Biology subjects

Liu, P.

Publications and source records attributed to Liu, P..

At least 289 records · Page 16Linked to original sources

bioRxiv2020

Effects of SARS-CoV-2 Mutations on Protein Structures and Intraviral Protein-Protein Interactions

Since 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) has infected ten millions of people across the globe, and massive mutations in virus genome have occurred during the rapid spread of this novel coronavirus. Variance in protein sequence might lead to change in protein structure and interaction, then further affect the viral physiological characteristics, which could bring tremendous influence on the pandemic. In this study, we investigated 18 non-synonymous mutations in SARS-CoV-2 genome which incidence rates were all [≥]1% as of July 15th, 2020, then modeled the mutated protein structures and compared them with the reference ones. The results showed that four types of mutations could cause dramatic changes in protein structures (RMSD [≥]5.0 [A]), which were Q57H and G251V in open reading frames 3a (ORF3a), S194L and R203K/G204R in nucleocapsid (N). Next, we found that these mutations could affect the binding affinity of intraviral protein interactions. In addition, the hot spots within these docking complexes were altered, among which the mutation Q57H was involved in both Orf3a-Orf8 and Orf3a-S protein interactions. Besides, these mutations were widely distributed all over the world, and their occurrences fluctuated as time went on. Notably, the incidences of R203K/G204R in N and Q57H in Orf3a were both over 50% in some countries. Overall, our findings suggest that SARS-CoV-2 mutations can change viral protein structure, binding affinity and hot spots of the interface, thereby may have impacts on SARS-CoV-2 transmission, diagnosis and treatment of COVID-19.

microbiology↗

bioRxiv2020

UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import

As organisms develop, individual cells generate mitochondria to fulfill physiologic requirements. However, it remains unknown how mitochondrial network expansion is scaled to cell growth and impacted by environmental cues. The mitochondrial unfolded protein response (UPRmt) is a signaling pathway mediated by the transcription factor ATFS-1 which harbors a mitochondrial targeting sequence (MTS)1. Here, we demonstrate that ATFS-1 mediates an adaptable mitochondrial expansion program that is active throughout normal development. Developmental mitochondrial network expansion required the relatively inefficient MTS2 in ATFS-1, which allowed the transcription factor to be responsive to parameters that impact protein import capacity of the entire mitochondrial network. Increasing the strength of the ATFS-1 MTS impaired UPRmt activity throughout development due to increased accumulation within mitochondria. The insulin-like signaling-TORC13 and AMPK pathways affected UPRmt activation4,5 in a manner that correlated with protein synthesis. Manipulation to increase protein synthesis caused UPRmt activation. Alternatively, S6 kinase inhibition had the opposite effect due to increased mitochondrial accumulation of ATFS-1. However, ATFS-1 with a dysfunctional MTS6 constitutively increased UPRmt activity independent of TORC1 function. Lastly, expression of a single protein with a strong MTS, was sufficient to expand the muscle cell mitochondrial network in an ATFS-1-dependent manner. We propose that mitochondrial network expansion during development is an emergent property of the synthesis of highly expressed mitochondrial proteins that exclude ATFS-1 from mitochondrial import, causing UPRmt activation. Mitochondrial network expansion is attenuated once ATFS-1 can be imported.

molecular biology↗

bioRxiv2020

Designed Variants of Recombinant ACE2-Fc that Decouple Anti-SARS-CoV-2 Activities from Unwanted Cardiovascular Effects

Angiotensin-converting enzyme 2 (ACE2) is the entry receptor for SARS-CoV-2, and recombinant ACE2 decoys are being evaluated as new antiviral therapies. We designed and tested an antibody-like ACE2-Fc fusion protein, which has the benefit of long pharmacological half-life and the potential to facilitate immune clearance of the virus. Out of a concern that the intrinsic catalytic activity of ACE2 may unintentionally alter the balance of its hormonal substrates and cause adverse cardiovascular effects in treatment, we performed a mutagenesis screening for inactivating the enzyme. Three mutants, R273A, H378A and E402A, completely lost their enzymatic activity for either surrogate or physiological substrates. All of them remained capable of binding SARS-CoV-2 and could suppress the transduction of a pseudotyped virus in cell culture. This study established new ACE2-Fc candidates as antiviral treatment for SARS-CoV-2 without potentially harmful side effects from ACE2s catalytic actions toward its vasoactive substrates.

biochemistry↗

bioRxiv2020

A novel compound that disrupts mitotic spindle poles in human cells

We characterize the mechanism of action of a new microtubule-targeting compound in cells. Microtubule-targeting drugs are used as successful anti-cancer therapies. We synthesized a family of compounds that share a common scaffold and have several functional groups amenable to modifications. We found that one of the active derivatives, C75, reduces cell viability and prevents microtubule polymerization in vitro. In this study, we explore the phenotypes caused by C75 in cells. It causes mitotic arrest and spindle phenotypes in several cancer cell lines in the nanomolar range. C75 can bind to the Colchicine-pocket on tubulin in vitro, but causes different effects on microtubules in cells. While Colchicine causes a decrease in microtubules and spindle pole collapse without re-growth, similar concentrations of C75 cause a rapid loss of microtubules and spindle pole fragmentation followed by microtubule re-growth to form multipolar spindles. In addition, C75 and Colchicine synergize for reduced viability and spindle phenotypes. Importantly, the phenotypes caused by C75 are similar to those caused by the depletion of ch-TOG, a microtubule polymerase, and tubulin and ch-TOG are displaced and oscillate in C75-treated cells. This suggests that C75 causes microtubule depolymerization in cells either directly or indirectly via inhibiting ch-TOG. This unique effect of C75 on microtubules warrants further exploration of its anti-cancer potential.

cell biology↗

bioRxiv2020

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization

BackgroundMicrobiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome. ResultsIn this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions. ConclusionsStandardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.

microbiology↗

bioRxiv2020

Effects of Starter Feeds of Different Physical Forms on Rumen Fermentation and Microbial Composition for Pre-weaning and Post-weaning Lambs

This study aimed to evaluate the effects of starter feeds of different physical forms on rumen fermentation and microbial composition for lambs. Twenty-four eight-day-old male Hu lambs (5.04 {+/-} 0.75 kg body weight) were fed either milk replacer (MR) and pelleted starter feed (PS), or MR and textured starter feed (TS) in pre-weaning (day 8 to 35) and post-weaning (day 36 to 42) lambs. And the MR was fed by bottles to lambs at 2% of body weight at day 8 divided as three equal amounts at 08:00, 14:00 and 20:00 in pre-weaning. And the lambs were readily availed starter feeds and clean fresh water in the whole experiment. Six lambs for each treatment were euthanized at day 21 or 42 for sampling. The results showed the total volatile fatty acids, propionate and butyrate of rumen liquid in TS groups were all higher than them in PS groups respectively for pre-weaning and post-weaning lambs (P < 0.05), and the pH of rumen liquid in TS group was lower than it in PS group for post-weaning lambs (P < 0.05). Moreover, the pH of rumen and OTUs in TS group had trends to lower than them in PS group for pre-weaned lambs (P = 0.061, P = 0.066). TS established the predominant Phylum, Bacteroidetes, earlier than PS, and increased significantly the relative abundances of Sharpea compared to PS at level of genus (P < 0.05) for pre-weaning and post-weaning lambs. TS were more benefits to trigger rumen development for lambs. IMPORTANCEEarly use of starter feed could trigger rumen fermentation and establishment of dominant flora, which were in favour of growth and development of rumen for ruminants. The physical form of starter feed is one of the important factors to promote rumen fermentation and establishment of dominant flora for ruminants of transition. However, limited study on effects of physical forms of starter feeds, especially the texturized starters containing steam-flaked grains, to rumen fermentative pattern and microbial composition for pre-weaning and post-weaning lambs to date. It was necessary to investigate the effects of physical form of starter feed on rumen fermentation and microbial composition for lambs. The significance of our research showed TS were better benefits to promote the rumen fermentation and establishment of dominant flora for lambs, which will greatly enhance our understanding of physical forms of starter feeds, leading to broader studies on rumen development for lambs.

developmental biology↗

bioRxiv2020

The direct regulation of Aalbdsx on AalVgR is Indispensable for ovarian development in Aedes albopictus

BACKGROUNDAedes albopictus is an important vector with an extensive worldwide distribution. Only female mosquitoes play a significant role in the transmission of pathogens. Doublesex (dsx) is a central nexus gene in the insect somatic sex determination hierarchy. RESULTSIn this study, we characterized the full-length sex-specific splicing forms of the Ae. albopictus dsx gene (Aalbdsx). Then, we identified 15 direct target genes of DSX in adult females using digital gene expression (DGE) combined with qPCR following a chromatin immunoprecipitation assay (ChIP) with specific DSX antibodies. The knockdown of Aalbdsx suppressed ovarian development, and the transcript levels of the Aalbdsx target vitellogenin receptor (VgR) gene decreased, whereas vitellogenin (Vg) expression showed an increase in the fat body. Genes in the major Vg regulatory pathway were also upregulated. Our results suggest that the effects of Aalbdsx RNAi on ovarian development are exerted mainly via VgR rather than Vg. CONCLUSIONThe results of our study not only provide a reference for the further elucidation of the sex determination cascade and comparative analyses of dsx target interactions in mosquitoes but also reveal potential molecular targets for application to the development of sterile male mosquitoes to be released for vector control.

developmental biology↗

bioRxiv2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Microbial and viral communities transform the chemistry of Earths ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles, and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

microbiology↗

bioRxiv2020

stLFRsv: a germline SV analysis pipeline using co-barcoded reads

Co-barcoded reads originated from long DNA fragment (mean length larger than 50Kbp) with barcodes, maintain both single base level accuracy and long range genomic information. We propose a pipeline stLFRsv to detect structure variation using co-barcoded reads. stLFRsv identifies abnormally large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structure variations. The barcodes enabled co-barcoded reads phasing increases the signal to noise ratio and barcode sharing profiles are used to filter out false positives. We integrate the short reads SV caller smoove for smaller variations with stLFRsv. The integrated pipeline was evaluated on the well characterized genome HG002/NA24385 and obtained precision and recall rate of 74.2% and 22.3% for deletion on the whole genome. stLFR found some large variations not included in the benchmark set and verified by means of long reads or assembly. Our work indicates that co-barcoded reads technology has the potential to improve genome completeness.

bioinformatics↗

bioRxiv2020

Fibroblasts as an Alternative to Mesenchymal Stem Cells with Successful Treatment and Immune Modulation in EAE Model of Multiple Sclerosis

The immune modulatory potential of mesenchymal stem cells (MSCs) is well known and is the basis for multiple clinical trials in treatment of autoimmune conditions. Unfortunately, MSCs are relatively rare, difficult to expand in culture, and methods of obtaining MSCs are complicated and expensive. In contrast, fibroblasts are found in copious amounts in various tissues, are a robust cellular population, and can be cultured without need for costs associated with culture media. Previous studies by our group and others have demonstrated fibroblasts possess regenerative activities. In the current study we demonstrated: a) fibroblasts inhibit mixed lymphocyte reaction; b) suppress T cell activation; c) inhibit DC maturation; and d) stimulate T regulatory (Treg) cell formation. Importantly, administration of fibroblasts in the experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis resulted in disease inhibition, which was abrogated upon depletion of Treg cells. This data, combined with existing clinical safety data on fibroblast administration, supports the clinical translation of fibroblast-based therapies for multiple sclerosis.

immunology↗

bioRxiv2020

High-Throughput Human Primary Cell-Based Airway Model for Evaluating Influenza, Coronavirus, or other Respiratory Viruses in vitro

Influenza and other respiratory viruses represent a significant threat to public health, national security, and the world economy, and can lead to the emergence of global pandemics such as the current COVID-19 crisis. One of the greatest barriers to the development of effective therapeutic agents to treat influenza, coronaviruses, and many other infections of the respiratory tract is the absence of a robust preclinical model. Preclinical studies currently rely on high-throughput, low-fidelity in vitro screening with cell lines and/or low-throughput animal models that often provide a poor correlation to human clinical responses. Here, we introduce a human primary airway epithelial cell-based model integrated into a high-throughput platform where tissues are cultured at an air-liquid interface (PREDICT96-ALI). We present results on the application of this platform to influenza and coronavirus infections, providing multiple readouts capable of evaluating viral infection kinetics and potentially the efficacy of therapeutic agents in an in vitro system. Several strains of influenza A virus are shown to successfully infect the human primary cell-based airway tissue cultured at an air-liquid interface (ALI), and as a proof-of-concept, the effect of the antiviral oseltamivir on one strain of Influenza A is evaluated. Human coronaviruses NL63 (HCoV-NL63) and SARS-CoV-2 enter host cells via ACE2 and utilize the protease TMPRSS2 for protein priming, and we confirm expression of both in our ALI model. We also demonstrate coronavirus infection in this system with HCoV-NL63, observing sufficient viral propagation over 96 hours post-infection to indicate successful infection of the primary cell-based model. This new capability has the potential to address a gap in the rapid assessment of therapeutic efficacy of various small molecules and antiviral agents against influenza and other respiratory viruses including coronaviruses.

microbiology↗

bioRxiv2020

Lipid Droplet Is an Ancient and Inheritable Organelle in Bacteria

Lipid droplet (LD) is a monolayer phospholipid membrane-bound organelle found in all eukaryotes and several prokaryotes which plays key roles in cellular lipid homeostasis and human health. The origin and evolution of the organelle remains unknown. Here, we report that through screening over 660 bacteria using biophysical and biochemical methods, plus LD isolation and proteomic tool, LDs were identified in most of these microbes, affiliated with five main bacterial phyla. Moreover, LDs were also identified in E. coli overexpressing lipid synthesis enzymes, indicating that bacteria without detectable LDs possessed the ability of LD biogenesis. The similarity of isolated LDs from representative strains and evolutionary analysis of LD major protein PspA demonstrate that LDs were conserved in bacteria. Furthermore, time-lapse imaging revealed that LDs were inheritable accompanying with bacterial growth and division. Finally, a common ancestor of LD-containing bacteria was predicted to originate 3.19 billion years ago by a phylogenetic analysis. Our findings suggest that LD is a widespread and inheritable organelle from an ancient common ancestor.

cell biology↗

bioRxiv2020

Identification of Lipid Droplets in Gut Microbiota

Recent research has accumulating evidence to support that gut microbiota can be a newly discovered organ/tissue for humans. Although the functions of gut microbiota have been linked to almost all aspects of human physiological, most findings so far are still either belonged to correlational research or at preliminary stage of causal study due to the complexity of gut microbiota as well as lack of proper tools and methods. Thus, development of new approaches is essential and necessary. Lipid droplet is a cellular organelle governing cell lipid homeostasis that is directly related to human metabolic syndromes. Previously we and other groups found lipid droplets in several bacterial strains. We wonder if gut bacteria have lipid droplets. If so, these bacteria may play key roles to regulate gut lipid content, remove unnecessary lipids and produce useful lipid molecules for host. Here we identified lipid droplet-like structures in freshly isolated bacteria from mouse small and large intestines, as well as mouse and human feces. We also purified and analyzed lipid droplets from a cloned human gut bacterium Streptomyces thermovulgaris. Together, we demonstrate the existence of lipid droplets in gut microbiota and established an approach to study them.

microbiology↗

bioRxiv2020

Rab18 Binds PLIN2 and ACSL3 to Mediate Lipid Droplet Dynamics

Rab18 has been linked to lipid metabolism and metabolic diseases in different model systems, but the mechanism of Rab18-mediated lipid droplet (LD) dynamics in muscle cells remains elusive. Here, we report that Rab18 plays an essential role in oleic acid (OA)-induced LD growth and formation in mouse myoblast cell line C2C12. Rab18 was translocated from endoplasmic reticulum (ER) to LDs during the LD growth induced by OA in C2C12 cells, which was directly regulated by perilipin 2 (PLIN2), a LD resident protein. LD-associated Rab18 bound with the C terminus of PLIN2, and the LD localization of Rab18 was diminished after PLIN2 deletion. Moreover, loss of function of Rab18 led to less triacylglycerol (TAG) accumulation and fewer but larger LD formation. In contrast, expression of wild type Rab18 and a constitutively active Rab18 (Q67L) mutant resulted in elevated TAG content and LD number. Furthermore, LD-associated Rab18 interacted with acyl-CoA synthetase long-chain family member 3 (ACSL3) and in turn, promoted the LD localization of ACSL3, which may play an important role in the accumulation of TAG induced by OA. These data showed that Rab18 was recruited to LD after OA treatment, and formed a complex with PLIN2 and ACSL3, which contributes to TAG accumulating and LD growth.

cell biology↗

bioRxiv2020

Dietary S. maltophilia promotes fat storage by enhancing lipogenesis and ER-LD contacts in C. elegans

Dietary and symbiotic bacteria can exert powerful influence on metazoan lipid metabolism. Here, we demonstrate that feeding Caenorhabditis elegans (C. elegans) with the opportunistic pathogenic bacteria Stenotrophomonas maltophilia (S. maltophilia) retards growth and promotes excessive fat storage. Gene expression analysis reveals that dietary S. maltophilia induces a lipogenic transcriptional response that includes the SREBP ortholog SBP-1, and fatty acid desaturases FAT-6 and FAT-7. Live imaging and ultrastructural analysis suggest that excess fat is stored in greatly expanded lipid droplets (LDs), as a result of enhanced endoplasmic reticulum-LD interaction. We also report that loss of function mutations in cyp-35B1 or dpy-9 in C. elegans confers resistance to S. maltophilia. Our work delineates a new model for understanding microbial regulation of metazoan physiology.

cell biology↗

bioRxiv2020

Adiposome Targeting and Enzymatic Activity of Lipid Droplet-Specific Proteins

New strategies to decode the specific protein targeting mechanism on lipid droplet (LD) are urgently needed. Using adiposome, the LD binding of perilipin 2 (PLIN2), perilipin 3 (PLIN3), and adipose triglyceride lipase (ATGL) were studied. Scatchard analysis found that the binding of PLIN2 to the adiposome surface was saturable, pointing to a specific membrane binding partner. Phosphatidylinositol (PI) was found to inhibit PLIN2 binding while it did not impede PLIN3. Structural analysis combined with mutagenesis revealed that the 73rd glutamic acid of PLIN2 is significant for the effect of PI on the protein binding. The presence of PI significantly stimulated the activity of ATGL in vitro. The phosphorylation site mutants of ATGL were found reducing the lipase activity in the adiposome system. Our study demonstrates the utility of adiposome as a powerful, manipulatable model system for the characterization of LD binding and enzymatic activity of LD proteins in vitro.

biochemistry↗

bioRxiv2020

De novo mutation in ancestral generations evolves haplotypes contributing to disease

PurposeThe variome of the Turkish (TK) population, a population with a considerable history of admixture and consanguinity, has not been deeply investigated deeply for its potential impact on the genomic architecture of disease traits. MethodsWe generated and analyzed a database of variants derived from exome sequencing (ES) data of 773 TK unrelated, clinically affected individuals with various suspected Mendelian disease traits, and 643 unaffected relatives. ResultsUsing uniform manifold approximation and projection (UMAP), we showed that the TK genomes are more similar to those of Europeans and consist of two main subpopulations: clusters 1 and 2 (N=235 and 1,181) that differ in admixture proportion and variome (https://turkishvariomedb.shinyapps.io/tvdb/). Furthermore, the higher inbreeding coefficient (F) values observed in the TK affected compared to unaffected individuals correlated with a larger median span of long-sized (>2.64 Mb) runs of homozygosity (ROH) regions (p-value=2.09e-18). We show that long-sized ROHs are more likely to be formed on recently configured haplotypes enriched for rare homozygous deleterious variants in the TK-affected compared to TK-unaffected individuals (p-value= 3.35e-11). Analysis of genotype-phenotype correlations reveals that genes with rare homozygous deleterious variants in long-sized ROHs provide the most comprehensive set of molecular diagnoses for the observed disease traits with a systematic quantitative analysis of HPO (Human Phenotype Ontology) terms. ConclusionOur findings support the notion that novel rare variants on newly configured haplotypes arising within the recent past generations of a family or clan contribute significantly to recessive disease traits in the TK population.

genomics↗

bioRxiv2020

Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

Influenza virus infections are major causes of morbidity and mortality. Research using cultured cells, bulk tissue, and animal models cannot fully capture human disease dynamics. Many aspects of virus-host interactions in a natural setting remain unclear, including the specific cell types that are infected and how they and neighboring bystander cells contribute to the overall antiviral response. To address these questions, we performed single-cell RNA sequencing (scRNA-Seq) on cells from freshly collected nasal washes from healthy human donors and donors diagnosed with acute influenza during the 2017-18 season. We describe a previously uncharacterized goblet cell population, specific to infected individuals, with high expression of MHC class II genes. Furthermore, leveraging scRNA-Seq reads, we obtained deep viral genome coverage and developed a model to rigorously identify infected cells that detected influenza infection in all epithelial cell types and even some immune cells. Our data revealed that each donor was infected by a unique influenza variant and that each variant was separated by at least one unique non-synonymous difference. Our results demonstrate the power of massively-parallel scRNA-Seq to study viral variation, as well as host and viral transcriptional activity during human infection.

genomics↗