Biology subjects

Liu, L.

Publications and source records attributed to Liu, L..

At least 739 records · Page 41Linked to original sources

bioRxiv2020

A scale-free, fully connected global transition network underlies known microbiome diversity

Microbiomes are inherently linked by their structural similarity, yet the global features of such similarity are not clear. Here we propose as solution a search-based microbiome transition network. By traversing a composition-similarity based network of 177,022 microbiomes, we show that although the compositions are distinct by habitat, each microbiome is on-average only seven neighbors from any other microbiome on Earth, indicating the inherent homology of microbiome at the global scale. This network is scale-free, suggesting a high degree of stability and robustness in microbiome transition. By tracking the minimum spanning tree in this network, a global roadmap of microbiome dispersal was derived that tracks the potential paths of formulating and propagating microbiome diversity. Such search-based global microbiome networks, reconstructed within hours on just one computing node, provide a readily expanded reference for tracing the origin and evolution of existing or new microbiomes.

microbiology↗

bioRxiv2020

The regulation of liver gene expression by carbohydrates is mouse strain specific

C57BL/6J and BALB/cJ mouse strains were analyzed by deep mRNA sequencing of the liver in the fasted state and following ingestion of standard laboratory mouse chow supplemented with plain drinking water or water containing 20% glucose, sucrose or fructose. Supplementation with these carbohydrates induced unique extents and temporal changes in gene expressions in a strain specific manner. Fructose and sucrose stimulated gene changes peaked at 3 h postprandial, whereas glucose effects peaked at 12 h postprandial in C57BL/6J mice and at 6 h postprandial in BABL/cJ mice. Network analyses revealed that fructose changed genes were primarily involved in lipid metabolism and were more complex in C57BL/6J than in BALB/cJ mice. These data demonstrate that there are qualitative and quantitative differences in the normal physiological responses of the liver between these two strains of mice and C57BL/6J is more sensitive to sugar intake than BALB/cJ.

genomics↗

bioRxiv2020

Identification and phenotype of MAIT cells in cattle and their response to bacterial infections

Mucosal-associated invariant T (MAIT) cells are a population of innate-like T cells that utilise a semi-invariant T cell receptor (TCR) chain and are restricted by the highly conserved antigen presenting molecule MR1. MR1 presents microbial riboflavin biosynthesis derived metabolites produced by bacteria and fungi. Consistent with their ability to sense ligands derived from bacterial sources, MAIT cells have been associated with the immune response to a variety of bacterial infections, such as Mycobacterium spp., Salmonella spp. and Escherichia coli. To date, MAIT cells have been studied in humans, non-human primates and mice. However, they have only been putatively identified in cattle by PCR based methods; no phenotypic or functional analyses have been performed. Here, we identified a MAIT cell population in cattle utilising MR1 tetramers and high-throughput TCR sequencing. Phenotypic analysis of cattle MAIT cells revealed features highly analogous to those of MAIT cells in humans and mice, including expression of an orthologous TRAV1-TRAJ33 TCR chain, an effector memory phenotype irrespective of tissue localisation, and expression of the transcription factors PLZF and EOMES. We determined the frequency of MAIT cells in peripheral blood and multiple tissues, finding that cattle MAIT cells are enriched in mucosal tissues as well as in the mesenteric lymph node. Cattle MAIT cells were responsive to stimulation by 5-OP-RU and riboflavin biosynthesis competent bacteria in vitro. Furthermore, MAIT cells in milk increased in frequency in cows with mastitis. Following challenge with virulent Mycobacterium bovis, a causative agent of bovine tuberculosis and a zoonosis, peripheral blood MAIT cells expressed higher levels of perforin. Thus MAIT cells are implicated in the immune response to two major bacterial infections in cattle. These data suggest that MAIT cells are functionally highly conserved and that cattle are an excellent large animal model to study the role of MAIT cells in important zoonotic infections.

immunology↗

bioRxiv2020

Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago

Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The SARS-CoV-2 pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, we used a combinatorial human antibody library constructed 20 years before the COVID-19 pandemic to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in crystal structures with SARS-CoV-2 spike RBD. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of human immune responses to SARS-CoV-2.

microbiology↗

bioRxiv2020

Single-cell Multi-omics reveal heterogeneity and metastasis potential in different liver cancer cell lines

Hepatocellular carcinoma (HCC) is a malignant neo-plasm with a high recurrence and metastatic rate, accounted for poor prognosis. Commonly existed heterogeneity is concerned with neoplasia, cancer progression, therapeutic resistance and metastasis is the principal cause of cancer lethality. As development of multi-omics methods in single-cell technology provides multi-faceted insight into disease processes in the era of precision medicine. Here, we interrogated single-cell transcriptomes, proteomes and epigenetic information, revealing metastasis potential heterogeneity in 5 HCC cell lines across different metastasis capacity. We confirmed that higher mesenchymal (M) status but not proliferation rate was associated with stronger metastasis ability of cell lines. Besides, we identified a subgroup being common in several cell lines, showing a higher hypoxic signature. A gene set involving 14 genes were chosen to represent the hypoxia state, much consistent than previous reported gene set, and showed worse prognosis association in TCGA data. This hypoxic subgroup prefers glycolysis metabolism than OXPO, and showed non-cycling, quiescent state which could be resistant to many proliferation-targeting drugs. Our results provide a comprehensive understanding of characteristic associated with metastasis capacity of HCC cell line, which will guide the metastasis mechanism study of HCC.

cancer biology↗

bioRxiv2020

Molecular and morphological analyses clarify species delimitation and reveal a new Betula species in section Costatae

Background and AimsDelineating closely related and morphologically similar species with overlapping ranges can be difficult. Here, we use section Costatae (genus Betula) as a model to resolve species and subspecies boundaries in four morphologically similar trees: Betula ashburneri, Betula costata, Betula ermanii and Betula utilis (including ssp. utilis, and diploid and tetraploid races of ssp. albosinensis). MethodsWe genotyped 298 individuals (20-80 per species) from 38 populations at 15 microsatellite markers and a subset of 34 individuals from 21 populations using restriction-site associated DNA sequencing (RAD-seq). Morphometric analysis was conducted to characterise leaf variation for a subset of 89 individuals. Key ResultsMolecular analyses and leaf morphology found little differentiation between B. ashburneri, diploid B. utilis ssp. albosinensis and some samples of B. utilis ssp. utilis suggesting that these should be treated as a single species. By contrast, tetraploid Betula utilis ssp. albosinensis was divided into two groups with group I genetically similar to B. utilis ssp. utilis based on SNPs and group II, a very distinct cluster, which we propose as a new species, namely, Betula buggsii. Phylogenomic analysis based on 2,285,620 SNPs show a well-supported monophyletic clade of B. buggsii, forming a sister with a well-supported clade of B. ashburneri, diploid B. albosinensis and some samples of B. utilis ssp. utilis. Morphologically, Betula buggsii is characterised by elongated lenticels and a distinct pattern of bark peeling. Betula buggsii is geographically restricted to the Qinling-Daba Mountains. ConclusionsOur study reveals six genetically distinguishable species: B. ashburneri, B. buggsii, B. costata, B. utilis ssp. utilis, B. utilis ssp. albosinensis and B. ermanii. Our research demonstrates an integrative approach in delimitating species using morphological and genetic samples from their nearly entire distributions. Analyses based on subsets of species distributions may lead to erroneous species or subspecies delineation.

evolutionary biology↗

bioRxiv2020

Transferrin receptor is another receptor for SARS-CoV-2 entry

Angiotensin-converting enzyme 2 (ACE2) has been suggested as a receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry to cause coronavirus disease 2019 (COVID-19). However, no ACE2 inhibitors have shown definite beneficiaries for COVID-19 patients, applying the presence of another receptor for SARS-CoV-2 entry. Here we show that ACE2 knockout dose not completely block virus entry, while TfR directly interacts with virus Spike protein to mediate virus entry and SARS-CoV-2 can infect mice with over-expressed humanized transferrin receptor (TfR) and without humanized ACE2. TfR-virus co-localization is found both on the membranes and in the cytoplasma, suggesting SARS-CoV-2 transporting by TfR, the iron-transporting receptor shuttling between cell membranes and cytoplasma. Interfering TfR-Spike interaction blocks virus entry to exert significant anti-viral effects. Anti-TfR antibody (EC50 ~16.6 nM) shows promising anti-viral effects in mouse model. Collectively, this report indicates that TfR is another receptor for SARS-CoV-2 entry and a promising anti-COVID-19 target.

microbiology↗

bioRxiv2020

Cancer immunotherapy by NC410, a LAIR-2 Fc protein blocking LAIR-collagen interaction

Collagens are a primary component of the extracellular matrix and are functional ligands for the inhibitory immune receptor leukocyte associated immunoglobulin-like receptor-1 (LAIR-1). Leukocyte associated immunoglobulin-like receptor-2 (LAIR-2) is a secreted protein that can act as a decoy receptor by binding collagen with higher affinity than LAIR-1. We propose that collagens promote immune evasion by interacting with LAIR-1 and that LAIR-2 could release LAIR-1 mediated immune suppression. Analysis of public datasets shows high LAIR-2 expression being associated with a favorable outcome in certain tumors. We designed a dimeric LAIR-2 with a functional IgG1 Fc tail, NC410, and showed that NC410 reduces tumor growth and increases T cell expansion and effector function in humanized tumor models. Immunohistochemical analysis of human tumors shows that NC410 binds to collagen-rich areas where LAIR-1+ immune cells are localized. Our findings show that NC410 might be a powerful new strategy for cancer immunotherapy for immune-excluded tumors.

cancer biology↗

bioRxiv2020

Multiple glacial refugia across northern and southern China and unexpected patterns of spatial genetic diversity in Betula albosinensis: a widespread temperate deciduous tree species

The central-marginal hypothesis (CMH) predicts high genetic diversity at the species geographic centre and low genetic diversity at the species geographic margins. However, most studies examining the CMH have neglected potential effect of past climate. Here, we test six hypotheses, representing effects of past climate and contemporary range position, for their ability to explain the spatial patterns of genetic diversity in 37 populations of Betula albosinensis. Ecological niche modelling (ENM) revealed large and continuous suitable habitats in north, southwest and southeast China during the last glacial maximum (LGM) but a contraction of suitable habitats since the LGM. Pollen records further confirmed the existence of multiple refugia in north and south China. The spatial pattern of genetic diversity (i.e., expected heterozygosity, gene diversity and allele richness) were best explained by distance to the southern edge and distance to the range edge but also showed longitudinal and latitudinal gradients. Hypotheses accounting for the effects of climate (climatic suitability, climatic stability and climatic variability) had comparatively little support. Our findings show partial support for the CMH and illustrates that the existence of multiple LGM refugia, and suggests species abundance and past species movement play a role in shaping genetic diversity across species ranges.

evolutionary biology↗

bioRxiv2020

Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

BackgroundExisting computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells, rather than the miRNA regulation unique to individual cells. Recent advance in single-cell miRNA-mRNA co-sequencing technology has opened a way for investigating miRNA regulation at single-cell level. However, as currently single-cell miRNA-mRNA co-sequencing data is just emerging and only available at small-scale, there is a strong need of novel methods to exploit existing single-cell data for the study of cell-specific miRNA regulation. ResultsIn this work, we propose a new method, CSmiR (Cell-Specific miRNA regulation) to use single-cell miRNA-mRNA co-sequencing data to identify miRNA regulatory networks at the resolution of individual cells. We apply CSmiR to the miRNA-mRNA co-sequencing data in 19 K562 single-cells to identify cell-specific miRNA-mRNA regulatory networks for understanding miRNA regulation in each K562 single-cell. By analyzing the obtained cell-specific miRNA-mRNA regulatory networks, we observe that the miRNA regulation in each K562 single-cell is unique. Moreover, we conduct detailed analysis on the cell-specific miRNA regulation associated with the miR-17/92 family as a case study. Finally, through exploring cell-cell similarity matrix characterized by cell-specific miRNA regulation, CSmiR provides a novel strategy for clustering single-cells to help understand cell-cell crosstalk. ConclusionsTo the best of our knowledge, CSmiR is the first method to explore miRNA regulation at a single-cell resolution level, and we believe that it can be a useful method to enhance the understanding of cell-specific miRNA regulation.

bioinformatics↗

bioRxiv2020

Interaction Landscape of K29-Linked Ubiquitin Signaling Revealed by a Linkage-Specific Synthetic Antigen-Binding Fragment

Protein ubiquitination shows remarkable topological and functional diversity through the polymerization of ubiquitin via different linkages. Deciphering the cellular ubiquitin code is of central importance to understand the physiology of the cell. Among the eight possible linkages, K29-linked polyubiquitin is a relatively abundant type of polyubiquitin in both human and yeast cells. However, our understanding of its function is rather limited due to the lack of specific binders as tools to detect K29-linked polyubiquitin. In this study, we screened and characterized a synthetic antigen-binding fragment, termed sAB-K29, that can specifically recognize K29-linked polyubiquitin using chemically synthesized K29-linked diubiquitin. We further determined the crystal structure of this fragment bound to the K29-linked diubiquitin, which revealed the molecular basis of specificity. Using sAB-K29 as a tool, we uncovered that K29-linked ubiquitination is involved in different kinds of cellular proteotoxic stress response as well as cell cycle regulation. In particular, we showed that K29-linked ubiquitination is enriched in the midbody and downregulation of the K29-linked ubiquitination signal arrests cells in G1/S phase.

cell biology↗

bioRxiv2020

Piezo2 mediates ultrasonic hearing via cochlear outer hair cells in mice

Ultrasonic hearing is exploited for hunting and navigation as in echolocation by microbats and bottleneck dolphins, and for social communication like ultrasonic vocalization by mice and rats. However, the molecular and cellular basis for ultrasonic hearing is not known yet. Here we show that knockout of the mechanosensitive ion channel PIEZO2 in cochlea disrupts the ultrasonic hearing but not the low-frequency hearing in mice, as shown by audiometry and acoustically-associative freezing behavior. Deletion of Piezo2 in the outer hair cells specifically abolishes the associative learning of the mice upon hearing the ultrasonic frequency. Ex vivo cochlear Ca2+ imaging revealed that the ultrasonic transduction requires both PIEZO2 and the hair-cell mechanotransduction channel. Together, our study demonstrates that the outer hair cells are the effector cells with PIEZO2 as an essential molecule for ultrasonic hearing in mice. Significance StatementSome animals have evolved an incredible ability for vocalizing and hearing ultrasonic frequencies that is inaudible for humans (> 20 kHz). For many years, it has been considered that animals hear ultrasonic frequencies with their cochlear hair cells, using the identical set of mechanotransduction molecules in the hair bundles for hearing audible frequencies. Here, we show that the mice lacking the mechanosensitive ion channel PIEZO2 hardly hear ultrasonic frequencies, while can still be sensitive to audible frequencies. Thus, animals may use a partially different mechanism for sensing physiological ultrasound.

neuroscience↗

bioRxiv2020

MFG-E8 Signaling Promotes Elastolysis and Calcification in the Aging Aortic Wall

Milk fat globule-EGF factor 8 (MFG-E8) protein increases with age and is mainly secreted by vascular smooth muscle cells in the arterial wall. Here, we investigated the role of MFG-E8 signaling during proinflammation, elastolysis, fibrosis, and calcification within the aging arterial wall. In vivo studies indicated that (1) Elastic lamina breaks collagen deposition and calcium-phosphorus products were markedly increased in the aging arterial wall of rats; (2) MFG-E8 protein abundance was markedly increased while intact tropoelastin (TPELN), an element of repair of the elastic fibers, was markedly decreased in the aging arterial wall of rats; (3) The absence of MFG-E8 markedly alleviated age-associated increases in elastic lamina breaks, collagen deposition and calcium-phosphorus products in mice; and (4) MFG-E8 deficiency significantly decreased age-associated increases in matrix metalloproteinase type II (MMP-2) activation, alkaline phosphatase, and runt-related transcription factor 1 (Runx1) expression in the aortic walls of mice. The in vitro studies demonstrated that (1) treating either young or old rat VSMCs with recombinant human MFG-E8 protein (rhMFG-E8) significantly reduced TPELN levels while MFG-E8 gene silencing significantly increased TPELN levels; (2) rhMFG-E8 treatment activated MMP-2 levels in both young and old VSMCs; and (3) MMP-2 bound to and cleaved TPELN secreted from VSMCs. Thus, these findings suggest that MFG-E8 signaling promotes age-associated adverse structural remodeling, including elastolysis, fibrosis, and calcification; however, MFG-E8 deficiency markedly mitigates these adverse effects in mice.

pathology↗

bioRxiv2020

Cellular Anatomy of the Mouse Primary Motor Cortex

An essential step toward understanding brain function is to establish a cellular-resolution structural framework upon which multi-scale and multi-modal information spanning molecules, cells, circuits and systems can be integrated and interpreted. Here, through a collaborative effort from the Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based description of one brain structure - the primary motor cortex upper limb area (MOp-ul) of the mouse. Applying state-of-the-art labeling, imaging, computational, and neuroinformatics tools, we delineated the MOp-ul within the Mouse Brain 3D Common Coordinate Framework (CCF). We defined over two dozen MOp-ul projection neuron (PN) types by their anterograde targets; the spatial distribution of their somata defines 11 cortical sublayers, a significant refinement of the classic notion of cortical laminar organization. We further combine multiple complementary tracing methods (classic tract tracing, cell type-based anterograde, retrograde, and transsynaptic viral tracing, high-throughput BARseq, and complete single cell reconstruction) to systematically chart cell type-based MOp input-output streams. As PNs link distant brain regions at synapses as well as host cellular gene expression, our construction of a PN type resolution MOp-ul wiring diagram will facilitate an integrated analysis of motor control circuitry across the molecular, cellular, and systems levels. This work further provides a roadmap towards a cellular resolution description of mammalian brain architecture.

neuroscience↗

bioRxiv2020

Droplet microfluidic sequencing of HIV genomes and integration sites

Sequencing individual HIV-proviruses and their adjacent cellular junctions can elucidate mechanisms of infected cell persistence in vivo. Here, we present a high throughput microfluidic method to sequence entire proviruses in their native integration site context. We used the method to analyze infected cells from people with HIV on suppressive antiretroviral therapy, demonstrating >90% capture and sequencing of paired proviral genomes and integration sites. This method should enable comprehensive genetic analysis of persistent HIV-infected cell reservoirs, providing important insights into the barriers to HIV cure.

genomics↗

bioRxiv2020

Virus-Like Particle Based-Vaccines Elicit Neutralizing Antibodies against the HIV-1 Fusion Peptide

Broadly neutralizing antibodies (bnAbs) isolated from HIV-infected individuals delineate vulnerable sites on the HIV envelope glycoprotein that are potential vaccine targets. A linear epitope at the N-terminal region of the HIV-1 fusion peptide (FP8) is the primary target of VRC34.01, a bnAb that neutralizes ~50% of primary HIV isolates. FP8 has attracted attention as a potential HIV vaccine target because it is a simple linear epitope. Here, we used platform technologies based on RNA bacteriophage virus-like particles (VLPs) to develop multivalent vaccines targeting the FP8 epitope. We produced recombinant MS2 VLPs displaying the FP8 peptide and we chemically conjugated synthetic FP8 peptides to Q{beta} VLPs. Both recombinant and conjugated FP8-VLPs induced high titers of FP8-specific antibodies in mice. A heterologous prime-boost-boost regimen employing the two FP8-VLP vaccines and native envelope trimer was the most effective approach for eliciting HIV-1 neutralizing antibodies. Given the potent immunogenicity of VLP-based vaccines, this vaccination strategy - inspired by bnAb-guided epitope mapping, VLP bioengineering, and optimal prime-boost immunization strategies - may be an effective strategy for eliciting bnAb responses against HIV.

immunology↗

bioRxiv2020

Is there a need for preoperative α-blocker in patients missed preoperative diagnosis of extra-adrenal retroperitoneal paraganglioma undergoing paraganglioma resection? A retrospective study of 167 cases at a single center

BackgroundPreoperative -adrenergic blockade is believed to decrease perioperative risks and mortality in adrenal pheochromocytoma surgeries. The aim of this study is to evaluate the effects of the preoperative -adrenergic blockade on patients outcomes in extra-adrenal retroperitoneal paraganglioma surgeries. MethodsWe searched our clinical database for the diagnosis extra-adrenal retroperitoneal paraganglioma by postoperative histopathology in the General Hospital of Peoples Liberation Army from 2000 till 2017. And we recorded preoperative status of patients, preoperative medication preparation, intraoperative and postoperative cardiovascular events, intake and output, length of stay in ICU, length of hospital stay, and short time outcomes. ResultsThe intraoperative morbidity of heart rate elevation and highest heart rate were higher in patients undergoing tumor manipulation with preoperative -adrenergic blockade than those without (P<0.05), while there were no significant differences in intraoperative morbidity of blood pressure elevation and SAP decreased following tumorectomy in these two groups (P>0.05). There were no significant differences in postoperative complications and outcomes (P>0.05). ConclusionUnder the current medical techniques, either with or without preoperative medicine, resection of extra-adrenal retroperitoneal paraganglioma could be carried out successfully.

physiology↗

bioRxiv2020

Primary sex determination in chickens depends on DMRT1 dosage, but gonadal sex does not determine secondary sexual characteristics in adult birds

In birds, males are the homogametic sex (ZZ) and females the heterogametic sex (ZW), and primary sex determination is thought to depend on a sex chromosome gene dosage mechanism. Previous studies have suggested that the most likely sex-determinant is the Z chromosome gene DMRT1 (Doublesex and Mab-3 Related Transcription factor 1). To clarify this issue, we used a CRISPR-Cas9 based mono-allelic targeting approach and sterile surrogate hosts to generate birds with targeted mutations in the DMRT1 gene. The resulting chromosomally male (ZZ) chicken with a single functional copy of DMRT1 developed ovaries in place of testes, demonstrating the avian sex determining mechanism is based on DMRT1 dosage. These ZZ ovaries expressed typical female markers and showed clear evidence of follicular development. However, these ZZ adult birds with an ovary in place of testes were indistinguishable in appearance to wild type adult males, supporting the concept of cell-autonomous sex identity (CASI) in birds. In experiments where oestrogen synthesis was blocked in control ZW embryos, the resulting gonads developed as testes. In contrast, if oestrogen synthesis was blocked in ZW embryos that lacked DMRT1, the gonads invariably adopted an ovarian fate. Our analysis shows that DMRT1 is the key sex determination switch in birds and that it is essential for testis development, but that production of oestrogen is also a key factor in primary sex determination in chickens, and that this production is linked to DMRT1 expression.

developmental biology↗