Biology subjects

Peng, Z.

Publications and source records attributed to Peng, Z..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation

As a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica. Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.

plant biology↗

bioRxiv2020

PacC-dependent adaptation and modulation of host cellular pH controls hemibiotrophic invasive growth and disease development by the rice blast fungus

Many of the worlds most serious crop diseases are caused by hemibiotrophic fungi. These pathogens have evolved the ability to colonize living plant cells, suppressing plant immunity responses, before switching to necrotrophic growth, in which host cells die, providing the energy to fuel sporulation and spread of the fungus. How hemibiotrophic pathogens switch between these two lifestyles remains poorly understood. Here, we report that the devastating rice blast fungus, Magnaporthe oryzae, manipulates host cellular pH to regulate hemibiotrophy. During infection by M. oryzae, host plant cells are alkalinized to pH 7.8 during biotrophic growth, but later acidified to pH 6.5 during necrotrophy. Using a forward genetic screen, we identified alkaline-sensitive mutants of M. oryzae that were blocked in biotrophic proliferation and impaired in induction of host cell acidification and necrotrophy. These mutants defined components of the PacC-dependent ambient pH signal transduction pathway in M. oryzae. We report that PacC exists as a full-length repressor, PacC559, and a truncated transcriptional activator, PacC222, which localize to the fungal nucleus during biotrophic growth and to the cytoplasm during necrotrophy. During biotrophy, PacC222 directly activates genes associated with nutrient acquisition and fungal virulence, while PacC559 represses genes associated with saprophytic mycelial growth and sporulation, which are subsequently de-repressed during necrotrophy. When considered together, our results indicate that temporal regulation of hemibiotrophy by M. oryzae requires PacC-dependent sensing and manipulation of host cellular pH. Author SummaryCrop diseases caused by fungi represent some of the most serious threats to global food security. Many fungal pathogens have evolved the ability to invade living plant tissue and suppress host immunity, before switching to a completely different mode of growth, in which they are able to kill host plant cells. This lifestyle- called hemibiotrophy -is exemplified by the blast fungus, Magnaporthe oryzae, which causes devastating diseases of rice, wheat and many other grasses. We found that during infection by M. oryzae, host cells initially have an alkaline pH, when the fungus is growing in living tissue, but pH rapidly becomes acidic, as host tissue is killed. We identified mutants of the blast fungus that were sensitive to alkaline pH and this enabled us to identify the signal transduction pathway by which the fungus responds to changes in ambient pH. We found that mutants in the pH response pathway were blocked in invasive fungal growth and could not cause acidification of host tissue. Consequently, they are unable to cause blast disease. We characterized the central regulator of this pathway, the PacC transcription factor, which unusually can act as both a repressor and an activator of fungal gene expression. During biotrophic invasive growth, PacC activates many genes previously reported to be required for virulence, including several associated with nutrient acquisition, and at the same time represses genes associated with vegetative growth and sporulation. The PacC signaling pathway is therefore necessary for regulating the switch in fungal lifestyle associated with causing blast disease.

microbiology↗

bioRxiv2020

Performance characterization of PCR-free whole genome sequencing for clinical diagnosis

PurposeTo evaluate the performance of PCR-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection. MethodsAll the 5 NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing DNA input and library preparation protocol (PCR-based versus PCR-free protocols for library preparation). The DP (depth of coverage) and GQ (genotype quality) of each sample were compared. We developed a systematic WGS pipeline for the analysis of down-sampling samples of the 5 NA12878 samples. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes and CNVs. ResultsIn general, NA12878-2 (PCR-free WGS) showed better DP and GQ distribution than NA12878-1 (PCR-based WGS). With a mean depth of ~40X, the sensitivity of homozyous and heterozygous SNPs of NA12878-2 showed higher sensitivity (>99.77% and > 99.82%) than NA12878-1, and positive predictive value (PPV) exceeded 99.98% and 99.07%. The sensitivity and PPV of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and CNVs are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. ConclusionDifferent experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.

genetics↗

bioRxiv2020

Probing the functions of microglial cyclin-dependent kinase 5 under physiological and pathological conditions

Cyclin dependent kinase 5 (Cdk5) regulates various developmental and physiological processes in the central nervous system. Deregulation of Cdk5 activity in neurons induces severe neurodegeneration and has been implicated in Alzheimers disease (AD) and other neurodegenerative conditions. A large fraction of AD risk genes are highly expressed in microglia, highlighting an important role for these cells in AD pathogenesis. While Cdk5 function in neurons is well characterized, our understanding of its roles in microglial function under physiological and neurodegenerative conditions remain rudimentary. Here, we investigate the roles of Cdk5 in microglia using myeloid-specific Cdk5 conditional knockout mice. Using microglia-specific transcriptome profiling, histological analyses, and behavioral assessments, we found that knockout of Cdk5 in microglia for 1 month induced transcriptional changes characterized by upregulation of cell cycle processes and type I interferon signaling genes in both physiological conditions and AD-related amyloidogenesis. In contrast to the robust transcriptional changes, conditional loss of microglial Cdk5 produced minimal effects on the density and morphology of microglia and their phagocytic activity toward myelin debris. Moreover, Cdk5cKO mice exhibited little change in synaptic density and tasks associated with locomotor, anxiety-like, and memory-related behaviors. Our findings indicate that the conditional loss of Cdk5 in microglia induces rapid alterations of microglial transcriptome with minimal or delayed effects on histological and behavioral responses.

neuroscience↗

bioRxiv2020

Structures of microRNA-precursor apical junctions and loops reveal non-canonical base pairs important for processing

Metazoan pri-miRNAs and pre-miRNAs fold into characteristic hairpins that are recognized by the processing machinery. Essential to the recognition of these miR-precursors are their apical junctions where double-stranded stems meet single-stranded hairpin loops. Little is known about how apical junctions and loops fold in three-dimensional space. Here we developed a scaffold-directed crystallography method and determined the structures of eight human miR-precursor apical junctions and loops. Six structures contain non-canonical base pairs stacking on top of the hairpin stem. U-U pair contributes to thermodynamic stability in solution and is highly enriched at human miR-precursor apical junctions. Our systematic mutagenesis shows that U-U is among the most efficiently processed variants. The RNA-binding heme domain of pri-miRNA-processing protein DGCR8 binds longer loops more tightly and non-canonical pairs at the junction appear to modulate loop length. Our study provides structural and biochemical bases for understanding miR-precursors and molecular mechanisms of microRNA maturation.

molecular biology↗

bioRxiv2020

scSTATseq: Diminishing Technical Dropout Enables Core Transcriptome Recovery and Comprehensive Single-cell Trajectory Mapping

The advent of single-cell RNA sequencing has provided illuminating information on complex systems. However, large numbers of genes tend to be scarcely detected in common scRNAseq approaches due to technical dropout. Although bioinformatics approaches have been developed to approximate true expression profiles, assess the dropout events on single-cell transcriptomes is still consequently challenging. In this report, we present a new plate-based method for scRNAseq that relies on Tn5 transposase to tagment cDNA following second strand synthesis. By utilizing pre-amplification tagmentation step, scSTATseq libraries are insulated against technical dropout, allowing for detailed analysis of gene-gene co-expression relationships and mapping of pathway trajectories. The entire scSTATseq library construction workflow can be completed in 7 hours, and recover transcriptome information on up to 8,000 protein-coding genes. Investigation of osteoclast differentiation using this workflow allowed us to identify novel markers of interest such as Rab15. Overall, scSTATseq is an efficient and economical method for scRNAseq that compares favorably with existing workflows.

genomics↗

bioRxiv2020

Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders

BackgroundWith the reduce of cost and incomparable advantages, WGS is likely to change the way of clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated, especially for CNV detection. MethodsAll the samples underwent WGS using MGISEQ-2000. The performance of NA12878, YH cell line, and the Chinese trios were measured for sensitivity, PPV, depth and breadth of coverage. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using family-based trio design in the Chinese trios. We also developed a systematic WGS pipeline for the analysis of 8 clinical cases with known disease-causing variants. ResultsIn general, the sensitivity and PPV for SNV/indel detection increased with mean depth, and reached a plateau at a ~40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozyous and heterozygous SNPs of NA12878 was >99.25% and >99.50% respectively, and PPVs were 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV is still not 100% even with a mean depth of ~150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size of less than 1kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~40X) is better than WES (~120X). Among the Chinese trios with ~40X mean depth, the sensitivity in the offspring was >99.48% and >96.36% for SNP and indel detection, and PPVs were 99.86% and 97.93%. All the 12 previously validated variants in the 8 clinical cases were successfully detected by our WGS pipeline. ConclusionsThe current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. Clinical scientists should know the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.

genomics↗

bioRxiv2020

Modelling the epidemic trend of the 2019 novel coronavirus outbreak in China

We present a timely evaluation of the Chinese 2019-nCov epidemic in its initial phase, where 2019-nCov demonstrates comparable transmissibility but lower fatality rates than SARS and MERS. A quick diagnosis that leads to case isolation and integrated interventions will have a major impact on its future trend. Nevertheless, as China is facing its Spring Festival travel rush and the epidemic has spread beyond its borders, further investigation on its potential spatiotemporal transmission pattern and novel intervention strategies are warranted.

microbiology↗

bioRxiv2019

Improved protein structure prediction using predicted inter-residue orientations

The prediction of inter-residue contacts and distances from co-evolutionary data using deep learning has considerably advanced protein structure prediction. Here we build on these advances by developing a deep residual network for predicting inter-residue orientations in addition to distances, and a Rosetta constrained energy minimization protocol for rapidly and accurately generating structure models guided by these restraints. In benchmark tests on CASP13 and CAMEO derived sets, the method outperforms all previously described structure prediction methods. Although trained entirely on native proteins, the network consistently assigns higher probability to de novo designed proteins, identifying the key fold determining residues and providing an independent quantitative measure of the "ideality" of a protein structure. The method promises to be useful for a broad range of protein structure prediction and design problems.

bioinformatics↗

bioRxiv2019

OR1D2 receptor mediates bourgeonal-induced human CatSper activation in a G-protein dependent manner

During fertilization, sperm are guided towards eggs by physiological chemokines, a process named sperm chemotaxis. Human sperm chemotaxis is speculated to be mediated by olfactory receptor OR1D2 in a pathway requiring calcium influx. Bourgeonal, an artificial ligand of OR1D2, can activate CatSper, the primary calcium channel in human sperm. However, whether bourgeonal-induced CatSper activation requires OR1D2 and how CatSper is activated remain unclear. Herein, we show that OR1D2 antibody can inhibit bourgeonal-induced CatSper activation and sperm chemotaxis, proving that OR1D2 mediates bourgeonal-induced CatSper activation. Furthermore, bourgeonal-evoked CatSper currents can be greatly suppressed by either GDP-{beta}-S or antibody of Gs. Interestingly, bourgeonal can transiently increase sperm cAMP level, and this effect can be abolished by OR1D2 antibody. Consistently, bourgeonal-induced CatSper activation can be inhibited by membrane adenylate cyclases inhibitor. Overall, our results indicate that bourgeonal activates CatSper via OR1D2-G protein-cAMP pathway. Although CatSper can be activated by various physiological and environmental factors, this study represents the most recent progress proving that CatSper can be indirectly activated by extracellular regulators through a G-protein-dependent intracellular signaling pathway.

physiology↗

bioRxiv2019

Impact of ultrasonography on identifying noninvasive prenatal screening false-negative aneuploidy

PurposeTo evaluate the impact of ultrasonography (US) on identifying noninvasive prenatal screening (NIPS) false-negative aneuploidy.\n\nMethodsAnalysis of large population-based NIPS false-negative aneuploidy data comprising karyotypes, clinical outcomes, and US results.\n\nResultsFrom December 2010 to July 2018, a total of 3,320,457 pregnancies were screened by NIPS performed in BGI; among them, 69 NIPS false-negative aneuploidy cases with informed consent were confirmed, and US examination data for 48 cases were not available. Of the 21 cases with US results, 19 (90.5%) had various abnormalities on ultrasound, and 2 (9.5%) cases were shown to be normal on ultrasound. Additionally, 6 out of 7 live born fetuses (approximately 85.7%) were found to have abnormalities on ultrasound. Ventricular septal defects constituted the most frequently observed ultrasound abnormality type among the 21 NIPS false-negative aneuploidy cases.\n\nConclusionNIPS has expanded rapidly worldwide and now accounts for a large proportion of prenatal screening tests in China. This study suggests that abnormal US findings should not be neglected, even when NIPS produces a negative result. Combining NIPS with an US examination can further reduce the incidence of livebirths with aneuploidy.

genetics↗

bioRxiv2019

AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants

Null variants are prevalent within human genome, and their accurate interpretation is critical for clinical management. In 2018, the ClinGen Sequence Variant Interpretation (SVI) Working Group refined the only criterion (PVS1) for pathogenicity in the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. The refinement may improve interpretation consistency, but it also brings hurdles to biocurators because of the complicated workflows and multiple bioinformatics sources required. To address these issues, we developed an automatic classification tool called AutoPVS1 to streamline PVS1 interpretation. We assessed the performance of AutoPVS1 using 56 variants manually curated by ClinGens SVI Working Group and achieved an interpretation concordance of 95% (53/56). A further analysis of 28,586 putative loss-of-function variants by AutoPVS1 demonstrated that at least 27.6% of them do not reach a very strong strength level, with 17.4% based on variant-specific issues and 10.2% on disease mechanism considerations. Moreover, 40.7% (1,918/4,717) of splicing variants were assigned a decreased PVS1 strength level, significantly higher than frameshift and nonsense variants. Our results reinforce the necessity of considering variant-specific issues and disease mechanisms in variant interpretation, and demonstrate that AutoPVS1 is an accurate, reproducible, and reliable tool which facilitates PVS1 interpretation and will thus be of great importance to curators.

genetics↗

bioRxiv2019

Noninvasive Prenatal Diagnosis for Duchenne Muscular Dystrophy Based on the Direct Haplotype Phasing

ObjectiveWe aimed to investigate the validity of noninvasive prenatal diagnosis (NIPD) based on direct haplotype phasing without the proband and its feasibility for clinical application in the case of Duchenne Muscular Dystrophy (DMD).\n\nMethodsThirteen singleton-pregnancy families affected by DMD were recruited. Firstly, we resolved maternal haplotypes for each family by performing targeted linked-read sequencing of their high molecular weight DNA, respectively. Then, we identified SNPs of the DMD gene in all carrier mothers and inferred the DMD gene mutation status of all fetuses. Finally, the fetal genotypes were further validated by using chorionic villus sampling.\n\nResultsThe method of directly resolving maternal haplotype through targeted linked-read sequencing was smoothly performed in all participated families. The predicted mutational status of 13 fetuses was correct, which had been confirmed by invasive prenatal diagnosis.\n\nConclusionDirect haplotyping of NIPD based on linked-read sequencing for DMD is accurate.

genetics↗

bioRxiv2019

Loss of SHMT2 mediates 5-FU chemoresistance by inducing autophagy in colorectal cancer

Serine hydroxymethyltransferase 2 (SHMT2) plays a vital role in one-carbon metabolism and drives colorectal carcinogenesis. In our study, loss of SHMT2 induced 5-Fluorouracil (5-FU) chemoresistance and was associated with poor prognosis in colorectal cancer (CRC). To elucidate the possible mechanism and generate a strategy to sensitize CRC to 5-FU chemotherapy, we first identified the binding proteins of SHMT2 in cancer cells by mass spectrometry. We found that SHMT2 inhibited autophagy through binding cytoplasmic p53. In fact, SHMT2 prevented cytoplasmic p53 degradation by inhibiting the binding of p53 and HDM2. Under treatment with 5-FU, depletion of SHMT2 promoted autophagy and inhibited apoptosis. Autophagy inhibitors CQ decreased low SHMT2-induced 5-FU resistance in vitro and in vivo. Finally, we enhanced the lethality of 5-FU treatment to CRC cells through the autophagy inhibitor or knockdown of SHMT2 in patient-derived and CRC cell xenograft models. Our findings identified the low SHMT2-induced autophagy on 5-FU resistance in CRC. These results reveal SHMT2-p53 as a novel cancer therapeutic target to reduce chemotherapeutic drug resistance.

cancer biology↗

bioRxiv2019

APOC2 accelerates colorectal cancer progression via modulating lipid metabolism and transcriptional activity of PHF8

The apolipoproteins (APOs) are the major proteins in blood lipid transportation. Emerging evidence has demonstrated that APOs might exert important function in tumor cells, but the underlying mechanism remains inclusive. In this study, we aim to explore the relationship between APOC2 dysfunction and colorectal cancer (CRC) malignancy. By analyzing the expression of APOC2 in 507 patients with CRC, we demonstrated that the APOC2 was overexpressed and associated with poor prognosis in CRC. We then found that high levels of APOC2 resulted in proliferation, invasion and metastasis of CRC cells in vitro and in vivo. Mechanistically, we revealed that APOC2 directly interacted with FASN which resulted in decreased levels of omega-3 fatty acids and increased levels of alpha-ketoglutarate (-KG). Both RNA-seq and ChIP-seq analysis revealed that APOC2 overexpression resulted accumulation of -KG leads to activation on the transcriptional program of PHF8 and thereby contributed to activation on genes involved in cell proliferation, invasion and metastasis. Together, our study unveiled the oncogenic role of APOC2 in tumor cells, which sheds new light on the potential of APOC2 as a biomarker in the prognosis of CRC.

cancer biology↗

bioRxiv2019

VGLUT2/ Cdk5/p25 Signaling Pathway Contributed to Inflammatory Pain By CFA

Vesicular glutamate transporter type 2 (VGLUT2) is known to play an important role in mediating the heat hyperalgesia induced by inflammation. However, the underlying mechanism for this activity is poorly understood. Cyclin-dependent kinase 5 (Cdk5), serving as a key regulator in mediating release of glutamate, contributed to the inflammatory heat. It remains unknown whether there is a bridge between Cdk5 and VGLUT2 for mediating inflammatory pain. Therefore, we designed the experiment to determine whether VGLUT2 signaling pathway is involved in Inflammatory pain mediated by Cdk5 and the heat hyperalgesia induced by complete Freunds adjuvant (CFA) can be reversed by roscovitine, a selective inhibitor for Cdk5 through inhibition of VGLUT2 expression. Immunohistochemistry results suggest that when compared with rats in a control group, rats in an experimental group showed significant coexpression of Cdk5/VGLUT2 in small and medium-sized neuronal cells of the dorsal root ganglion (DRG) and spinal cord between days 1 and 3 following subcutaneous injection of CFA. Moreover, our study revealed that the expression of VGLUT2 protein in DRG and spinal cord was remarkably increased between days 1 and 3 following CFA injection. Additionally, p25 but not p35, a activator of Cdk5, protein was significantly increased and reduced by roscovitine. The increased expressions of VGLUT2 protein was significantly reduced by roscovitine as well. Our study showed that VGLUT2/Cdk5 signaling pathway contributed to the inflammatory pain medicated by Cdk5/p25.

neuroscience↗

bioRxiv2019

A New Minimally Invasive Technique for Repairing Achilles Tendon Rupture: A Biomechanical Study

IntroductionThe incidence of Achilles tendon rupture shows a gradually increasing trend, which is mainly managed by minimally invasive treatment due to its advantages, such as low wound infection rate. At present, the firmness of the commonly applied minimally invasive suture method for Achilles tendon remains controversial. Our research group has developed a novel suture method for Achilles tendon, which has achieved favorable clinical outcomes. Therefore, this experiment aimed to explore the optimal approach to repair Achilles tendon rupture through comparing the biomechanical strength of the commonly used Achilles tendon suture methods currently.\n\nMaterials and methods6 fresh frozen human cadaveric Achilles tendon specimens were sutured by three kinds of technique, and were tested through the cyclical loading after repair.\n\nResultsResults of cyclical loading showed that, the repair using the new technique was stronger after 10 cycles, 1000 cycles, and rupture. Moreover, the new technique had displayed superior anti-deformation strength to that of the Ma-Griffith technique.\n\nConclusionsOur experimental results demonstrate that, the new technique proposed by our research group can attain comparable biomechanical properties to those of the Krachow technique. However, the sample size in this study is small, and further clinical trials are warranted.

biochemistry↗

bioRxiv2019

Genomic acquisitions in emerging populations of Xanthomonas vasicola pv. vasculorum infecting corn in the U.S. and Argentina

Xanthomonas vasicola pv. vasculorum (Xvv) is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this bacteria have greatly increased in the past years in South America and in the U.S., where it is now present in most of the corn producing states. Phenotypic characterization showed that the emerging U.S. and South American Xvv populations may have increased virulence in corn compared to older strains. To understand the genetic mechanisms behind the increased virulence in this group, we used comparative genomics to identify gene acquisitions in Xvv genomes from the U.S. and Argentina. We sequenced 41 genomes of Xvv and the related sorghum-infecting X. vasicola pv. holcicola (Xvh). A comparison of all available X. vasicola genomes showed the phylogenetic relationships in the group and identified clusters of genes associated with the emerging Xvv populations. The newly acquired gene clusters showed evidence of horizontal transfer to Xvv and included candidate virulence factors. One cluster, in particular, corresponded to a prophage transferred from Xvh to all Xvv from Argentina and the U.S. The prophage contains putative secreted proteins, which represent candidates for virulence determinants in these populations and await further molecular characterization.

microbiology↗