Biology subjects

Hu, Z.

Publications and source records attributed to Hu, Z..

13 recordsLinked to original sources

bioRxiv2018

Sonodynamic therapy as an adjunctivw treatment on porphyromonas gingivalis induced periodontitis in rats with diabetes

ObjectivesThe purpose of our research was to examine the effects of Minocycline combined hyaluronic acid (HA)-mediated Ultrasound therapy of infected wound in wister rats.\n\nMethods40 female wister rats were made wound on the two side of the backbone, then infected in Staphylococcus aureus at the comic for three times. then, they are divided into four groups: control group, minocycline combined HA alone, ultasound alone, minocycline combined HA-mediated ultasound group, respective. After 3 times of treatments, the rats were killed and made into specimens. Assessments consisted of visual inspection in the change of the skin, scar formation pathological morphology by hematoxylin and eosin(HE) stain with optical microscopy, IL-1B assaying and TNF-a were performed.\n\nResultCompared with control group, minocycline combined HA alone, ultasound alone, minocycline combined HA-mediated ultasound group all have effect for wound healing, there was a obvious improvement in all parameters over the duration of the experiment(P<0.05). Compared with the control group, minocycline combined HA-mediated ultasound group indicated less inflammation cells (P<0.001) and the reduce of and IL-1B and TNF-a (P<0.001).\n\nConclusionMinocycline combined HA-mediated ultrasound can accelerate tissue regrowth, which exert significant benefits in healing the wounds.

microbiology↗

bioRxiv2018

Construction and Characterization of a Synthetic Baculovirus-inducible 39K Promoter

The low expression activity and specificity of natural promoters limit the applications of genetic engineering. To construct a highly efficient synthetic inducible promoter in the Bombyx mori (Lepidoptera), we analyzed the regulatory elements and functional regions of the B. mori nucleopolyhedrovirus (BmNPV) 39K promoter. The results of truncated mutation analysis of the 39K promoter showed that the transcriptional regulatory region spanning positions -573 to -274 and +1 to +62 is essential for virus-inducible promoter activity. Further investigation using electrophoretic mobility shift assay (EMSA) revealed that the baculovirus IE-1 protein binds to the 39K promoter at the -310 to -355 region, and transcription activates the expression of 39K promoter assay. Finally, we successfully constructed a synthetic inducible promoter that increase the virus-inducing activity of other promoters using the baculovirus-inducible transcriptional activation region that binds to specific core elements of 39K (i.e., spanning the region -310 to -355). In summary, we describes a novel, synthetic, and highly efficient biological tool, namely, a virus-inducible 39K promoter, which provides endless possibilities for future gene function research, gene therapy, and pest control in genetic engineering.

bioengineering↗

bioRxiv2018

Heterodimerization of UNC-13/RIM regulates synaptic vesicle release probability but not priming

UNC-13 proteins play an essential role in synaptic transmission by recruiting synaptic vesicles (SVs) to become available for release, which is termed SV priming. Here we show that the C2A domain of UNC-13L, like the corresponding domain in mammalian Munc13-1, displays two conserved binding modes: forming C2A/C2A homodimers, or forming a heterodimer with the zinc finger domain of UNC-10/RIM (C2A/RIM). Functional analysis revealed that UNC-13Ls C2A promotes synaptic transmission by regulating a post-priming process. Stimulus-evoked release but not SV priming, was impaired in unc-10 mutants deficient for C2A/RIM heterodimerization, leading to decreased release probability. Disrupting C2A/C2A homodimerization in UNC-13L-rescued animals had no effect on synaptic transmission, but fully restored the evoked release and the release probability of unc-10/RIM mutants deficient for C2A/RIM heterodimerization. Thus, our results support the model that RIM binding C2A releases UNC-13L from an autoinhibitory homodimeric complex to become fusion-competent by functioning as a switch only.

neuroscience↗

bioRxiv2018

Basal Forebrain Deep Brain Stimulation Impacts the Regulation of Extracellular Vesicle Related Proteins in the Rat Brain

Extracellular vesicle (EV) signaling has attracted considerable attention in recent years because EVs play a key role in long distance cellular communication functions. EV studies have begun to reveal aspects of physiological and physiopathological regulation in numerous applications, although many areas remain to date largely unexplored. Deep brain stimulation (DBS) has shown remarkable therapeutic benefits of patients with neuropsychiatric disorders, but despite of the long and successful history of use, the mechanisms of action on neural ensemble activity are not yet fully understood. Here we explore how DBS of the basal forebrain impacts EV signaling in the rat brain. We employed differential centrifugations to isolate the EVs prefrontal cortex (PFC), hippocampus and striatum. We then performed quantitative analysis of EV-associated proteins using an MS-based proteomics method. We identified a considerable number of EV-associated proteins are modulated by DBS in three brain regions, some of which have been previously linked with central nervous system disorders. Particularly, neurofilament proteins NFL and NFM were both significantly changed in EVs of PFC, hippocampus and striatum after DBS stimulation compared with controls. The SOD1 protein, associated previously with neurodegenerative diseases, was significantly increased only in PFC. Our study is the first, to our knowledge, to use EV protein analysis to examine DBS effects on brain physiological regulation. Our findings open an entirely new perspective on brain area specific DBS effects.

neuroscience↗

bioRxiv2018

β-lactam Antibiotics Stimulate the Pathogenicity of Methicillin-resistant Staphylococcus aureus Via SarA-controlled Tandem Lipoprotein Expression

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of nosocomial infections worldwide. MRSA resists nearly all {beta}-lactam antibiotics that have a bactericidal activity and a signal inducer effect. However, studies have yet to clarify whether the inducer effect of empirically used {beta}-lactams stimulates MRSA pathogenicity in vivo. Here, we showed that a new cluster of tandem lipoprotein genes (tlpps) was upregulated in MRSA in response to the subinhibitory concentrations of {beta}-lactam induction. The increased Tlpps significantly altered immune responses by macrophages with high IL-6 and TNF levels. The deletion of the tlpps mutant (N315{Delta}tlpps) significantly decreased the proinflammatory cytokine levels in vitro and in vivo. The bacterial loads of N315{Delta}tlpps in the mouse kidney were also reduced compared with those of the wild type N315. The {beta}-lactam-treated MRSA exacerbated cutaneous infections with increased lesion size, extended illness, and flake-like abscess-formation compared with those of the nontreatment. The {beta}-lactam antibiotics that promoted the MRSA pathogenicity were SarA dependent, and the increasing expression of tlpps after {beta}-lactam treatment was directly controlled by the global regulator SarA. Overall, our findings suggested that {beta}-lactams should be used carefully because it might lead to a worse outcome of MRSA infection than inaction in the treatment.\n\nAuthor summary{beta}-lactams are widely used in practice to treat infectious diseases, however, {beta}-lactams worsening the outcome of a certain disease is poorly understood. In this study, we have identified a new cluster of tandem lipoprotein genes (tlpps) that is upregulated in the major clinically prevalent MRSA clones in response to the subinhibitory concentrations of {beta}-lactams induction. The major highlight in this work is that {beta}-lactams induce SarA expression, and then SarA directly binds to the tlpp cluster promoter region and upregulates the tlpp expression in MRSA. Moreover, the {beta}-lactam stimulated Tlpps are important virulence factors that enhance MRSA pathogenicity. The deletion of the tlpps mutant significantly decreases the proinflammatory cytokine levels in vitro and in vivo. The {beta}-lactam induced Tlpps enhance the host inflammatory responses by triggering the expression of IL-6 and TNF, thereby promoting bacterial colonization and abscess formation. These data elucidate that {beta}-lactams can worsen the outcome of MRSA infection through the induction of tlpps that are controlled by the global regulator SarA.

pathology↗

bioRxiv2018

Dominant negative FADD/MORT1 inhibits the development of intestinal intraepithelial lymphocytes with a marked defect on CD8αα+TCRγδ+ T cells

Intestinal intraepithelial lymphocytes are considered to be distinct from thymus-derived cells and are thought to derive locally from cryptopatch (CP) precursors. Although the development and homing of IELs have been studied in some details, the factors controlling their homeostasis are incompletely understood. Here, we demonstrate that FADD, a classic adaptor protein required for death-receptor-induced apoptosis, is a critical regulator of the intestinal IEL development. The mice with a dominant negative mutant of FADD (FADD-DN) display a defective localized intestinal IELs with a marked defect on CD8+TCR{gamma}{delta}+ T cells. Since Lin- LPLs have been identified as precursors CP cells for CD8+ development, we analyzed lamina propria lymphocytes (LPLs) and found the massive accumulation of IL-7R-lin- LPLs in FADD-DN mice. IL-7 plays a differentiation inducing role in the development of intestinal IELs and its receptor IL-7R is a transcriptional target of Notch1. The level of Notch1 expression also showed very low in Lin- LPLs cells from FADD-DN mice compared with normal mice, indicating a possible molecular mechanism of FADD in the early IEL development. In addition, loss of {gamma}{delta} T-IELs induced by FADD-DN results in a worsening inflammation in murine DSS-induced colitis model, suggesting a protective role of FADD in the intestinal homeostasis.

immunology↗

bioRxiv2018

Lymphoid origin of a lineage of intrinsically activated plasmacytoid dendritic cell in mice and humans

We identified a novel mouse plasmacytoid dendritic cell (pDC) lineage derived from the common lymphoid progenitors (CLPs) that is dependent on expression of Bcl11a. These CLP-derived pDCs, which we refer to as "B-pDCs", have a unique gene expression profile that includes hallmark B cell genes, normally not expressed in conventional pDCs. Despite expressing most classical pDC markers such as SIGLEC-H and PDCA1, B-pDCs lack IFN- secretion, exhibiting a distinct inflammatory profile. Functionally, B-pDCs induce T cell proliferation more robustly than canonical pDCs following Toll-like receptor 9 (TLR9) engagement. B-pDCs, along with another homogeneous subpopulation of myeloid derived pDCs, display elevated levels of the cell-surface receptor tyrosine kinase AXL, mirroring human AXL+ transitional DCs in function and transcriptional profile. Murine B-pDCs therefore represent a phenotypically and functionally distinct CLP-derived DC lineage specialized in T cell activation and previously not described in mice.

immunology↗

bioRxiv2018

A hierarchical Bayesian model for detecting convergent rate changes of conserved elements on phylogenetic trees

Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved non-exonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.

evolutionary biology↗

bioRxiv2018

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds

The relative roles of regulatory and protein evolution in the origin and loss of convergent phenotypic traits is a core question in evolutionary biology. Here we combine phylogenomic, epigenomic and developmental data to show that convergent evolution of regulatory regions, but not protein-coding genes, is associated with flightlessness in palaeognathous birds, a classic example of a convergent phenotype. Eleven new genomes, including a draft genome from an extinct moa, resolve palaeognath phylogeny and show that the incidence of independent, convergent accelerations among 284,000 conserved non-exonic elements is significantly more frequent in ratites than other bird lineages. Ratite-specific acceleration of conserved regions and measures of open chromatin across eight tissues in the developing chick identify candidate regulatory regions that may have modified or lost function in ratites. Enhancer activity assays conducted in the early developing chicken forelimb confirm that volant versions of a conserved element in the first intron of the TEAD1 gene display conserved enhancer activity, whereas an accelerated flightless version fails to drive reporter gene expression. Our results show that convergent molecular changes associated with loss of flight are largely regulatory in nature.

evolutionary biology↗

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

The 10,000 Immunomes Project: A resource for human immunology

New immunological assays now enable rich measurements of human immune function, but difficulty attaining enough measurements across sufficiently large and diverse cohorts has hindered describing normal human immune physiology on a large scale. Here we present the 10,000 Immunomes Project (10KIP), a diverse human immunology reference derived from over 44,000 individuals across 242 studies from ImmPort, a publicly available resource of raw immunology study data and protocols. We carefully curated datasets, aggregating subjects from healthy/control arms and harmonizing data across studies. We demonstrate 10KIPs utility by describing variations in serum cytokines and leukocytes by age, race, and sex; defining a baseline cell-cytokine network; and using 10KIP as a common control to describe immunologic changes in pregnancy. Subject-level data is available for interactive visualization and download at http://10kImmunomes.org/. We believe 10KIP can serve as a common control cohort and will accelerate hypothesis generation by clinical and basic immunologists across diverse populations.\n\nOne Sentence SummaryAn open online resource of human immunology data from more than 10,000 normal subjects including interactive data visualization and download enables a new look at immune system differences across age and sex, rapid hypothesis generation, and creation of custom control cohorts.

immunology↗

bioRxiv2017

Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells

While meta-analysis has demonstrated increased statistical power and more robust estimations in studies, the application of this commonly accepted methodology to cytometry data has been challenging. Different cytometry studies often involve diverse sets of markers. Moreover, the detected values of the same marker are inconsistent between studies due to different experimental designs and cytometer configurations. As a result, the cell subsets identified by existing auto-gating methods cannot be directly compared across studies. We developed MetaCyto for automated meta-analysis of both flow and mass cytometry (CyTOF) data. By combining clustering methods with a silhouette scanning method, MetaCyto is able to identify commonly labeled cell subsets across studies, thus enabling meta-analysis. Applying MetaCyto across a set of 10 heterogeneous cytometry studies totaling 2926 samples enabled us to identify multiple cell populations exhibiting differences in abundance between White and Asian adults. Software is released to the public through GitHub (github.com/hzc363/MetaCyto).

bioinformatics↗

bioRxiv2017

xCell: Digitally portraying the tissue cellular heterogeneity landscape

Tissues are complex milieu consisting of numerous cell-types. Numerous recent methods attempt to enumerate cell subsets from transcriptomes. However, available method used limited source for training and displayed only partial portrayal of the full cellular landscape. Here we present xCell, a novel gene-signature based method for inferring 64 immune and stroma cell-types. We harmonized 1,822 pure human cell-types transcriptomes from various sources, employed curve fitting approach for linear comparison of cell-types, and introduced a novel spillover compensation technique for separating between cell-types. Using extensive in silico analyses and comparison to cytometry immunophenotyping we show that xCell outperforms other methods: http://xCell.ucsf.edu/.

bioinformatics↗