Biology subjects

Sun, K.

Publications and source records attributed to Sun, K..

83 records · Page 5Linked to original sources

bioRxiv2020

Disease mutation study identifies essential residues for phosphatidylserine flippase ATP11A

PS flippase (P4-ATPase) transports PS from the outer to the inner leaflet of the lipid bilayer in the membrane to maintain PS asymmetry, which is important for biological activity of the cell. ATP11A is expressed in multiple tissues and plays a role in myotube formation. However, detailed cellular function of ATP11A remains elusive. Mutation analysis revealed that I91, L308 and E897 residues in ATP8A2 are important for flippase activity. In order to investigate the roles of these corresponding amino acid residues in ATP11A, we assessed the expression and flippase activity of the respective ATP11A mutant proteins. ATP11A mainly localizes to the Golgi when co-expressed with TMEM30A, the {beta}-subunit of the complex. Y300F and D913K mutations affect correct Golgi localization and PS stimulated flippase activity. In addition, Y300F mutation causes reduced ATP11A expression. Our data provides insight into essential residues for expression and flippase activity of ATP11A.

biochemistry↗

bioRxiv2019

LARP7 is a BRCA1 ubiquitinase substrate and regulates genome stability and tumorigenesis

Attenuated DNA repair leads to genomic instability and tumorigenesis. BRCA1/BARD1 are the best known tumor suppressors that promote homology recombination (HR) and arrest cell cycle at G2/M checkpoint. As E3 ubiquitin ligases, their ubiquitinase activity has been known to involve in the HR and tumor suppression, but the mechanism remains ambiguous. Here, we demonstrated upon genotoxic stress, BRCA1 together with BARD1 catalyzed the K48 ployubiquitination on LARP7, a 7SK RNA binding protein known to control RNAPII pausing, and thereby degraded it through 26S ubiquitin-proteasome pathway. Depleting LARP7 suppressed the expression of CDK1 complex, arrested cell at G2/M DNA damage checkpoint and reduced BRCA2 phosphorylation which thereby facilitated RAD51 recruitment to damaged DNA to enhance HR. Importantly, LARP7 depletion observed in breast patients lead to the chemoradiotherapy resistance both in vitro and in vivo. Together, this study unveils a mechanism by which BRCA1/BARD1 utilizes their E3 ligase activity to control HR and cell cycle, and highlights LARP7 as a potential target for cancer prevention and therapy.\n\nHighlightsO_LIDNA damage response downregulates LARP7 through BRCA1/BARD1\nC_LIO_LIBRCA1/BARD1 catalyzes the K48 polyubiquitination on LARP7\nC_LIO_LILARP7 promotes G2/M cell cycle transition and tumorigenesis via CDK1 complex\nC_LIO_LILARP7 disputes homology-directed repair that leads to tumor therapy resistance\nC_LI

molecular biology↗

bioRxiv2019

Targeting the Pregnane X Receptor Using Microbial Metabolite Mimicry

The human pregnane X receptor (PXR), a master regulator of drug metabolism, has important roles in intestinal homeostasis and abrogating inflammation. Existing PXR ligands have substantial off-target toxicity. Based on prior work that established microbial (indole) metabolites as PXR ligands, we proposed microbial metabolite mimicry as a novel strategy for drug discovery that allows to exploit previously unexplored parts of chemical space. Here we report functionalized indole-derivatives as first-in-class non-cytotoxic PXR agonists, as a proof-of-concept for microbial metabolite mimicry. The lead compound, FKK6, binds directly to PXR protein in solution, induces PXR specific target gene expression in, cells, human organoids, and mice. FKK6 significantly represses pro-inflammatory cytokine production cells and abrogates inflammation in mice expressing the human PXR gene. The development of FKK6 demonstrates for the first time that microbial metabolite mimicry is a viable strategy for drug discovery and opens the door to mine underexploited regions of chemical space.

biochemistry↗

bioRxiv2019

A new strategy for selection of crop cultivated varieties based on yield factors driving and meteorological prediction

Meteorological conditions, as an uncontrollable factor, have a direct impact on the growth and yield of crops in the field. Its particularly important to choose the cultivated varieties suitable for environmental change. As for this problem, a new strategy for selection of crop cultivated varieties is proposed in this paper. The experiment selected Harbin pilot (Heilongjiang, China) and Changchun pilot (Jilin, China). In the experiment, the cultivated varieties suitable for forecasting meteorological conditions in 2015 could be provided according to the meteorological data of 2005-2014 years and the yield data of different soybean varieties in Harbin pilot. The same method was also taken in Changchun pilot. The results showed that the recommended varieties of Harbin pilot and Changchun pilot had 70% and 50% probability respectively for selection of soybean cultivated varieties when the yield evaluation trait was 100-seed-weight. As for seed weight per plant, the possibility of more than 60% of the recommended varieties in two pilots is to provide prejudgment. Therefore, this method can help to improve the current situation of the impact of uncontrollable meteorological conditions on crop yield and also can be applied to the selection of any other crops cultivated varieties under a certain environment.

plant biology↗

bioRxiv2019

Bacterial Hyperswarming as a Protective Response to Intestinal Stress

Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. Here, we report for the first time that bacterial swarmers are associated with protection against intestinal inflammation. We show that bacterial swarmers are highly predictive of intestinal stress in mice and humans. We isolated a novel Enterobacter swarming strain, SM3, from mouse feces. SM3 and other known commensal swarmers contrast to their respective swarming-deficient, but swimming-competent isogenic strains abrogated intestinal inflammation in mice. Treatment of colitic mice with SM3, but not its mutants, enriched beneficial fecal anaerobes belonging to the family, Bacteroidales S24-7. We observed SM3 swarming associated pathways in the in vivo fecal metatranscriptomes. In vitro growth of S24-7 was enriched in presence of SM3 or its mutants conjecturing that bacterial swarming in vivo might influence SM3s access to S24-7 in the intestines. Overall, our work identifies a new paradigm in which intestinal stress allows for the emergence of swarming bacteria, which can counterintuitively heal intestinal inflammation.

microbiology↗

bioRxiv2019

A Topological Data Analysis Network Model of Asthma Based on Blood Gene Expression Profiles

Stratified medicine requires discretisation of disease populations for targeted treatments. We have developed and applied a discrete Morse theory clustering algorithm to a Topological Data Analysis (TDA) network model of 498 gene expression profiles of peripheral blood from asthma and healthy participants. The Morse clustering algorithm defined nine clusters, BC1-9, representing molecular phenotypes with discrete phenotypes including Type-1, 2 & 17 cytokine inflammatory pathways. The TDA network model and clusters were also characterised by activity of glucocorticoid receptor signalling associated with different expression profiles of glucocorticoid receptor (GR), according to microarray probesets targeted to the start or end of the GR mRNAs 3 UTR; suggesting differential GR mRNA processing as a possible driver of asthma phenotypes including steroid insensitivity.

molecular biology↗

bioRxiv2018

Transient Overexpression of VEGF-A in Adipose Tissue Promotes Energy Expenditure via Activation of the Sympathetic Nervous System

Adipose-derived VEGF-A stimulates functional blood vessel formation in obese fat pads which in turn facilitates healthy expansion of the adipose tissue. However, the detailed mechanism(s) governing the process remains largely unknown. Here, we investigated the role of sympathetic nervous system activation in the process. To this end, we induced overexpression of VEGF-A in an adipose-specific doxycycline (Dox)-inducible transgenic mouse model for a short period of time during high fat-diet (HFD) feeding. We found that local overexpression of VEGF-A in adipose tissue stimulated lipolysis and browning rapidly after Dox induction. Immunofluorescent staining against tyrosine hydroxylase (TH) indicated higher levels of sympathetic innervation in adipose tissue of transgenic mice. In response to the increased norepinephrine (NE) level, expression of {beta}3-andrenoceptor was significantly upregulated and the downstream protein kinase A (PKA) pathway was activated, as indicated by the enhanced phosphorylation of the whole PKA substrates, in particular the hormone sensitive lipase (HSL) in adipocytes. As the result, the adipose tissue exhibited increased lipolysis, browning, and energy expenditure. Importantly, all these effects were abolished upon the treatment with {beta}3-adrenoceptor antagonist SR59230A. Collectively, these results demonstrate that transient overexpressed VEGF-A activates sympathetic nervous system which hence promotes lipolysis and browning in adipose tissue.

physiology↗

bioRxiv2018

Impact of exogenous nitrogen on cyanobacterial abundance and community in oil-contaminated sediment mesocosms

High concentrations of crude oil are toxic to cyanobacteria but can facilitate the emergence of cyanobacterial aggregation at an appropriate concentration range; however, the exact inducing factor has never been clearly elucidated. We hypothesized that increasing exposure to elevated concentrations of nitrogen would inhibit the accumulation of cyanobacteria in oil-contaminated sediments. To test this hypothesis, we simulated an oil spill in estuarine sediment microcosms with and without the removal of nitrogen limitation by supplementation of exogenous nitrogen. An integrated MiSeq sequencing of 16S rRNA gene analysis along with metatranscriptome sequence was performed to achieve a comprehensive study of cyanobacterial blooms. The number of cyanobacterial sequences increased over time in both oil-contaminated and non-oil-contaminated sediments at different time points after 42 days of incubation. And, supplementation with a nitrogen resource could accelerate cyanobacterial blooms under uncontaminated microcosms but delay the bloom phenomenon and reduce the cyanobacterial abundance to a great degree when exposed to oil. Our results clearly illustrated that nitrogen limitation was a vital driver of the increased abundance of cyanobacteria in oil-contaminated mesocosms. In addition, the abundance and compositions of blooming cyanobacteria varied significantly among the different treatment groups, and Oscillatoria may play a potential and non-negligible role in oil-contaminated mesocosms.

microbiology↗

bioRxiv2018

Quantifying the risk of local Zika virus transmission in the continental US during the 2015-2016 ZIKV epidemic

BackgroundLocal mosquito-borne Zika virus (ZIKV) transmission has been reported in two counties of the continental United State (US), prompting the issuance of travel, prevention, and testing guidance across the continental US. Large uncertainty, however, surrounds the quantification of the actual risk of ZIKV introduction and autochthonous transmission across different areas of the US.\n\nMethodWe present a framework for the projection of ZIKV autochthonous transmission in the continental US during the 2015-2016 epidemic, using a data-driven stochastic and spatial epidemic model accounting for seasonal, environmental and detailed population data. The model generates an ensemble of travel-related case counts and simulate their potential to trigger local transmission at individual level.\n\nResultsWe estimate the risk of ZIKV introduction and local transmission at the county level and at the 0.025{degrees} x 0.025{degrees} cell level across the continental US. We provide a risk measure based on the probability of observing local transmission in a specific location during a ZIKV epidemic modeled after the one observed during the years 2015-2016. The high spatial and temporal resolutions of the model allow us to generate statistical estimates of the number of ZIKV introductions leading to local transmission in each location. We find that the risk is spatially heterogeneously distributed and concentrated in a few specific areas that account for less than 1% of the continental US population. Locations in Texas and Florida that have actually experienced local ZIKV transmission are among the places at highest risk according to our results. We also provide an analysis of the key determinants for local transmission, and identify the key introduction routes and their contributions to ZIKV spread in the continental US.\n\nConclusionsThis framework provides quantitative risk estimates, fully captures the stochas-ticity of ZIKV introduction events, and is not biased by the under-ascertainment of cases due to asymptomatic infections. It provides general information on key risk determinants and data with potential uses in defining public health recommendations and guidance about ZIKV risk in the US.

epidemiology↗

bioRxiv2018

A compromised gsdf signaling leads to gamatogenesis confusion and subfertility in medaka

Summary statementGsdf signals trigger the gamatogenesis, alter the somatic expression of Fsh/Lh receptors and brain type aromatase in medaka brain and gonad.\n\nAbstractGonadal soma-derived factor (gsdf) and anti-Mullerian hormone (amh) are somatic male determinants in several species of teleosts, although the mechanisms by which they trigger the indifferent germ cells into the male pathway remain unknown. This study aimed to decipher the roles of gsdf/amh in directing the sexual fate of germ cells using medaka as a model. Transgenic lines (TgcryG) that restrictively and persistently express a Gsdf-Gfp fusion protein in the lens and the hypothalamus-pituitary-gonad (HPG) axis, were generated under the control of a mouse {gamma}F-crystallin promoter. A high frequency (44.4%) of XX male sex reversals was obtained in TgcryG lines, indicating that signals of gsdf-expressing cells in HPG were enough for the spermatogenesis activation in the genetic females. Furthermore, all TgcryG XY individuals with endogenous gsdf depletion (named Sissy) displayed intersex (100%) with enlarged ovotestis in contrast to a giant ovary developed in XY gsdf deficiency. The heterogeneous expression of gsdf led to the confusion of gamatogenesis and ovotestis development, similar to some hotei (amhr2) mutants, suggests that the signaling balance of gsdf/amh is essential for proper gamatogenesis, maintaining sex steroid production and gonadotropin secretion, which are evolutionarily conserved across phyla.

evolutionary biology↗

bioRxiv2017

Preliminary results of models to predict areas in the Americas with increased likelihood of Zika virus transmission in 2017.

Numerous Zika virus vaccines are being developed. However, identifying sites to evaluate the efficacy of a Zika virus vaccine is challenging due to the general decrease in Zika virus activity. We compare results from three different modeling approaches to estimate areas that may have increased relative risk of Zika virus transmission during 2017. The analysis focused on eight priority countries (i.e., Brazil, Colombia, Costa Rica, Dominican Republic, Ecuador, Mexico, Panama, and Peru). The models projected low incidence rates during 2017 for all locations in the priority countries but identified several subnational areas that may have increased relative risk of Zika virus transmission in 2017. Given the projected low incidence of disease, the total number of participants, number of study sites, or duration of study follow-up may need to be increased to meet the efficacy study endpoints.

epidemiology↗