Biology subjects

Yuan, X.

Publications and source records attributed to Yuan, X..

9 recordsLinked to original sources

bioRxiv2018

The biochemical properties of a novel paraoxonase-like enzyme in Trichoderma atroviride strain T23 involved in the degradation of 2,2-dichlorovinyl dimethyl phosphate

Dichlorvos, is a broad-spectrum organophosphorus pesticide that is widely applied in the agricultural industry and considered a pollutant to fish and bees. T. atroviride strain T23, an efficient DDVP-degrading strain, could convert DDVP to dichloroacetic acid, 2,2-dichloroethanol and phosphoric acid through mineralization. RT-qPCR analysis showed TaPon1-like encoding an organophosphorus hydrolase, is continuously highly expressed in the process of degrading DDVP. TaPon1-like contained an open reading frame of 1317 bp, and the deduced amino acid sequence shared 21% homology with HuPON1, which also exhibits excellent hydrolysis of organophosphate-oxons compounds. By analysis of gene knockout, we found the {Delta}TaPon1-like knockout strain KO1 lost 35.6% of its DDVP-degradation capacity at 24 h, but this loss of degradation activity was recovered when the gene was complemented. Furthermore, the purified recombinant protein reTAPON1-LIKE, could transform DDVP only to dimethyl phosphate and showed significant paraoxonase activity (1028 U L-1). The reTAPON1-LIKE enzyme showed a broad degradation spectrum, degrading not only DDVP but also organophosphate-oxons and lactone. The kinetic parameters (Km and kcat) of the purified reTAPON1-LIKE were determined to be 0.23 mM and 204.3 s-1 for DDVP, respectively. The highest activity was obtained at 35 {degrees}C, and the optimal pH was 8.5. The activity of reTAPON1-LIKE was enhanced most significantly when 1.0 mM Ca2+ was added but declined when 1.0 mM Cu2+ was added. These results showed TAPON1-LIKE play an important role for DDVP degradation in the first step by T23 and provided clue to comprehensively understanding the degradation mechanism of organophosphate-oxons pesticides by filamentous fungi.\n\nImportanceThe large amounts of residues of organophosphate pesticides in agroecological system has become a great threat to the safety of environment and humans. Bioremediation in association with microbial is innovative technology having a potential to alleviate such pollution problems. The genus Trichoderma is genetically diverse with capabilities to degrade chemical pesticides among different strains with agricultural significance. As a typical organophosphorus pesticide, it is one of the most employed compounds of the family. Though it was classified as a highly toxic pesticide by WHO due to its hazardous properties, it plays an important role in the control of plant pests, food storage and homes, as well as to treat infections in livestock. Therefore, we use DDVP as a model of organophosphate pesticide to study the mechanism of Trichoderma degrading organophosphate pesticides, for the aim of globally understanding molecular mechanism of enzymatic degradation of organophosphate pesticides by beneficial fungi.

microbiology↗

bioRxiv2018

Diagnostic Whole Exome Sequencing in Patients with Short Stature

Short stature is among the most common reasons for children being referred to the pediatric endocrinology clinics. The cause of short stature is broad, in which genetic factors play a substantial role, especially in primary growth disorders. However, identifying the molecular causes for short stature remains as a challenge because of the high heterogeneity of the phenotypes. Here, whole exome sequencing (WES) was used to identify the genetic causes of short stature with unknown etiology for 20 patients aged from 1 to 16 years old. The genetic causes of short stature were identified in 9 of the 20 patients, corresponding to a molecular diagnostic rate of 45%. Notably, in 2 of the 9 patients identified with genetic causes, the diagnosed diseases based on WES are different from the original clinical diagnosis. Our results highlight the clinical utility of WES in the diagnosis of rare, high heterogeneity disorders.

genetics↗

bioRxiv2018

Cyclin B3 is specifically required for metaphase to anaphase transition in mouse oocyte meiosis I

Meiosis, a cell division to generate gametes for sexual reproduction in eukaryotes, executes a single round of DNA replication and two successive rounds of chromosome segregation [1]. The extraordinary reliability of the meiotic cycle requires the activities of cyclin-dependent kinases (Cdks) associated with specific cyclins [2-4]. Cyclins are the regulatory subunits of protein kinases, which are the main regulators of maturation promoting factor or mitosis promoting factor (MPF) [5, 6] and anaphase-promoting complex/cyclosome (APC/C) [7, 8] in eukaryotic cell division. But how cyclins collaborate to control meiosis is still largely unknown. Cyclin B3 (Ccnb3) shares homology with A- and B-type cyclins [9], and is conserved during higher eukaryote evolution [10-17]. Previous studies have shown that Ccnb3-deleted females are sterile with oocytes unable to complete meiosis I in Drosophila [18], implying that Ccnb3 may have a special role in meiosis. To clarify the function of Ccnb3 in meiosis in mammalian species, we generated Ccnb3 mutant mice by CRISPR/Cas9, and found that Ccnb3 mutation caused female infertility with the failure of metaphase-anaphase transition in meiosis I. Ccnb3 was necessary for APC/C activation to initiate anaphase I, but not required for oocytes maturation, meiosis II progression, or early embryonic development. Our study reveals the differential cell cycle regulation between meiosis I and meiosis II, as well as meiosis between males and females, which shed light on the cell cycle control of meiosis.\n\nHighlightsO_LIIdentification of a female meiosis-specific cyclin in mouse\nC_LIO_LICyclin B3 is required for metaphase-anaphase transition in oocyte meiosis I\nC_LIO_LICyclin B3 is not essential for oocyte maturation and sister chromosome segregation\nC_LIO_LICyclin B3 is necessary for APC/C activation and MPF kinase activity through Cdk1\nC_LI

cell biology↗

bioRxiv2018

Uric acid lowering treatment alleviates perivascular carotid collar placement induced neointimal lesions in Uricase knockout mice

Hyperuricemia (HU) is a cause of gout. Clinical studies show a link between HU and cardiovascular disease. However, the role of soluble serum urate on atherosclerosis development remains elusive. We aimed to use a new HU mouse model (Uricase/Uox knockout (KO)) to further investigate the relationship between HU and atherosclerosis. Mouse model of induced carotid atherosclerosis was established in the novel spontaneous HU Uox-KO mouse and their wild type littermates (C57BL/6J background). Mice were implanted with a perivascular collar placement around the right carotid artery in combination with a western-type diet. To investigate urate-lowering treatment (ULT) effects on intima, the mice were gavaged daily from the age of 6 weeks with allopurinol. Human umbilical vein endothelial cells (HUVECs) were co-incubated with soluble urate, with and without probenecid, to study the mechanism of urate-related atherosclerosis. The Uox-KO mice had significantly elevated serum urate levels combined with higher blood urea nitrogen and serum creatinine. Western blot analysis showed enhanced levels of atherosclerosis inflammatory response proteins. However, there were no other risk indicators for the pathogenesis of atherosclerosis, including increased fasting glucose, altered lipid and atherosclerosis characterized cardiovascular and histological manifestations. In contrast, collar placement Uox-KO mice showed severe neointimal changes in histology staining consistent with increases in intimal area and increases in proliferating cell nuclear antigen (PCNA) - and F4/80-positive cells. Allopurinol reduced neointimal areas induced by the perivascular collar in hyperuricemic mice accompanied by decreased expression of PCNA- and F4/80-positive cells (P< 0.05). ULT alleviated atherosclerosis inflammatory response factors and reactive oxygen species intensities in both collar placement Uox-KO mice and urate-stimulated HUVECs. In vitro results using HUVECs showed ROS was induced by urate and ROS induction was abrogated using antioxidants. These data demonstrate that urate per se does not trigger atherosclerosis intima lesions in mice. Urate worsens carotid neointimal lesions induced by the perivascular collar and urate-lowering therapy partially abrogates the effects. The current study warrants the further human based study on the possible benefits of urate-lowering therapy in atherosclerosis patients with HU.\n\nSummary statementWe generated a carotid collar placement atherosclerosis model in the novel spontaneous HU Uox-KO mouse and demonstrate that urate plays a contributing rather than a causal role in the carotid neointimal lesions, while urate-lowering treatment may bring additional benefits in this HU mouse model.

physiology↗

bioRxiv2018

PRL-1 is required for neuroprotection against olfactory CO2 stimulation in Drosophila

The Mammalian phosphatase of regenerating liver (PRL) family is primarily recognized for its oncogenic properties. Here we found that in Drosophila, loss of prl-1 resulted in CO2-induced brain disorder presented as irreversible wing hold up with enhancement of Ca2+ responses at the neuron synaptic terminals. Overexpression of Prl-1 in the nervous system could rescue the mutant phenotype. We show that Prl-1 is particularly expressed in CO2-responsive neural circuit and the higher brain centers. Ablation of the CO2 olfactory receptor, Gr21a, suppressed the mutant phenotype, suggesting that CO2 acts as a neuropathological substrate in absence of Prl-1. Further studies found that the wing hold up is an obvious consequence upon knockdown of Uex, a magnesium transporter, which directly interacts with Prl-1. Conditional expression of Uex in the nervous system could rescue the phenotype of prl-1 mutants. We demonstrate that Uex acts genetically downstream of Prl-1. Our findings provide important insights into mechanisms of Prl-1 protection against olfactory CO2 stimulation induced brain disorder at the level of detailed neural circuits and functional molecular connections.

neuroscience↗

bioRxiv2018

Heart enhancers with deeply conserved regulatory activity are established early in development

During the phylotypic period embryos from different genera show similar gene expression patterns, implying common regulatory mechanisms. To identify enhancers involved in the initial events of cardiogenesis, which occurs during the phylotypic period, we isolated early cardiac progenitor cells from zebrafish embryos and characterized 3838 open chromatin regions specific to this cell population. Of these regions, 162 overlapped with conserved non-coding elements (CNEs) that also mapped to open chromatin regions in human. Most of the zebrafish conserved open chromatin elements tested drove gene expression in the developing heart. Despite modest sequence identity, human orthologous open chromatin regions could recapitulate the spatial temporal expression patterns of the zebrafish sequence, potentially providing a basis for phylotypic gene expression patterns. Genome-wide, we discovered 5598 zebrafish-human conserved open chromatin regions, suggesting that a diverse repertoire of ancient enhancers is established prior to organogenesis and the phylotypic period.

genomics↗

bioRxiv2017

Single-cell transcriptional regulations and accessible chromatin landscape of cell fate decisions in early heart development

Formation and segregation of the cell lineages forming the vertebrate heart have been studied extensively by genetic cell tracing techniques and by analysis of single marker gene expression both in embryos and differentiating ES cells. However, the underlying gene regulatory networks driving cell fate transitions during early cardiogenesis is only partially understood, in part due to limited cell numbers and substantial cellular heterogeneity within the early embryo. Here, we comprehensively characterized cardiac progenitor cells (CPC) marked by Nkx2-5 and Isl1 expression from embryonic days E7.5 to E9.5 using single-cell RNA sequencing. By leveraging on cell-to-cell heterogeneity, we identified different previously unknown cardiac sub-populations. Reconstruction of the developmental trajectory revealed that Isl1+ CPC represent a transitional cell population maintaining a prolonged multipotent state, whereas extended expression of Nkx-2.5 commits CPC to a unidirectional cardiomyocyte fate. Correlation-based analysis of cells in the unstable multipotent state uncovered underlying gene regulatory networks associated with differentiation. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states, which critically depend on Isl1 for accessibility of enhancers. In contrast, forced expression of Nkx2-5 eliminated multipotency of Isl1+ cells and established a unidirectional cardiomyocyte fate. Our data provides a transcriptional map for early cardiogenic events at single-cell resolution and establishes a general model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions.

developmental biology↗

bioRxiv2017

Hey2 restricts cardiac progenitor addition to the developing heart

A key event in vertebrate heart development is the timely addition of second heart field (SHF) progenitor cells to the poles of the heart tube. This accretion process must occur to the proper extent to prevent a spectrum of congenital heart defects (CHDs). However, the factors that regulate this critical process are poorly understood. Here we demonstrate that Hey2, a bHLH transcriptional repressor, restricts SHF progenitor accretion to the zebrafish heart. hey2 expression demarcated a distinct domain within the cardiac progenitor population. In the absence of Hey2 function an increase in myocardial cell number and SHF progenitors was observed. We found that Hey2 limited proliferation of SHF-derived cardiomyocytes in a cell-autonomous manner, prior to heart tube formation, and further restricted the developmental window over which SHF progenitors were deployed to the heart. Taken together, our data suggests a role for Hey2 in controlling the proliferative capacity and cardiac contribution of late-differentiating cardiac progenitors.

developmental biology↗

bioRxiv2017

Effect of vertical slit turbulence on metabolism and swimming behavior of juvenile grass carp (ctenopharyngodon idella)

Baffles were incorporated into the swim chamber of a flume-type swimming respirometer, and the effect of vertical slit turbulence on the swimming behavior and metabolism of juvenile grass carp were investigated. Results showed a significant lower TBF in turbulent flow than in laminar flow (p< 0.05). However, differences in TBF at different inlet velocities were not significant (p> 0.05), whether the fish passed through the baffles or not. In turbulent flow, the residence time ratios of test fish at different flow zone were low water velocity > medium velocity > high velocity. Oxygen consumption rate (MO2) increased with flow velocity and was higher in turbulent flow than in laminar flow. Further, the speed exponent c, in turbulent flow, was significantly higher than in laminar flow, indicated a decrease swimming efficiency. This study of fish swimming in turbulent flow extends knowledge of fish ecology and provides data for guiding the design of hydrokinetic turbulent where needed, so preventing ecological impacts.

animal behavior and cognition↗