Biology subjects

Ma, Q.

Publications and source records attributed to Ma, Q..

215 records · Page 12Linked to original sources

bioRxiv2018

Thylakoid-integrated recombinant Hcf106 participates in the chloroplast Twin Arginine Transport (cpTat) system

The chloroplast Twin arginine transport (cpTat) system distinguishes itself as a protein transport pathway by translocating fully-folded proteins, using the proton-motive force (PMF) as the sole source of energy. The cpTat pathway is evolutionarily conserved with the Tat pathway found in the plasma membrane of many prokaryotes. The cpTat (E. coli) system uses three proteins, Tha4 (TatA), Hcf106 (TatB), and cpTatC (TatC), to form a transient translocase allowing the passage of precursor proteins. Briefly, cpTatC and Hcf106, with Tha4, form the initial receptor complex responsible for precursor protein recognition and binding in an energy-independent manner, while a separate pool of Tha4 assembles with the precursor-bound receptor complex in the presence the PMF. Analysis by blue-native polyacrylamide gel electrophoresis (BN-PAGE) shows that the receptor complex, in the absence of precursor, migrates near 700 kDa and contains cpTatC and Hcf106 with little Tha4 remaining after detergent solubilization. To investigate the role that Hcf106 may play in receptor complex oligomerization and/or stability, systematic cysteine substitutions were made in positions from the N-terminal transmembrane domain to the end of the predicted amphipathic helix of the protein. BN-PAGE analysis allowed us to identify the locations of amino acids in Hcf106 that were critical for interacting with cpTatC. Oxidative cross-linking allowed us to map interactions of the transmembrane domain and amphipathic helix region of Hcf106. In addition, we showed that in vitro expressed, integrated Hcf106 can interact with the precursor signal peptide domain and imported cpTatC, strongly suggesting that a subpopulation of the integrated Hcf106 is participating in competent cpTat complexes.

plant biology↗

bioRxiv2018

Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development

Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCFTIR1/AFB functionality as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin1 to 4 (RN1 to 4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical and morphological levels. This selective activity is explained by their ability to promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, via a genetic screen using RN4, we revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions.

plant biology↗

bioRxiv2018

Corilagin controls post-parasiticide schistosome egg-induced liver fibrosis by inhibiting Stat6 signalling pathway

This study aims to explore the effect of Corilagin (Cor) on post-parasiticide schistosome egg-induced hepatic fibrosis through the Stat6 signalling pathway in vitro and in vivo. Cellular and animal models were established and treated by Corilagin. The inhibitory effect of Corilagin was also confirmed in RAW264.7 cells in which Stat6 was overexpressed based on the GV367-Stat6-EGFP lentiviral vector system and in which Stat6 was knock-downed by gene specific siRNAs. As a result, Corilagin prevented increases in the protein level of Phospho-Stat6 (P-Stat6). Both the mRNA and protein levels of the downstream mediators SOCS1, KLF4, and PPAR{gamma}/{delta} were markedly suppressed after Corilagin treatment. Expression of ARG1 and FIZZ1/Retnla, Ym1, TGF-{beta} and PDGF in serum were also inhibited by Corilagin. The pathological changes, area of granulomas of liver sections, and degree of hepatic fibrosis were significantly alleviated in the Corilagin group. The areas of CD68- and CD206-positive cells stained by immunofluorescence were significantly decreased by Corilagin. In conclusion, Corilagin can suppress post-parasiticide schistosome egg-induced hepatic fibrosis by inhibiting the Stat6 signalling pathway and provide a new therapeutic strategy for schistosomiasis liver fibrosis.

pharmacology and toxicology↗

bioRxiv2018

The interplay between small RNA pathways shapes chromatin landscape in C. elegans

The nematode C. elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both \"silencing\" siRNAs bound by Worm-specific Argonautes (WAGO) and \"activating\" siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partial loss-of-function mutant this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in both drh-3 and csr-1 partial loss-of-function mutants and describe small RNAs matching enhancers. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to increase in silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.

molecular biology↗

bioRxiv2018

NDUFAB1 Protects Heart by Coordinating Mitochondrial Respiratory Complex and Supercomplex Assembly

The impairment of mitochondrial bioenergetics, often coupled with exaggerated reactive oxygen species (ROS) production, is emerging as a common mechanism in diseases of organs with a high demand for energy, such as the heart. Building a more robust cellular powerhouse holds promise for protecting these organs in stressful conditions. Here, we demonstrate that NDUFAB1 (NADH:ubiquinone oxidoreductase subunit AB1), acts as a powerful cardio-protector by enhancing mitochondrial energy biogenesis. In particular, NDUFAB1 coordinates the assembly of respiratory complexes I, II, and III and supercomplexes, conferring greater capacity and efficiency of mitochondrial energy metabolism. Cardiac-specific deletion of Ndufab1 in mice caused progressive dilated cardiomyopathy associated with defective bioenergetics and elevated ROS levels, leading to heart failure and sudden death. In contrast, transgenic overexpression of Ndufab1 effectively enhanced mitochondrial bioenergetics and protected the heart against ischemia-reperfusion injury. Our findings identify NDUFAB1 as a central endogenous regulator of mitochondrial energy and ROS metabolism and thus provide a potential therapeutic target for the treatment of heart failure and other mitochondrial bioenergetics-centered diseases.

cell biology↗

bioRxiv2018

IRIS-DGE: An integrated RNA-seq data analysis and interpretation system for differential gene expression

MotivationNext-Generation Sequencing has made available much more large-scale genomic and transcriptomic data. Studies with RNA-sequencing (RNA-seq) data typically involve generation of gene expression profiles that can be further analyzed, many times involving differential gene expression (DGE). This process enables comparison across samples of two or more factor levels. A recurring issue with DGE analyses is the complicated nature of the comparisons to be made, in which a variety of factor combinations, pairwise comparisons, and main or blocked main effects need to be tested.\n\nResultsHere we present a tool called IRIS-DGE, which is a server-based DGE analysis tool developed using Shiny. It provides a straightforward, user-friendly platform for performing comprehensive DGE analysis, and crucial analyses that help design hypotheses and to determine key genomic features. IRIS-DGE integrates the three most commonly used R-based DGE tools to determine differentially expressed genes (DEGs) and includes numerous methods for performing preliminary analysis on user-provided gene expression information. Additionally, this tool integrates a variety of visualizations, in a highly interactive manner, for improved interpretation of preliminary and DGE analyses.\n\nAvailabilityIRIS-DGE is freely available at http://bmbl.sdstate.edu/IRIS/.\n\nContactqin.ma@sdstate.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2018

ViDGER: An R package for integrative interpretation of differential gene expression results of RNA-seq data

Differential gene expression (DGE) is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes (DEGs) across two or more conditions. Interpretation of the DGE results can be non-intuitive and time consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. Here we present an R package, ViDGER (Visualization of Differential Gene Expression Results using R), which contains nine functions that generate information-rich visualizations for the interpretation of DGE results from three widely-used tools, Cuffdiff, DESeq2, and edgeR.

bioinformatics↗

bioRxiv2018

GeneQC: A quality control tool for gene expression estimation based on RNA-sequencing reads mapping

MotivationOne of the main benefits of using modern RNA-sequencing (RNA-Seq) technology is the more accurate gene expression estimations compared with previous generations of expression data, such as the microarray. However, numerous issues can result in the possibility that an RNA-Seq read can be mapped to multiple locations on the reference genome with the same alignment scores, which occurs in plant, animal, and metagenome samples. Such a read is so-called a multiple-mapping read (MMR). The impact of these MMRs is reflected in gene expression estimation and all downstream analyses, including differential gene expression, functional enrichment, etc. Current analysis pipelines lack the tools to effectively test the reliability of gene expression estimations, thus are incapable of ensuring the validity of all downstream analyses.\n\nResultsOur investigation into 95 RNA-Seq datasets from seven species (totaling 1,951GB) indicates an average of roughly 22% of all reads are MMRs for plant and animal species. Here we present a tool called GeneQC (Gene expression Quality Control), which can accurately estimate the reliability of each genes expression level. The underlying algorithm is designed based on extracted genomic and transcriptomic features, which are then combined using elastic-net regularization and mixture model fitting to provide a clearer picture of mapping uncertainty for each gene. GeneQC allows researchers to determine reliable expression estimations and conduct further analysis on the gene expression that is of sufficient quality. This tool also enables researchers to investigate continued re-alignment methods to determine more accurate gene expression estimates for those with low reliability.\n\nAvailabilityGeneQC is freely available at http://bmbl.sdstate.edu/GeneQC/home.html.\n\nContactqin.ma@sdstate.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2018

Computational elucidation of regulatory network responding to acid stress in Lactococcus lactis MG1363

Acid stress caused by lactate increment can lead to the growth inhibition of bacteria and yes has not been fully defined. Regulons, serve as co-regulated gene groups contribute to the transcriptional regulation of microbe genome, have the potential in understanding the underlying regulatory mechanism. Lactococcus lactis is one of the most important Gram-positive lactic acid-producing bacteria, widely used in food industry and has been proved to have advantages in oral delivery of drug and vaccine. In this study, we designed a novel computational pipeline, RECTA, for regulon prediction. The pipeline carried out differentially expressed gene prediction, gene co-expression analysis, cis-regulatory motif finding, and comparative genomic study to predict and validate regulons related to acid stress response in Lactococcus lactis MG1363. A total of 51 regulons were identified, and 14 of them have computational verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response with (i) known transcriptional factors in MEME suite database successfully mapped in Lactococcus lactis MG1363; and (ii) differentially expressed genes between pH values of 6.5 (control) and 5.1 (treatment). Validated by 36 literature confirmed acid stress response related proteins and genes, 33 genes in Lactococcus lactis MG1363 were found having orthologous genes using BLAST, associated to six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A, rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated to acid stress. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network based on regulon elucidation. The predicted resistance pathways could serve as promising candidates for better acid tolerance engineering in Lactococcus lactis. It has a strong application power and can be effectively applied to other bacterial genomes, where the elucidation of the transcriptional regulation network is needed.

systems biology↗

bioRxiv2018

Gallic Acid Disrupts Aβ1-42 Aggregation and Rescues Cognitive Decline of APP/PS1 Transgenic Mouse

Alzheimers disease (AD) treatment represents one of the largest unmet medical needs. Developing drugs capable of preventing A{beta} aggregation is an excellent approach to prevent and treat AD. Here, we show that gallic acid (GA), a naturally occurring polyphenolic small molecule rich in grape seeds and fruits, has the capacity to alleviate cognitive decline of APP/PS1 transgenic mouse through reduction of A{beta}1-42 aggregation and neurotoxicity. Oral administration of GA not only improved the spatial reference memory and spatial working memory of early stage AD mice (4-month-old), but also significantly reduced the more severe deficits in spatial learning, reference memory, short-term recognition and spatial working memory of the late stage AD mice (9-month-old). The hippocampal long-term-potentiation (LTP) was also significantly elevated in the GA-treated late stage APP/PS1 AD mice. Atomic force microscopy (AFM), dynamic light scattering (DLS) and thioflavin T (ThT) fluorescence densitometry analyses showed that GA can reduce A{beta}1-42 aggregation from forming toxic oligomers and fibrils. Indeed, pre-incubating GA with oligomeric A{beta}1-42 reduced A{beta} 1-42-mediated intracellular calcium influx and neurotoxicity. Molecular docking studies identified that the 3,4,5-hydroxyle groups of GA were essential in noncovalently stabilizing GA binding to the Lys28-Ala42 salt bridge and the -COOH group is critical for disrupting the salt bridge of A{beta}1-42. The predicated covalent interaction through Schiff-base formation between the carbonyl group of the oxidized product and {varepsilon}-amino group of Lys16 is also critical for the disruption of A{beta}1-42 S-shaped triple-{beta}-motif and toxicity. Together, these studies demonstrated that GA can prevent and protect the AD brain through disrupting A{beta}1-42 aggregation.

neuroscience↗

bioRxiv2017

Identification of methylation and hydroxymethylation haplotype blocks as distal regulatory elements aids in deconvolution of heterogeneous brain tissues

5-Hydroxymethylcytosine (5hmC) is an oxidation product of 5-methylcytosine (5mC), and adjacent CpG sites in the mammalian genome can be co-methylated and co-hydroxymethylated due to the processivity of DNMT and TET enzymes. We applied TAB-seq and oxBS-seq to selectively detect 5hmC and 5mC, respectively, at base resolution in the mouse cortex, olfactory bulb and cerebellum tissues. We found that majority of the called 5hmC CpG sites frequently had 5mC modification simultaneously and enriched in gene body regions of neuron development related genes in brain tissues. These results supported a prominent role of oxidizing 5mC to 5hmC as new epigenetic mark. Strikingly, by a systematic search of regions that show highly coordinated methylation and hydroxymethylation (MHBs and hMHBs), we found that MHBs significantly overlapped with hMHBs in gene body regions which further supported that oxidized 5mC to 5hmC co-ordinately in a subset of cells within heterogeneous brain tissues. Consistently, using a metric called methylation haplotype load, we defined a subset of 1,361 tissue-specific MHBs and 3,818 shared MHBs which were predominantly regulatory elements, and aids in deconvolution of heterogeneous brain tissues. Our results provide new insights into the role of co-ordinately oxidized 5mC to 5hmC as distal regulatory elements may involve in regulating tissue identity.

genetics↗

bioRxiv2017

Dynamic protein aggregation regulates bacterial dormancy depth critical for antibiotic tolerance

The ability of some bacteria within a population to tolerate antibiotic treatment is often attributed to prolonged bacterial infection1-3. Unlike antibiotic resistance, which generally results from genetic mutations or plasmid transfer4,5, antibiotic tolerance usually refers to the phenomenon that a subgroup of cells can survive high dose antibiotic treatment as a result of phenotypic heterogeneity6,7. Previous studies mainly associate antibiotic tolerance with cell dormancy, by hypothesizing that the lethal effects of antibiotics are disabled due to the extremely slow metabolic and proliferation rates in dormant bacteria 8,9. However, less is known about how surviving bacteria subsequently escape from the dormant state and resuscitate, which is equally important for disease recurrence. Here we monitored the process of bacterial antibiotic tolerance and regrowth at the single-cell level, and found that each individual survival cell shows different dormancy depth, which in return regulates whether and when it can resume growth after removal of antibiotic. The persister cells are considered to be in shallow dormancy depth, while the viable but non-culturable cells (VBNC cells) are in deep dormancy depth. We further implemented time-lapse fluorescent imaging and biochemical analysis to establish that dynamic endogenous protein aggregation is an important indicator of bacterial dormancy depth. For cells to leave the dormant state and resuscitate, clearance of cellular protein aggregates and recovery of proteostasis are required. Through additional mutagenesis studies, we found the ability to recruit functional DnaK-ClpB machineries, which facilitate protein disaggregation in an ATP-dependent manner, determines the timeline (whether and when) for bacterial regrowth. Better understanding of the key factors regulating bacterial regrowth after surviving antibiotic attack could lead to new therapeutic strategies for combating bacterial antibiotic tolerance.

microbiology↗

bioRxiv2017

Genetic load and mutational meltdown in cancer cell populations

ABSRACTLarge and non-recombining genomes are prone to accumulating deleterious mutations faster than natural selection can purge (Mullers ratchet). A possible consequence would then be the extinction of small populations. Relative to most single-cell organisms, cancer cells, with large and non-recombining genomes, could be particularly susceptible to such \"mutational meltdown\". Curiously, deleterious mutations in cancer cells are rarely noticed despite the strong signals in cancer genome sequences. Here, by monitoring single-cell clones from HeLa cell lines, we characterize deleterious mutations that retard cell proliferation. The main mutational events are copy number variations (CNVs), which happen at an extraordinarily high rate of 0.29 events per cell division. The average fitness reduction, estimated to be 18% per mutation, is also very high. HeLa cell populations therefore have very substantial genetic load and, at this level, natural population would likely experience mutational meltdown. We suspect that HeLa cell populations may avoid extinction only after the population size becomes large. Because CNVs are common in most cell lines and cancer tissues, the observations hint at cancer cells vulnerability, which could be exploited by therapeutic strategies.

evolutionary biology↗

bioRxiv2017

A probabilistic model-based bi-clustering method for single-cell transcriptomic data analysis

We present here novel computational techniques for tackling four problems related to analyses of single-cell RNA-Seq data: (1) a mixture model for coping with multiple cell types in a cell population; (2) a truncated model for handling the unquantifiable errors caused by large numbers of zeros or low-expression values; (3) a bi-clustering technique for detection of sub-populations of cells sharing common expression patterns among subsets of genes; and (4) detection of small cell sub-populations with distinct expression patterns. Through case studies, we demonstrated that these techniques can derive high-resolution information from single-cell data that are not feasible using existing techniques.

bioinformatics↗

bioRxiv2017

Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity

Cells of multi-cellular organisms evolve toward uni-cellularity in the form of cancer and, if humans intervene, continue to evolve in cell culture. During this process, gene dosage relationships may evolve in novel ways to cope with the new environment and may regress back to the ancestral unicellular state. In this context, the evolution of sex chromosomes vis-a-vis autosomes is of particular interest. Here, we report the chromosomal evolution in ~600 cancer cell lines. Many of them jettisoned either Y or the inactive X; thus, free-living male and female cells converge by becoming \"de-sexualized\". Surprisingly, the active X often doubled, accompanied by the addition of one haploid complement of autosomes, leading to an X:A ratio of 2:3 from the extant ratio of 1:2. Theoretical modeling of the frequency distribution of X:A karyotypes suggests that the 2:3 ratio confers a higher fitness and may reflect aspects of sex chromosome evolution.

genomics↗

bioRxiv2017

ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) underlies a major Al resistance QTL and interacts with natural variation in the genetic background to quantitatively regulate Al resistance in rice.

Transcription factors (TFs) mediate stress resistance indirectly via physiological mechanisms driven by the genes they regulate. When studying TF-mediated stress resistance, it is important to understand how TFs interact with different genetic backgrounds. Here, we fine-mapped the aluminum (Al) resistance QTL Alt12.1 to a 44 Kb region containing six gene models. Among them is ART1, which encodes a C2H2-type zinc finger TF required for Al resistance in rice. The parents of the mapping population, Al-resistant Azucena (tropical japonica) and Al-sensitive IR64 (indica), showed similar ART1 expression levels but extensive sequence polymorphism within the ART1 coding region. Using reciprocal near-isogenic lines (NILs) in the Azucena and IR64 genetic backgrounds, we examined how allele-swapping Alt12.1 would affect plant responses to Al. Analysis of global transcriptional responses to Al stress in roots of the NILs alongside their recurrent parents demonstrated that the ART1 from Al-resistant Azucena led to greater changes in gene expression in response to Al when compared to the ART1 from IR64 in both genetic backgrounds. The presence of the ART1 allele from the opposite parent affected the expression of several genes not previously implicated in rice Al tolerance. We highlight examples where putatively functional variation in cis-regulatory regions of ART1-regulated genes interacts with ART1 to determine gene expression in response to Al. This ART1-promoter interaction may be associated with transgressive variation for Al resistance in the Azucena x IR64 population. These results illustrate how ART1 interacts with the genetic background to contribute to quantitative phenotypic variation in rice Al resistance.

plant biology↗

bioRxiv2017

Worldwide Population Structure Of Escherichia coli Reveals Two Major Subspecies

Recombination is one of the most important mechanisms of prokaryotic species evolution but its exact roles are still in debate. Here we try to infer genome-wide recombination events within a species uti-lizing a dataset of 104 complete genomes of Escherichia coli from diverse origins, among which 45 from world-wide animal-hosts are in-house sequenced using SMRT (single-molecular real time) technology.Two major clades are identified based on evidences of ecological and physiological characteristics, as well as distinct genomic features implying scarce inter-clade genetic exchange. By comparing the synteny of identical fragments genome-widely searched for each genome pair, we achieve a fine-scale map of re-combination within the population. The recombination is rather extensive within clade, which is able to break linkages between genes but does not interrupt core genome framework and primary metabolic port-folios possibly due to natural selection for physiological compatibility and ecological fitness. Meanwhile,the recombination between clades declines drastically as the phylogenetic distance increases, generally 10-fold reduced than those of the intra-clade, which establishes genetic barrier between clades. These empirical data of recombination suggest its critical role in the early stage of speciation, where recombina-tion rate differs according to phylogentic distance. The extensive intra-clade recombination coheres sister strains into a quasi-sexual group and optimizes genes or alleles to streamline physiological activities,whereas shapely declined inter-clade recombination split the population into clades adaptive to divergent ecological niches.\n\nSignificance StatementRoles of recombination in species evolution have been debated for decades due to difficulties in inferring recombination events during the early stage of speciation, especially when recombination is always complicated by frequent gene transfer events of bacterial genomes. Based on 104 high-quality complete E. coli genomes, we infer gene-centric dynamics of recombination in the formation of two E. coli clades or subpopulations, and recombination is found to be rather intensive in a within-clade fashion, which forces them to be quasi-sexual. The recombination events can be mapped among individual genomes in the context of genes and their variations; decreased between-clade and increased intra-claderecombination engender a genetic barrier that further encourages clade-specific secondary metabolic portfolios for better environmental adaptation. Recombination is thus a major force that accelerates bacterial evolution to fit ecological diversity.

microbiology↗