to original sources

bioRxiv2021

Chicken peripheral blood lymphocyte response to ALV-J infection assessed by single-cell RNA sequencing

Chicken peripheral blood lymphocytes (PBLs) exhibit wide-ranging cell types, but current understanding of their subclasses, immune cell classification, and function is limited and incomplete. Previously, we found that viremia caused by avian leukosis virus subgroup J (ALV-J) was eliminated by 21 days post infection (DPI), accompanied by increased CD8+ T cell ratio in PBLs and low antibody levels. Here we performed single-cell RNA sequencing (scRNA-seq) of PBLs in ALV-J infected and control chickens at 21 DPI to determine chicken PBL subsets and their specific molecular and cellular characteristics, before and after viral infection. Eight cell clusters and their potential marker genes were identified in chicken PBLs. T cell populations (clusters 6 and 7) had the strongest response to ALV-J infection at 21 DPI, based on detection of the largest number of differentially expressed genes (DEGs). T cell populations of clusters 6 and 7 could be further divided into four subsets: activated CD4+ T cells (cluster A0), Th1-like cells (cluster A2), Th2-like cells (cluster A1), and cytotoxic CD8+ T cells. Hallmark genes for each T cell subset response to viral infection were initially identified. Furthermore, pseudotime analysis results suggested that chicken CD4+ T cells could potentially differentiate into Th1-like and Th2-like cells. Moreover, ALV-J infection probably induced CD4+ T cell differentiation into Th1-like cells in which the most immune related DEGs were detected. With respect to the control group, ALV-J infection also had an obvious impact on PBL cell composition. B cells showed inconspicuous response and their numbers decreased in PBLs of the ALV-J infected chickens at 21 DPI. Percentages of cytotoxic Th1-like cells and CD8+ T cells were increased in the T cell population of PBLs from ALV-J infected chicken, which were potentially key mitigating factors against ALV-J infection. More importantly, our results provided a rich resource of gene expression profiles of chicken PBL subsets for a systems-level understanding of their function in homeostatic condition as well as in response to viral infection.

immunology↗

bioRxiv2020

Collagen induced inflammations

Collagen-induced arthritis (CIA) mouse model is currently the most widely used and reliable autoimmune model to study rheumatoid arthritis. In this model, we used bovine type II collagen (CII) and complete Freunds adjuvant (CFA) or incomplete Freunds adjuvant (IFA) to form emulsifier, and mice were injected intradermal to induce autoimmune arthritis (CIA). In this model, we ground bovine collagen type II (CII) with complete Freunds adjuvant (CFA) or incomplete Freunds adjuvant (IFA) to form emulsifiers, and intradermal injection in mice induced autoimmune arthritis (CIA). This article describes the mouse, CFA strains, key emulsification, anesthesia, and injection immune techniques, as well as the incidence, date of onset, score, pathological results of arthritis. The total time for preparation of reagents and immunization of 20 mice was about 2-2.5 hours. In this protocol, we induced a high incidence of CIA with DBA/1J in genetically susceptible mice and assessed the severity and pathology of the disease, at the same time we found that CII also can induced enteritis, including ileitis and colitis. The initial symptoms of arthritis appear in the 24-26 days of the experiment, that is, 3-5 days after the second immunization, the peak period of inflammation was 30-36 days, the arthritis incidence about 90-100%, at the same time, the incidence of enteritis and arthritis were the same, small intestinal inflammation was more severe, but the duration was short; while the colonic inflammation was mild, and the duration was longer than enteritis, we named it collagen induced inflammations (CIIs).

immunology↗

bioRxiv2020

Long-term survival of salmon-attached SARS-CoV-2 at 4 degree as a potential source of transmission in seafood markets

Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. Here we showed that salmon-attached SARS-CoV-2 at 4{degrees}C could remain infectious for more than one week, suggesting that fish-attached SARS-CoV-2 may be a source of transmission.

microbiology↗

bioRxiv2020

Histone demethylase complexes KDM3A and KDM3B cooperate with OCT4/SOX2 to construct pluripotency gene regulatory network

The pluripotency gene regulatory network of porcine-induced pluripotent stem cells (piPSCs), especially in epigenetics, remains elusive. To determine this biological function of epigenetics, we cultured piPSCs in different culture conditions. We found that activation of pluripotent gene- and pluripotency-related pathways requires the erasure of H3K9 methylation modification which was further influenced by mouse embryonic fibroblast (MEF) served feeder. By dissecting the dynamic change of H3K9 methylation during loss of pluripotency, we demonstrated that the H3K9 demethylases KDM3A and KDM3B regulated global H3K9me2/me3 level and that their co-depletion led to the collapse of the pluripotency gene regulatory network. Immunoprecipitation-mass spectrometry (IP-MS) provided evidence that KDM3A and KDM3B formed a complex to perform H3K9 demethylation. The genome-wide regulation analysis revealed that OCT4 (O) and SOX2 (S), the core pluripotency transcriptional activators, maintained the pluripotent state of piPSCs depending on the H3K9 hypomethylation. Further investigation revealed that O/S cooperating with histone demethylase complex containing KDM3A and KDM3B promoted pluripotency genes expression to maintain the pluripotent state of piPSCs. Together, these data offer a unique insight into the epigenetic pluripotency network of piPSCs. SummaryErasure of H3K9 methylation in porcine pluripotent stem cells depends on the complex of transcription factors OCT4/SOX2 and histone demethylase KDM3A/KDM3B.

cell biology↗

bioRxiv2020

Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosome

Autosomal origins of heterogametic sex chromosomes have been inferred frequently from suppressed recombination and gene degeneration manifested in incompletely differentiated sex chromosomes. However, the initial transition of an autosome region to a proto-sex locus has been not explored in depth. By assembling and analyzing a chromosome-level draft genome, we found a recent (evolved 0.26 million years ago), highly homologous, and dmrt1 containing sex-determination locus with slightly reduced recombination in large yellow croaker (Larimichthys crocea), a teleost species with genetic sex determination (GSD) and with undifferentiated sex chromosomes. We observed genomic homology and polymorphic segregation of the proto-sex locus between sexes. Expression of dmrt1 showed a stepwise increase in the development of testis, but not in the ovary. We infer that the inception of the proto-sex locus involves a few divergences in nucleotide sequences and slight suppression of recombination in an autosome region. In androgen-induced sex reversal of genetic females, in addition to dmrt1, genes in the conserved dmrt1 cluster, and the rest of the sex determination network were activated. We provided evidence that broad functional links were shared by genetic sex determination and environmental sex reversal.

evolutionary biology↗

bioRxiv2020

A Scaling Law Governing Branching Morphogenesis in Neuronal Dendrites

The systematic variation of diameters in branched networks has tantalized biologists since the discovery of da Vincis rule for trees. Da Vincis rule can be formulated as a power law with exponent two: the square of the mother branchs diameter is equal to the sum of the squares of those of the daughters. Power laws, with different exponents, have been proposed for branching in circulatory systems and in neurons. The laws have been derived theoretically, based on optimality arguments, but, for the most part, have not been tested rigorously. In the case of neuronal dendrites, diameter changes across branch points have functional implications for the spread of electrical signals: for example, Ralls law with an exponent of 3/2 maximizes propagation speeds of action potentials across branch points. Using a super-resolution method to measure the diameters of all dendrites in highly branched Drosophila Class IV sensory neurons, we have tested Ralls law and shown it to be false. In its place, we have discovered a new diameter-scaling law: the cross-sectional area is proportional to the number of dendrite tips supported by the branch plus a constant, corresponding to a minimum dendrite diameter. The law accords with microtubules providing force and transport for dendrite tip growth. That the observed scaling differs from Ralls law suggests that constraints imposed by cell biological mechanisms may impact electrical signaling in neurons. Our new scaling law generalizes to other branched processes such as the vasculature of plants and the circulatory system of animals. Significance StatementTo study the systematic variation of dendrite diameters, we have established a super-resolution method that allows us to resolve dendrite diameters in Drosophila Class IV dendritic arborization neurons, a model cell for studying branching morphogenesis. Interestingly, they do not follow any of the known scaling laws. We propose a new scaling law that follows from two concepts: there is an incremental cross-sectional area needed to support each terminal branch, and there is a minimum branch diameter. The law is consistent with dendrite growing by tip extension and being supported by microtubule-based transport. If the law generalizes to other neurons, it may facilitate segmentation in connectomic studies.

biophysics↗

bioRxiv2019

Multiple splitting of droplets using multi-furcating microfluidic channels

Removing volumes from droplets is a challenging but critical step in many droplet-based applications. Geometry-mediated droplet splitting has the potential to reliably divide droplets and thus facilitate the implementation of this step. In this paper, we report the design of multi-furcating microfluidic channels for efficient droplet splitting. We studied the splitting regimes as the size of the mother droplets varied and investigated the effect of channel lengths. We further examined the droplet breakup mechanisms. This study could potentially be applied in washing steps in droplet-based biological assays or assays that require aliquot.

biophysics↗

bioRxiv2019

Structure and function of a 9.6 megadalton bacterial iron storage compartment

Iron storage proteins are essential for maintaining intracellular iron homeostasis and redox balance. Iron is generally stored in a soluble and bioavailable form inside ferritin protein compartments. However, some organisms do not encode ferritins and thus rely on alternative storage strategies. Encapsulins, a class of protein-based organelles, have recently been implicated in microbial iron and redox metabolism. Here, we report the structural and mechanistic characterization of a 42 nm two-component encapsulin-based iron storage compartment from Quasibacillus thermotolerans. Using cryo-electron microscopy and x-ray crystallography, we reveal the assembly principles of a thermostable T = 4 shell topology and its catalytic ferroxidase cargo. We show that the cargo-loaded compartment has an exceptionally large iron storage capacity storing over 23,000 iron atoms. These results form the basis for understanding alternate microbial strategies for dealing with the essential element iron.

biochemistry↗

bioRxiv2018

Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis based on integrated RNA-Seq

Spermatogenesis is an important physiological process associated with male infertility. But whether there are RNA editings (REs) and whats the role of REs during the process are still unclear. In this study, we integrated published RNA-Seq datasets and established a landscape of REs during the development of mouse spermatogenesis. 7530 editing sites among all types of male germ cells were found, which enrich on some regions of chromosome, including chromosome 17 and both ends of chromosome Y. Totally, REs occur in 2012 genes during spermatogenesis, more than half of which harbor at two different sites of the same gene at least. We also found REs mainly occur in introns, coding regions (CDSs) and intergenic regions. Moreover, about half of the REs in CDSs can cause amino acids changes. Finally, based on our adult male Kunming mice, we verified that there is a non-synonymous A-to-I RNA editing site in Cog3 during spermatogenesis, which is conserved not only between species but also across tissues. In short, based on the power of integrating RNA-Seq datasets, we provided the landscape of REs and found their dynamic changes during mouse spermatogenesis. This research strategy is general for other types of sequencing datasets and biological problems.

developmental biology↗

bioRxiv2018

Cryo-electron microscopy structure of the lipid droplet-formation protein seipin

Sui et al. report the cryo-EM structure of the conserved luminal domain of the lipid droplet (LD)-formation protein seipin. The structure reveals key features of this domain and suggest a new model for seipins role in LD formation.\n\nMetabolic energy is stored in cells primarily as triacylglycerols in lipid droplets (LDs), and LD dysregulation leads to metabolic diseases. The formation of monolayer-bound LDs from the endoplasmic reticulum (ER) bilayer is poorly understood, but the ER protein seipin is essential to this process. Here, we report a cryo-electron microscopy structure and functional characterization of D. melanogaster seipin. The structure reveals a ring-shaped dodecamer, with the luminal domain of each monomer resolved at [~]4.0 [A]. Each luminal domain monomer exhibits two distinctive features: a hydrophobic helix positioned towards the ER bilayer, and a {beta}-sandwich domain that has structural similarity with lipid-binding proteins. This structure, and our functional testing in cells, suggest a model in which seipin oligomers initially detect forming LDs in the ER via hydrophobic helices and subsequently act as membrane anchors to enable lipid transfer and LD growth.

cell biology↗

bioRxiv2018

Differential expression of an alternative splice variant of IL-12Rβ1 impacts early dissemination in the mouse and associates with disease outcome in both mouse and humans exposed to tuberculosis

Experimental mouse models of TB suggest that early events in the lung impact immunity. Early events in the human lung in response to TB are difficult to probe and their impact on disease outcome is unknown. We have shown in mouse that a secreted alternatively-spliced variant of IL-12R{beta}1, lacking the transmembrane domain and termed {Delta}TM-IL-12R{beta}1, promotes dendritic cell migration to the draining lymph node, augments T cell activation and limits dissemination of M. tuberculosis (Mtb). We show here that CBA/J and C3H/HeJ mice (both highly susceptible to Mtb) express higher levels of {Delta}TM-IL-12R{beta}1 than resistant C57BL6 mice and limit early dissemination of Mtb from the lungs. Both CD11c+ cells and T cells express {Delta}TM-IL-12R{beta}1 in humans, and mice unable to make {Delta}TM-IL-12R{beta}1 in either CD4 or CD11c expressing cells permit early dissemination from the lung. Analysis of publically available blood transcriptomes indicates that pulmonary TB is associated with high {Delta}TM-IL-12R{beta}1 expression and that of all IL-12 related signals, the {Delta}TM-IL-12R{beta}1 signal best predicts active disease. {Delta}TM-IL-12R{beta}1 expression reflects the heterogeneity of latent TB infection and has the capacity to discriminate between latent and active disease. In a new Chinese TB patient cohort, {Delta}TM-IL-12R{beta}1 effectively differentiates TB from latent TB, healthy controls and pneumonia patients. Finally, {Delta}TM-IL-12R{beta}1 expression drops in drug-treated individuals in the UK and China where infection pressure is low. We propose that {Delta}TM-IL-12R{beta}1 regulates early dissemination from the lung and that it has diagnostic potential and provides mechanistic insights into human TB.

immunology↗

bioRxiv2017

Structure and function of accessory Sec proteins involved in the adhesin export pathway of Streptococcus gordonii

Many pathogenic bacteria, including Streptococcus gordonii, possess a pathway for the export of a single serine-rich-repeat protein that mediates the adhesion of bacteria to host cells and the extracellular matrix. These adhesins are O-glycosylated by several cytosolic glycosyltransferases and require three accessory Sec proteins (Asp1-3) for export, but how the adhesins are processed for secretion is not well defined. Here, we show that O-glycosylation of S. gordonii adhesin GspB occurs in a sequential manner by three enzymes (GtfA/B, Nss, Gly) that attach N-acetylglucosamine and glucose to Ser/Thr residues. The modified substrate is subsequently transferred from the last glycosyltransferase to the Asp1/2/3 complex. Crystal structures show that both Asp1 and Asp3 are related to carbohydrate binding proteins. Asp1 also has an affinity for phospholipids, which is attenuated by Asp2. These results suggest a mechanism for the modification of adhesin in the cytosol and its subsequent targeting to the export machinery.

biochemistry↗