Biology subjects

Zhu, C.

Publications and source records attributed to Zhu, C..

10 recordsLinked to original sources

bioRxiv2018

Nitric oxide synthase-mediated early nitric oxide-burst alleviates drought-induced oxidative damage in ammonium supplied-rice roots

Ammonium (NH4+) can enhance rice drought tolerance in comparison to nitrate (NO3-). The mechanism underpinning this relationship was investigated based on the time-dependent nitric oxide (NO) production and its protective role in oxidative stress of NH4+-/NO3--supplied rice under drought. An early burst of NO was induced by drought 3h after root NH4+ treatment but not after NO3- treatment. Root oxidative damage induced by drought was significantly higher in NO3- than in NH4+-treatment due to its reactive oxygen species accumulation. Inducing NO production by applying NO donor 3h after NO3- treatment alleviated the oxidative damage, while inhibiting the early NO burst increased root oxidative damage in NH4+ treatment. Application of nitric oxide synthase (NOS) inhibitor N(G)-nitro-L-arginine methyl ester (L-NAME) completely suppressed NO synthesis in roots 3h after NH4+ treatment and aggravated drought-induced oxidative damage, indicating the aggravation of oxidative damage might have resulted from changes in NOS-mediated early NO burst. Drought also increased root antioxidant enzymes activities, which were further induced by NO donor but repressed by NO scavenger and NOS inhibitor in NH4+-treated roots. Thus, the NOS-mediated early NO burst plays an important role in alleviating oxidative damage induced by drought by enhancing antioxidant defenses in NH4+-supplied rice roots.\n\nHighlightNOS-mediated early NO burst plays an important role in alleviating oxidative damage induced by water stress, by enhancing the antioxidant defenses in roots supplemented with NH4+

physiology↗

bioRxiv2018

De novo transcriptomic characterization of Betta splendens for identifying sex-biased genes potentially involved in aggressive behavior modulation and EST-SSR maker development

Betta splendens is not only a commercially important labyrinth fish but also a nice research model for understanding the biological underpinnings of aggressive behavior. However, the shortage of basic genetic resource severely inhibits investigations on the molecular mechanism in sexual dimorphism of aggressive behavior typicality, which are essential for further behavior-related studies. There is a lack of knowledge regarding the functional genes involved in aggression expression. The scarce marker resource also impedes research progress of population genetics and genomics. In order to enrich genetic data and sequence resources, transcriptomic analysis was conducted for mature B. splendens using a multiple-tissues mixing strategy. A total of 105,505,486 clean reads were obtained and by de novo assembly, 69,836 unigenes were generated. Of which, 35,751 unigenes were annotated in at least one of queried databases. The differential expression analysis resulted in 17,683 transcripts differentially expressed between males and females. Plentiful sex-biased genes involved in aggression exhibition were identified via a screening from Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways, such as htr, drd, gabr, cyp11a1, cyp17a1, hsd17b3, dax1, sf-1, hsd17b7, gsdf1 and fem1c. These putative genes would make good starting points for profound mechanical exploration on aggressive behavioral regulation. Moreover, 12,751 simple sequence repeats were detected from 9,617 unigenes for marker development. Nineteen of the 100 randomly selected primer pairs were demonstrated to be polymorphic. The large amount of transcript sequences will considerably increase available genomic information for gene mining and function analysis, and contribute valuable microsatellite marker resources to in-depth studies on molecular genetics and genomics in the future.

zoology↗

bioRxiv2018

Unaltered prion disease in mice lacking developmental endothelial locus-1 (Del 1)

Progression of prion diseases is driven by the accumulation of prions in the brain. Ablation of microglia or deletion of the eat-me-signal milk-fat globule EGF factor VIII (Mfge8) accelerate prion pathogenesis, suggesting that microglia defends the brain by phagocytosing prions. Like Mfge8, Developmental endothelial locus-1 (Del-1) is a secreted protein that acts as an opsonin bridging phagocytes and apoptotic cells to facilitate phagocytosis. We therefore asked whether Del-1 might play a role in controlling prion pathogenesis. We first determined the expression pattern of Del-1 in mice, and found that the brain expresses the highest level of Del-1. In mouse brains, Del-1 was mainly expressed by neurons. We then assessed the anti-inflammatory and phagocytosis-promoting functions of Del-1 in prion disease, and determined whether Del-1 complements Mfge8 in prion clearance in mice with a C57BL/6J genetic background. We found that Del-1 deficiency did not change prion disease progression and lesion patterns. Also, prion clearance and PrPSc deposition were unaltered in Del-1 deficient mice. Additionally, prioninduced neuroinflammation was not affected by Del-1 deficiency. We conclude that Del-1 is not a major determinant of prion pathogenesis in this context.

neuroscience↗

bioRxiv2018

Genetic determinants of resistance and virulence among carbapenemase-producing Klebsiella pneumoniae from Sri Lanka.

Whole genome sequencing of carbapenem-resistant Enterobacteriaceae from the intensive care units of a Sri Lankan teaching hospital revealed the presence of carbapenemase gene, blaOXA-181 among isolates of carbapenase-producing Klebsiella pneumoniae belonging to ST437 (2 strains) and ST147 (8 strains) in 2015. blaOXA-181 genes were carried in three variants of ColE-type plasmids. Elevated carbapemen resistance were observed in ompK36 mutant strains. ESBL genes, plasmid-mediated quinolone resistance (PMQR) determinants (qnr, aac(6)-Ib-cr, oqxAB) and mutations on chromosomal quinolone resistance-determining regions (QRDRs) with substitutions at ser83[->]I of gyrA and ser80[->]I of parC were observed. All strains possessed yersiniabactin on the mobile element ICEkp and other virulence determinants. Strict infection control and judicious use of antibiotics are warranted to prevent further spread of multidrug-resistant Klebsiella pneumoniae in the intensive care units.

microbiology↗

bioRxiv2018

NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells

NADHX and NADPHX are hydrated and redox inactive forms of the NADH and NADPH cofactors, known to inhibit several dehydrogenases in vitro. A metabolite repair system that is conserved in all domains of life and that comprises the two enzymes NAD(P)HX dehydratase and NAD(P)HX epimerase, allows reconversion of both the S- and R-epimers of NADHX and NADPHX to the normal cofactors. An inherited deficiency in this system has recently been shown to cause severe neurometabolic disease in children. Although evidence for the presence of NAD(P)HX has been obtained in plant and human cells, little is known about the mechanism of formation of these derivatives in vivo and their potential effects on cell metabolism. Here, we show that NAD(P)HX dehydratase deficiency in yeast leads to an important, temperature-dependent NADHX accumulation in quiescent cells with a concomitant depletion of intracellular NAD+ and serine pools. We demonstrate that NADHX potently inhibits the first step of the serine synthesis pathway in yeast. Human cells deficient in the NAD(P)HX dehydratase also accumulated NADHX and showed decreased viability. In addition, those cells consumed more glucose and produced more lactate, potentially indicating impaired mitochondrial function. Our results provide first insights into how NADHX accumulation affects cellular functions and pave the way for a better understanding of the mechanism(s) underlying the rapid and severe neurodegeneration leading to early death in NADHX repair deficient children.

biochemistry↗

bioRxiv2018

Metabolomics and proteomics analyses of grain yield reduction in rice under abrupt drought-flood alternation

HighlightAbrupt drought-flood alteration is a frequent meteorological disaster that occurs during summer in southern China and the Yangtze river basin, which often causes a large area reduction of rice yield. We previously reported abrupt drought-flood alteration effects on yield and its components, physiological characteristics, matter accumulation and translocation, rice quality of rice. However, the molecular mechanism of rice yield reduction caused by abrupt drought-flood alternation has not been reported.\n\nIn this study, four treatments were provided, no drought and no floods (control), drought without floods (duration of drought 10 d), no drought with floods (duration of floods 8 d), and abrupt drought-flood alteration (duration of drought 10 d and floods 8 d). The quantitative analysis of spike metabolites was proceeded by LC-MS (liquid chromatograph-mass spectrometry) firstly. Then the Heat-map, PCA, PLS-DA, OPLS-DA and response ranking test of OPLS-DA model methods were used to analysis the function of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alteration. In addition, relative quantitative analysis of spike total proteins under the treatment was conducted iTRAQ (isobaric tags for relative and absolute quantification) and LC-MS. In this study, 5708 proteins were identified and 4803 proteins were quantified. The identification and analysis of DEPs function suggested that abrupt drought-flood alteration treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process, etc, during panicle differentiation stage. In this study relative quantitative proteomics, metabolomics and physiology data (soluble protein content, superoxide dismutase activity, hydrogen peroxidase activity, peroxidase activity, malondialdehyde content, free proline content, soluble sugar content and net photosynthetic rate) analysis were applied to explicit the response mechanism of rice panicle differentiation stage under abrupt drought-flood alteration and provides a theoretical basis for the disaster prevention and mitigation.\n\nAbstractAbrupt drought-flood alternation is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, a quantitative analysis of spike metabolites was conducted via liquid chromatograph-mass spectrometry (LC-MS), and Heat-map, PCA, PLS-DA, OPLS-DA, and a response ranking test of OPLS-DA model methods were used to analyze functions of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alternation. The results showed that 102 DMs were identified from the rice spike between T1 (abrupt drought-flood alternation) and CK0 (control) treatment, 104 DMs were identified between T1 and CK1 (drought) treatment and 116 DMs were identified between T1 and CK2 (flood) treatment. In addition, a relative quantitative analysis of spike total proteins was conducted using isobaric tags for relative and absolute quantification (iTRAQ) and LC-MS. The identification and analysis of DEPs functions indicates that abrupt drought-flood alternation treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process during the panicle differentiation stage. In this study, relative quantitative metabolomics and proteomics analyses were applied to explore the response mechanism of rice panicle differentiation in response to abrupt drought-flood alternation.\n\nAbbreviations

plant biology↗

bioRxiv2018

YAP1 Oncogene is a Context-specific Driver for Pancreatic Ductal Adenocarcinoma

AbstractTranscriptomic profiling classifies pancreatic ductal adenocarcinoma (PDAC) into several molecular subtypes with distinctive histological and clinical characteristics. However, little is known about the molecular mechanisms that define each subtype and their correlation with clinical outcome. Mutant KRAS is the most prominent driver in PDAC, present in over 90% of tumors, but the dependence of tumors on oncogenic KRAS signaling varies between subtypes. In particular, squamous subtype are relatively independent of oncogenic KRAS signaling and typically display much more aggressive clinical behavior versus progenitor subtype. Here, we identified that YAP1 activation is enriched in the squamous subtype and associated with poor prognosis. Activation of YAP1 in progenitor subtype cancer cells profoundly enhanced malignant phenotypes and transformed progenitor subtype cells into squamous subtype. Conversely, depletion of YAP1 specifically suppressed tumorigenicity of squamous subtype PDAC cells. Mechanistically, we uncovered a significant positive correlation between WNT5A expression and the YAP1 activity in human PDAC, and demonstrated that WNT5A overexpression led to YAP1 activation and recapitulated YAP1-dependent but Kras-independent phenotype of tumor progression and maintenance. Thus, our study identifies YAP1 oncogene as a major driver of squamous subtype PDAC and uncovers the role of WNT5A in driving PDAC malignancy through activation of the YAP pathway.

cancer biology↗

bioRxiv2017

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed, paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here we present a new method, Smart-3SEQ, that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. We also obtain distinct biological profiles from FFPE single cells, which have been impossible to study with previous RNA-seq protocols, and we use these data to identify possible new macrophage phenotypes associated with the tumor microenvironment. We propose Smart-3SEQ as a highly cost-effective method to enable large gene-expression profiling experiments unconstrained by sample size and tissue availability. In particular, Smart-3SEQs compatibility with FFPE tissue unlocks an enormous number of archived clinical samples, and combined with LCM it allows unprecedented studies of small cell populations and single cells isolated by their in situ context.

genomics↗

bioRxiv2017

Insm1a regulates motor neuron development in zebrafish

Insulinoma-associated1a (Insm1a) is a zinc-finger transcription factor playing a series of functions in cell formation and differentiation of vertebrate central and peripheral nervous systems and neuroendocrine system. However, its roles on the development of motor neuron have still remained uncovered. Here, we provided evidences that insmla was a vital regulator of motor neuron development and provide a mechanistic understanding of how it contributes to this process. Firstly, we showed the localization of insmla in spinal cord and primary motor neurons (PMNs) of zebrafish embryos by in situ hybridization and imaging analysis of transgenic reporter line Tg(insmla: mCherry) ntu805. Then we demonstrated that the deficiency of insmla in zebrafish larvae lead to the defects of PMNs development, including the reduction of caudal primary motor neurons (CaP) and middle primary motor neurons (MiP), the excessive branching of motor axons, and the disorganized distance between adjacent CaPs. Additionally, knockout of insm1 impaired motor neuron differentiation in the spinal cord. Locomotion analysis showed that insmla-null zebrafish significantly reduced the swimming activity. Furthermore, we proved that the insmla loss of function significantly decreased the transcripts levels of both olig2 and nkx6.1. Microinjection of olig2 and nkx6.1 mRNA rescued the motor neuron defects in insmla deficient embryos. Taken together, these data indicate that insmla regulates the motor neuron development, at least in part, through modulation of the expressions of olig2 and nkx6.1.

developmental biology↗

bioRxiv2017

Gene fusion between CDKN1A and RAB44 caused by exon skipping like mechanism due to disruption of a splice site

Splicing contributes to gene regulation and protein diversity, while abnormal splicing underlies both hereditary diseases and cancers. Various mutations that disrupt splicing factors, exonic or intronic splicing enhancers or silencers, as well as splice sites, could be responsible for abnormal splicing. Characterization of abnormal splicing events is not only helpful for understanding the molecular processes linking mutations to disease phenotypes, but also provides promising targets for targeted therapies. In addition, CRISPR/Cas9 editing could be benefited once more attention is given to potential abnormal splicing outcomes other than off-target effects at the DNA level. Although large-scale multiplexed genome editing has been demonstrated in yeast, and has also been attempted for particular exons or genes in other eukaryotic cells to achieve saturation, in practice it is much more difficult to measure splicing consequences with genome-wide saturation editing in human cells. Instead, massive somatic mutations accumulated in cancer cohorts provide invaluable opportunities to study somatic mutation-associated splicing events. Abnormal splicing is not necessarily limited to single genes. Transcript fusion is a special form of abnormal splicing that connects two or more genes due to splicing on a transcriptional level (rather than chromosomal translocations such as BCR-ABL in chronic myeloid leukemia). It could arise from conventional splicing on read-through transcripts when the two genes are next to each other and on the same strand, or from trans-splicing when two genes are on different chromosomes, strands or far away - a few cases had been reported. However, it was found that these fusions not only occurred in tumors but also in normal tissues; there was limited investigation regarding how the fusion could happen, whether it be due to mutations or not, and what the downstream perturbations were. Here, in an effort to characterize somatic mutation-associated abnormal splicing (especially in its simplest form, exon skipping events), we identified over one hundred such events in various tumors, including those in MET, PTEN and TP53. Surprisingly, we detected a recurrent, but previously undescribed, tumor-specific transcript fusion event between the cyclin-dependent kinase inhibitor CDKN1A and the RAS oncogene family gene RAB44. By creating genome-edited cell lines, we demonstrate a causal relationship between splice-site mutations in CDKN1A and the fusion to the RAB44 transcript. We further provide evidence that the fusion arises from a readthrough transcript that escapes exosome-mediated degradation when the splice-site mutation occurred, and we show that the presence of the fusion transcript correlates with TP53 inactivation and CDK activation. The strong tissue specificity of RAB44 and the relatively high prevalence of this transcript fusion in multiple types of cancers warrants further study which could inform subclassifications of these cancers and the development of targeted therapies.

genetics↗