Biology subjects

Yu, L.

Publications and source records attributed to Yu, L..

At least 307 records · Page 17Linked to original sources

bioRxiv2020

CovProfile: profiling the viral genome and gene expressions of SARS-COV2

The SARS-CoV-2 virus has infected more than one million people worldwide to date. Knowing its genome and gene expressions is essential to understand the virus mechanism. Here, we propose a computational tool CovProfile to detect the viral genomic variations as well as viral gene expressions from the sequences obtained from Nanopore devices. We applied CovProfile to 11 samples, each from a terminally ill patient, and discovered that all the patients are infected by multiple viral strains, which might affect the reliability of phylogenetic analysis. Moreover, the expression of viral genes ORF1ab gene, S gene, M gene, and N gene are high among most of the samples. While performing the tests, we noticed a consistent abundance of transcript segments of MUC5B, presumably from the host, across all the samples.

bioinformatics↗

bioRxiv2020

Deep whole genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias

The diaphragm is a mammalian muscle critical for respiration and separation of the thoracic and abdominal cavities. Defects in the development of the diaphragm are the cause of congenital diaphragmatic hernia (CDH), a common birth defect. In CDH, weaknesses in the developing diaphragm allow abdominal contents to herniate into the thoracic cavity and impair lung development, leading to a high neonatal mortality. The genetic etiology of CDH is complex. Single nucleotide variants (SNVs), insertion/deletions (indels), and structural/copy number variants in more than 150 genes have been associated with CDH, although few genes are recurrently mutated in multiple patients and recurrently mutated genes can be incompletely penetrant. This suggests that multiple genetic variants in combination, other not yet investigated classes of variants, and/or nongenetic factors contribute to CDH susceptibility. However, to date no studies have comprehensively investigated the contribution of all possible classes of variants throughout the genome to the etiology of CDH. In our study, we used a unique cohort of four patients with isolated CDH with samples from blood, skin, and diaphragm connective tissue and parental blood samples and deep whole genome sequencing to assess germline and somatic de novo and inherited variants of various sizes (SNVs, indels, and structural variants) in exons, introns, UTRs, and intergenic regions. In each patient we found a different mutational landscape that included germline de novo, and inherited SNVs and indels in multiple genes. We also found in two patients an inherited 343 bp deletion interrupting an annotated enhancer of the CDH associated gene, GATA4, and we hypothesize that this common deletion (found in 1-2% of the population) acts as a sensitizing allele for CDH. Overall, our comprehensive reconstruction of the genetic architecture of four CDH individuals demonstrates that the etiology of CDH is heterogeneous and multifactorial. AUTHOR SUMMARYDeep whole genome sequencing of family trios shows that etiology of congenital diaphragmatic hernias is heterogeneous and multifactorial.

genetics↗

bioRxiv2020

Structure of intact human MCU supercomplex with the auxiliary MICU subunits

The mitochondrial Ca2+ uniporter (MCU) supercomplex is essential for mitochondrial Ca2+ uptake. Here, we present high-resolution cryo-EM structures of human MCU-EMRE supercomplex (MES, 3.41 [A]) and MCU-EMRE-MICU1-MICU2 supercomplex (MEMMS, 3.64 [A]). MES adopts a V-shaped dimer architecture comprising two hetero-octamers, and a pair of MICU1-MICU2 hetero-dimers form a bridge across the two halves of MES to constitute an O-shaped architecture of MEMMS. The MES and MEMMS pore profiles are almost identical, with Ca2+ in the selectivity filters and no obstructions, indicating both channels are conductive. Contrary to the current model in which MICUs block the MCU pore, MICU1-MICU2 dimers are located on the periphery of the MCU pores and do not occlude them. However, MICU1-MICU2 dimers may modulate MCU gating by affecting the matrix gate through the EMRE lever.

molecular biology↗

bioRxiv2020

Behavioral response of insecticide-resistant mosquitoes against spatial repellent: a modified self-propelled particle model simulation

Rapidly increasing pyrethroid insecticide resistance and changes in vector biting and resting behavior pose serious challenges in malaria control. Mosquito repellents, especially spatial repellents, have received much attention from industry. Many of these repellents contain the same or similar chemicals as those used in insecticides. Does resistance to insecticides affect the efficacy of spatial repellents? We attempted to simulate interactions between mosquitoes and repellents using a machine learning method, the self-propelled particle (SPP) model, which we modified to include attractiveness/repellency effects. We simulated a random walk scenario and scenarios with insecticide susceptible/resistant mosquitoes against repellent alone and against repellent plus attractant (to mimic a human host). We assumed attractant odors and repellent chemicals diffused randomly and omnidirectionally, and that mosquitoes were confined in a cubic cage. We modified the velocity and direction components of SPP using attraction/repulsion rates and concentrations. Simulation results indicated that without attractant/repellent, mosquitoes would fly anywhere in the cage at random. With attractant, mosquitoes might or might not fly toward the source (i.e., the human), depending on the simulation time (and thus the attractant concentration distribution). Eventually, however, all mosquitoes were attracted to the source of the odor. With repellent, results depended on the amount of chemical used and the level of mosquito insecticide resistance. All insecticide-susceptible mosquitoes eventually moved to the corner of the cage farthest from the repellent release point. Surprisingly, a high proportion of highly resistant mosquitoes might reach the attractant release point (the human) earlier in the simulation when repellent was present compare to no repellent was present. At fixed concentration, a high proportion of mosquitoes could be able to reach the host when the relative repellency efficacy (compare to attractant efficacy) was <1, whereas, no mosquitoes reached the host when the relative repellency efficacy was > 1. This result implies that repellent may not be sufficient against highly physiologically insecticide resistant mosquitoes, since very high concentrations of repellent are neither practically feasible nor cost-effective.

ecology↗

bioRxiv2020

Rottlerin ameliorates DSS-induced colitis by improving intestinal barrier function via activation of the Epac-2/Rap-1 signaling pathway.

OBJECTIVESRottlerin, a pan PDE inhibitor, has a variety of pharmacological activities, including enhancing barrier function and mediating anti-inflammatory activity by changing the distribution of occludin and ZO-1. Nevertheless, the function of rottlerin on Crohn disease (CD) keep unknown. Our aim of the study is to investigate the role of rottlerin on CD-like colitis and its mechanism. METHODSWild-type mice which were 8-10 weeks old were randomly divided into three treatment groups: (i) the normal feeding, no administration (control) group, (ii) the group administered 3% dextran sodium sulfate (DSS) alone, and (iii) the group administered rottlerin (100 mg/kg) and 3% DSS. In this study, the effect of rottlerin on the function and structure of the intestinal barrier was investigated, and the possible mechanism was discussed. We performed signaling pathway analysis and flow cytometry to identify the detailed mechanisms by which rottlerin (10 g/mL) treatment inhibits cell growth arrest and the attenuation of TJ proteins in LPS-treated FHs 74 int cells. RESULTSRottlerin treatment significantly ameliorated colitis induced by DSS in WT mice, which was manifested by a decrease in inflammation score, the attenuation of inflammatory factors and the inhibition of destruction on intestinal barrier structure. Rottlerin enhanced the levels of occludin and ZO-1, and improved the function of intestinal barrier, which may have been why rottlerin ameliorated colitis in WT mice. The anti-inflammatory effect of rottlerin may be partly due to the activation of Epac-2/Rap-1 signaling. CONCLUSIONSRottlerin may treat CD in humans via enhancing TJ proteins expression and improving the function of intestinal barrier.

cell biology↗

bioRxiv2020

Prediction of meiosis-essential genes based upon the dynamic proteomes responsive to spermatogenesis

Mammalian meiosis is a specific cell division process during sexual reproduction, whereas a comprehensive proteome of the different meiotic stages has not been systematically investigated. Here, we isolated different types of spermatocytes from the testes of spermatogenesis-synchronized mice and quantified the corresponding proteomes with high-resolution mass spectrometry. A total of 8,002 proteins were identified in nine types of germ cells, and the protein signatures of spermatogenesis were characterized using the dynamic proteomes. A supervised machine learning package, FuncProFinder, was developed to predict meiosis-essential candidate genes based on changes in their protein abundance. Of the candidates without functional annotation, four of the ten genes with the highest prediction scores, Zcwpw1, Tesmin, 1700102P08Rik, and Kctd19, were validated as meiosis-essential genes using knockout mouse models. The proteomic analysis of spermatogenic cells provides a solid foundation for studying the mechanism of mammalian meiosis.

developmental biology↗

bioRxiv2020

UFMylation regulates translational homeostasis and cell cycle progression

UFMylation, the posttranslational modification of proteins with ubiquitin fold modifier 1 (UFM1) is essential for metazoan life and is associated with multiple human diseases. Although UFMylation has been linked to endoplasmic reticulum (ER) stress, its biological functions and relevant cellular targets beyond the ER are obscure. Here, we show that UFMylation directly controls translation and cell division in a manner otherwise known for cellular homeostasis-sensing pathways such as mTOR. By combining cell cycle analyses, mass spectrometry and ribosome profiling we demonstrate that UFMylation is required for eIF4F translation initiation complex assembly and recruitment of the ribosome. Interference with UFMylation shuts down global translation, which is sensed by cyclin D1 and halts the cell cycle independently of integrated stress response signalling. Our findings establish UFMylation as a key regulator of translation and uncover a pathway that couples translational homeostasis to cell cycle progression via a ubiquitin-like modification.

cell biology↗

bioRxiv2019

Extensive Mammalian Germline Genome Engineering

Xenotransplantation, specifically the use of porcine organs for human transplantation, has long been sought after as an alternative for patients suffering from organ failure. However, clinical application of this approach has been impeded by two main hurdles: 1) risk of transmission of porcine endogenous retroviruses (PERVs) and 2) molecular incompatibilities between donor pigs and humans which culminate in rejection of the graft. We previously demonstrated that all 25 copies of the PERV elements in the pig genome could be inactivated and live pigs successfully generated. In this study, we improved the scale of porcine germline editing from targeting a single repetitive locus with CRISPR to engineering 13 different genes using multiple genome engineering methods. we engineered the pig genome at 42 alleles using CRISPR-Cas9 and transposon and produced PERVKO{middle dot}3KO{middle dot}9TG pigs which carry PERV inactivation, xeno-antigen KO and 9 effective human transgenes. The engineered pigs exhibit normal physiology, fertility, and germline transmission of the edited alleles. In vitro assays demonstrated that these pigs gain significant resistance to human humoral and cell mediated damage, and coagulation dysregulations, similar to that of allotransplantation. Successful creation of PERVKO{middle dot}3KO{middle dot}9TG pigs represents a significant step forward towards safe and effective porcine xenotransplantation, which also represents a synthetic biology accomplishment of engineering novel functions in a living organism. One Sentence SummaryExtensive genome engineering is applied to modify pigs for safe and immune compatible organs for human transplantation

synthetic biology↗

bioRxiv2019

Single-cell RNA-seq data reveals TNBC tumor heterogeneity through characterizing subclone compositions and proportions

Understanding subclonal architecture and their biological functions poses one of the key challenges to deeply portray and investigative the cause of triple-negative breast cancer (TNBC). Here we combine single-cell and bulk sequencing data to analyze tumor heterogeneity through characterizing subclone compositions and proportions. Based on sing-cell RNA-seq data (GSE118389) we identified five distinct cell subpopulations and characterized their biological functions based on their gene markers. According to the results of functional annotation, we found that C1 and C2 are related to immune functions, while C5 is related to programmed cell death. Then based on subclonal basis gene expression matrix, we applied deconvolution algorithm on TCGA tissue RNA-seq data and observed that microenvironment is diverse among TNBC subclones, especially C1 is closely related to T cells. Whats more, we also found that high C5 proportions would led to poor survival outcome, log-rank test p-value and HR [95%CI] for five years overall survival in GSE96058 dataset were 0.0158 and 2.557 [1.160-5.636]. Collectively, our analysis reveals both intra-tumor and inter-tumor heterogeneity and their association with subclonal microenvironment in TNBC (subclone compositions and proportions), and uncovers the organic combination of subclones dictating poor outcomes in this disease. HighlightsWe applied deconvolution algorithm on subclonal basis gene expression matrix to link single cells and bulk tissue together.

cancer biology↗

bioRxiv2019

Effects of a novel three-dimensional grid intrauterine device on the uterus, steroid receptor and PAX2 of rhesus macaques

Intrauterine devices (IUDs) is the most effective methods of the reversible and long-acting contraception. 1) To develop a novel three-dimensional grid intrauterine device (3-DGIUD) with nickel-titanium (Ni-Ti) and silicone rubber. 2) To observe the effect of the 3-DGIUD on contraceptive efficacy and the change of uterus, endometrial sex steroid receptor, PAX2 in rhesus macaques (Macaca mulatta). The materials of the 3-DGIUD were the nitinol wire and the silicone rubber. The frame of the 3-DGIUD was three-dimensional and grid-like. Twenty adult female rhesus macaques were divided into the 3-DGIUD group (placing the 3-DGIUD, n=9), the sham operation group (no placing the 3-DGIUD, n=9) and the control group (n=2). On the 10th-day after surgery, the 3-DGIUD group and the sham operation group macaques were caged together with male macaques (female: male = 1:1). The uterus, 3-DGIUD and pregnancy of 18 female rhesus monkeys were examined by abdominal ultrasound every month. The endometrium pathological examination was carried out and the expression of PAX2 and hormone receptor (ER, PR) was detected by immunohistochemical staining. After 3-DGIUD was placed in case group for 3 and 12 months, only 1 of female macaque was pregnant in 9. The contraceptive effective rate was 88.9% (8/9). The 3-DGIUD in the uterus of macaques was observed by ultrasound. In the sham operation group, 9 macaques were pregnant (9/9). There was significant difference in uterine size of the 3-DGIUD group between pre-placement and after surgery for 3 and 12 months (P<0.05). The endometrial epithelium was intact, just a small number of glands vacuoles and a few neutrophils infiltration around the 3-DGIUD. The expression of endometrial ER, PR and PAX2 in 3-DGIUD group on 12 months after surgery was similar to those in control macaque. The 3-DGIUD has a good contraceptive effect on female macaques, and has no significant affection on the expression of endometrial steroid receptor and PAX2 in rhesus monkeys.

zoology↗

bioRxiv2019

The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

The ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. We previously identified a composite domain in the BRG1 ATPase subunit that is capable of associating with both histones and DNA in a multivalent manner. Mapping the DNA binding pocket revealed that it contains several cancer mutations. Here, we utilize SELEX-seq to identify the DNA specificity of this composite domain and NMR spectroscopy and molecular modelling to determine the structural basis of DNA binding. Finally, we demonstrate that cancer mutations in this domain alter the mode of DNA association.

biochemistry↗

bioRxiv2019

Somatic genetic drift and multi-level selection in modular species

Cells in multicellular organisms are genetically heterogeneous owing to somatic mutations. The accumulation of somatic genetic variation in species undergoing asexual (or clonal) reproduction (termed modular species) may lead to phenotypic heterogeneity among modules. However, abundance and dynamics of somatic genetic variation under clonal growth, a widespread life history in nature, remain poorly understood. Here we show that branching events in a seagrass clone or genet leads to population bottlenecks at the cellular level and hence the evolution of genetically differentiated modules. Studying inter-module somatic genetic variation, we uncovered thousands of SNPs that segregated among modules. The strength of purifying selection on mosaic genetic variation was greater at the intra-module comparing with the inter-module level. Our study provides evidence for the operation of selection at multiple levels, of cell population and modules. Somatic genetic drift leads to the emergence of genetically unique modules; hence, modules in long-lived clonal species constitute an appropriate elementary level of selection and individuality.

evolutionary biology↗

bioRxiv2019

A multi-tier species delimitation approach resolves conflicts in delineating the primitively segmented spider genus Heptathela endemic to Japanese islands

Determining species boundaries forms an important foundation for biological research. However, the results of molecular species delimitation can vary with the data sets and methods that are used. Here we use a two-step approach to delimit species in the genus Heptathela, a group of primitively segmented trapdoor spiders that are endemic to Japanese islands. Morphological evidence suggests the existence of 19 species in the genus. We tested this initial species hypothesis by using six molecular species-delimitation methods to analyse 180 mitochondrial COI sequences of Heptathela sampled from across the known range of the genus. We then conducted a set of more focused analyses by sampling additional genetic markers from the subset of taxa that were inconsistently delimited by the single-locus analyses of mitochondrial DNA. Multilocus species delimitation was performed using two Bayesian approaches based on the multispecies coalescent. Our approach identified 20 putative species among the 180 sampled individuals of Heptathela. We suggest that our two-step approach provides an efficient strategy for delimiting species while minimizing costs and computational time.

evolutionary biology↗

bioRxiv2019

Whole-plant optimality predicts changes in leaf nitrogen under variable CO2 and nutrient availability

O_LIVegetation nutrient limitation is essential for understanding ecosystem responses to global change. In particular, leaf nitrogen (N) is known to be plastic under changed nutrient limitation. However, models can often not capture these observed changes, leading to erroneous predictions of whole-ecosystem stocks and fluxes.\nC_LIO_LIWe hypothesise that an optimality approach can improve representation of leaf N content compared to existing empirical approaches. Unlike previous optimality-based approaches, which adjust foliar N concentrations based on canopy carbon export, we use a maximisation criteria based on whole-plant growth and allow for a lagged response of foliar N to this maximisation criterion to account for the limited plasticity of this plant trait. We test these model variants at a range of Free-Air CO2 Enrichment (FACE) and N fertilisation experimental sites.\nC_LIO_LIWe show a model solely based on canopy carbon export fails to reproduce observed patterns and predicts decreasing leaf N content with increased N availability. However, an optimal model which maximises total plant growth can correctly reproduce the observed patterns.\nC_LIO_LIThe optimality model we present here is a whole-plant approach which reproduces biologically realistic changes in leaf N and can thereby improve ecosystem-level predictions under transient conditions.\nC_LI

ecology↗

bioRxiv2019

Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project

With more than 30,000 species, fish are the largest and most ancient vertebrate group. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Here, we announce the Fish10K project, an international collaborative project or initiative? aiming to sequence 10,000 representative fish genomes under a systematic context within ten years, and officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, and sequencing and assembly strategies. To illustrate, we present the genomes of ten fish species from a cohort of 93 species chosen for technology development.

genomics↗

bioRxiv2019

Studying the drug treatment pattern based on the action of drug and multi-layer network model

ObjectivesA drug can treat multiple diseases, indicating that the treatment of the drug has certain patterns. In this paper, we studied the treatment pattern of drugs from a new perspective based on the action of drug and multi-layer network model (STAM). Diseases affect the gene expression in related tissues and each disease corresponds to a tissue-specific protein-protein interaction (TSPPI) network. Therefore, a drug is associated with a multi-layer TSPPI network associated with diseases it treats. Single tissue-specific PPI network cannot consider all disease-related information, leading to find the potential treatment pattern of drugs difficultly. Research on multi-layer networks can effectively solve this disadvantage. Furthermore, proteins usually interact with other proteins in PPI to achieve specific functions, such as causing disease. Hence, studying the drug treatment patterns is equivalent to study common module structures in the multi-layer TSPPI network corresponding to drug-related diseases. Knowing the treatment patterns of the drug can help to understand the action mechanisms of the drug and to identify new indications of the drug.\n\nMethodsIn this paper, we were based on the action of drug and multi-layer network model to study the treatment patterns of drugs. We named our method as STAM. As a case of our proposed method STAM, we focused on a study to trichostatin A (TSA) and three diseases it treats: leukemia, breast cancer, and prostate cancer. Based on the therapeutic effects of TSA on various diseases, we constructed a tissue-specific protein-protein interaction (TSPPI) network and applied a multi-layer network module mining algorithm to obtain candidate drug-target modules. Then, using the genes affected by TSA and related to the three diseases, we employed Gene Ontology (GO), the modules significance, co-expression network and literatures to filter and analyze the identified drug-target modules. Finally, two modules (named as M17 and M18) were preserved as the potential treatment patterns of TSA.\n\nResultsThe processed results based on the above framework STAM demonstrated that M17 and M18 had strong potential to be the treatment patterns of TSA. Through the analysis of the significance, composition and functions of the selected drug-target modules, we validated the feasibility and rationality of our proposed method STAM for identifying the drug treatment pattern.\n\nConclusionThis paper studied the drug treatment pattern from a new perspective. The new method STAM used a multi-layer network model, which overcame the shortcomings of the single-layer network, and combined the action of drug. Research on drug treatment model provides new research ideas for disease treatment.

bioinformatics↗

bioRxiv2019

Rapid pacing by circulating traveling waves improves maturation of hiPSC-derived cardiomyocytes in self-organized tissue ring

Directed differentiation methods allow acquisition of high-purity cardiomyocytes (CMs) differentiated from human induced pluripotent stem cells (hiPSCs); however, their immaturity characteristic limits their application for drug screening and regenerative therapy. The rapid electrical pacing of cardiomyocytes have been used for efficiently promoting the maturation of cardiomyocytes, here we describe a simple device in modified culture plate on which hiPSC-derived CMs (hiPSC-CMs) can form three-dimensional self-organized tissue rings (SOTRs). Using calcium imaging, we show that within the ring, traveling waves (TWs) of action potential spontaneously originated and ran robustly at a frequency up to 4 Hz. After 2 weeks, SOTRs with TW training showed matured features including structural organization, increased cardiac-specific gene expression, enhanced Ca2+-handling properties, an increased oxygen-consumption rate, and enhanced contractile force. We subsequently used a mathematical model to interpret the origination, propagation, and long-term behavior of the TWs within the SOTRs. This new idea for spontaneous hiPSC-CM maturation also has potential for pacing the electrical excitable cells such as neuron and retina cells for various applications.

bioengineering↗

bioRxiv2019

Molecular mechanism of mitochondrial phosphatidate transfer by Ups1/Mdm35

Cardiolipin plays many important roles for mitochondrial physiological function and is synthesized from phosphatidic acid (PA) at inner mitochondrial membrane (IMM). PA synthesized from endoplasmic reticulum needs to transfer to IMM via outer mitochondrial membrane (OMM). The transfer of PA between IMM and OMM is mediated by Ups1/Mdm35 protein family. Although there are many structures of this family available, the detailed molecular mechanism of how PA is transferred between membranes is yet unknown. Here, we report another crystal structures of Ups1/Mdm35 in the authentic monomeric apo state and the DHPA bound state. By combining subsequent all-atom molecular dynamics simulations, extensive structural comparisons and biophysical assays, we discovered the conformational changes of Ups1/Mdm35, identified key structural elements and residues during membrane binding and PA entry. We found the monomeric Ups1 on membrane is an important transit for the success of PA transfer, and the equilibrium between monomeric Ups1 and Ups1/Mdm35 complex on membrane affects the PA transfer rate and can be regulated by many factors including environmental pH.

biochemistry↗