bioRxiv Science⌕ Search

Biology subjects

Zhang, W.

Publications and source records attributed to Zhang, W..

At least 937 records · Page 52Linked to original sources

Genomic evaluation of circulating proteins for drug target characterisation and precision medicine

Circulating proteins are vital in human health and disease and are frequently used as biomarkers for clinical decision-making or as targets for pharmacological intervention. By mapping and replicating protein quantitative trait loci (pQTL) for 90 cardiovascular proteins in over 30,000 individuals, we identified 467 pQTLs for 85 proteins. The pQTLs were used in combination with other sources of information to evaluate known drug targets, and suggest new target candidates or repositioning opportunities, underpinned by a) causality assessment using Mendelian randomization, b) pathway mapping using trans-pQTL gene assignments, and c) protein-centric polygenic risk scores enabling matching of plausible target mechanisms to sub-groups of individuals enabling precision medicine.

genetics↗

Pacific Biosciences long reads-based genome sequencing data from a widespread bee fungal parasite, Nosema ceranae

Nosema ceranae is a widespread fungal parasite that infects both adult honeybee and honeybee larvae, leading to microsporidiosis, which seriously affects bee health and apicultural industry. In this article, genome sequencing of clean spores of N. ceranae was conducted using third-generation Pacific Biosciences (PacBio) single molecule real time (SMRT) sequencing technology. In total, 152671 subreads were obtained after quality control of raw reads from PacBio SMRT sequencing, with a N50 and average length of 14422 bp and 11310 bp, respectively. Additionally, the length distribution of subreads was from 10000 bp to more than 50000 bp. Nineteen scaffords with a total length of 7354221 bp were assembled, and the N50, N90 and maximum scafford length were 728543 bp, 198795 bp and 1917792 bp, respectively. The GC content was 25.97%. Furthermore, by integration of genes predicted from de novo and homology-based methods, 3112 N. ceranae genes were finally assembled, with a total length of 2730179 bp and mean length of 877.31 bp. In addition, the total length and mean length of exons were 2657637 bp and 854 bp, respectively; and the total length and mean length of introns were 72542 bp and 23.31 bp, respectively. The genome sequencing data documented here will give deep insights into the molecular biology of N. ceranae, facilitate exploration of genes and pathways associated with toxin factors and infection-related factors, and benefit research on comparative genomics and phylogenetic diversity of Nosema species.

bioinformatics↗

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. The NuRD complex binds to all active enhancers to modulate transcription and here we use Hi-C experiments to show that it blurs TAD boundaries and increases the proximity of intermediate-range (~1 Mb) genomic sequences and enhancer-promoter interactions. To understand whether NuRD alters the dynamics of 3D genome structure, we developed an approach to segment and extract key biophysical parameters from 3D single-molecule trajectories of the NuRD complex determined using live-cell imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound enhancers move faster, increasing the overall volume of the nucleus that these key regulatory regions explore. Interestingly, we also uncovered a rare fast-diffusing state of NuRD bound enhancers that exhibits directed motion. The NuRD complex reduces the amount of time that enhancers remain in this fast-diffusing state, which we propose might otherwise re-organise enhancer-promoter proximity. Thus, we uncover an intimate connection between a chromatin remodeller and the spatial dynamics of the local regions of the genome to which it binds.

cell biology↗

ULTRASOUND-ASSISTED MAGNETIC NANOPARTICLE-BASED GENE DELIVERY

Low-intensity pulsed ultrasound (LIPUS), a special type of ultrasonic stimulation, is attracting a lot of attention for both clinical and scientific research. In this paper, we report a concept of a new method using magnetic nanoparticles (MNPs) for LIPUS-assisted gene delivery. The MNPs are iron oxide superparamagnetic nanoparticles, coated with polyethyleneimine (PEI), which introduces a high positive surface charge, favorable for the binding of genetic material. Due to the paramagnetic properties of the MNPs, the application of an external magnetic field increases transfection efficiency; meanwhile, LIPUS stimulation enhances cell permeability. We found out that stimulation at the intensity of 30 mW/cm2 for 10 minutes yields optimal results with a minimal adverse effect on the cells. Combining the effect of the external magnetic field and LIPUS, the genetic material (GFP or Cherry Red plasmid in our case) can enter the cells. The flow cytometry results showed that by using just a magnetic field to direct the genetic material, the transfection efficiency of HEK 293 cells that were treated with our MNPs was 56.1%. Coupled with LIPUS stimulation, it increased to 61.5% or 19% higher than the positive control (Lipofectamine 2000). In addition, compared with the positive control, our method showed less toxicity. Cell viability after transfection was 63.61%, 19% higher than with the standard transfection technique. In conclusion, we designed a new gene-delivery technique that is affordable, targeted, shows low-toxicity, yet high transfection efficiency, compared to other conventional approaches. The Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/018440v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@72028corg.highwire.dtl.DTLVardef@1057528org.highwire.dtl.DTLVardef@14ea607org.highwire.dtl.DTLVardef@764da1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex

Nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC from Xenopus laevis oocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes, and a Grid domain, which serves as a rigid base for the Finger domain. Two neighbouring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighbouring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC.

biophysics↗

Reusable and Sensitive Detection Method for Exonuclease III Activity by DNB Nanoarrays Based on cPAS Sequencing Technology

AbstractionIn this article, we have designed a sensitive and recycled DNB (DNA nanoball) nanoarrays sequencing complex structures based on BGISEQ-500RS sequencer for the monitoring performance of Exo III activity. In the shortage of Exo III, the effective number ratio of DNB would be captured by an optical system due to one fluorescent. In contrast, in the presence of Exo III, some DNB would disappear or discard from the fields of the optical system by fluorescence extinction and uncleaned fluorescent, respectively. As a result, the effective number of DNB of this strategy was relative to the concentration of Exo III. For Exo III, our strategy showed a highly sensitive linear response in the low detection range of 0.01 U/mL to 0.5 U/mL, with detection limits below 0.01 U/mL. With the comparison between DNB nanoarrays and other fluorescent sensors, this study possessed superior sensitivity, selectivity, and reusability, accompanying with the low cost and simple setup.

biochemistry↗

Morphological and physiological response strategies of Vallisneria natans at different water depths and light conditions

Phenotypic plasticity is an important adaptation to spatial and temporal environmental variations. For submerged macrophytes, adaptation to water depth and light variation is particularly important. To determine the morphological and physiological adaptive strategies of Vallisneria natans at different water depths and light conditions, we combined field investigation, light control experiment and in situ physiological response experiment. In the field investigation and the light control experiment, both water depth and light intensity had prominent effects on the morphological of V. natans, especially in fresh weight and leaf length. The leaf length elongated more rapidly at intermediate water depth sites with lower light intensity. In the in situ experiment, the survival boundary of V. natans is 5.5 m in Lake Erhai. Below this depth, the chlorophyll-a content increased gradually with increasing water depth. Our results demonstrated that V. natans can adapt to water depth and light availability by changing morphological, physiological and resource allocation. At low light condition, V. natans invested more resource for light acquisition, simultaneously, changing the photosynthetic pigment content to compensate for light attenuation; conversely, more resource was directed towards reproduction. These results will provide new insight for species selection when conducting aquatic plants restoration in freshwater ecosystem. HIGHLIGHTSO_LIWater depth and light availability affect the morphology, physiology, and resource allocation of V. natans. C_LIO_LIAn alternative resource allocation pattern of V. natans could shift between light acquisition and reproduction. C_LI

ecology↗

O-GlcNAcylation of SAMHD1 Indicating a Link between Metabolic Reprogramming and Anti-HBV Immunity

Viruses hijack the host cell machinery to promote viral replication; however, the mechanism by which metabolic reprogramming regulates innate antiviral immunity in the host remains elusive. Herein, we found that Hepatitis B virus (HBV) infection upregulates glucose transporter 1expression, promotes hexosamine biosynthesis pathway (HBP) activity, and enhances O-linked {beta}-N-acetylglucosamine (O-GlcNAc) modification of downstream proteins. HBP-mediated O-GlcNAcylation positively regulates host antiviral response against HBV in vitro and in vivo. Mechanistically, O-GlcNAc transferase (OGT)-mediated O-GlcNAcylation of sterile alpha motif and histidine/aspartic acid domain-containing protein 1 (SAMHD1) on Ser93 stabilizes SAMHD1 and enhances its antiviral activity. In addition, O-GlcNAcylation of SAMHD1 promoted its antiviral activity against human immunodeficiency virus-1 in vitro. In conclusion, the results of our study reveal a link between HBP, O-GlcNAc modification, and innate antiviral immunity by targeting SAMHD1. Therefore, the results of this study demonstrate a strategy for the potential treatment of HBV infection by modulating HBP activity.

microbiology↗

Surgery and Radioactive Iodine Therapeutic Strategy for Patients Greater than 60 Years of Age with Differentiated Thyroid Cancer

PurposeThe purpose of the current study was to determine whether older patients with differentiated thyroid cancer (DTC) who received surgical treatment had a better cause-specific survival (CSS) than patients who were recommended surgery, but declined, and whether patients who underwent post-operative RAI-131 therapy had an impact on CSS based on TNM staging and number of lymph node metastases for all total or near-total thyroidectomy patients. Patients and MethodsAll DTC patients information were obtained from the SEER*Stat 8.3.6 program, and only patients [&ge;] 60 years or older were considered. The patients were divided into two groups (underwent surgery and surgery recommend, but not performed). Furthermore, patients were grouped as follows: T4; N1b; M1; T1-3N0-1a; specific number of lymph node metastases; and total or near-total thyroidectomy. ResultsThe 120-month cause-specific survival (CSS) rate of females and males showed a gradual declining trend from 60-64 to [&ge;]80 years of age in the group that underwent surgery. The CSS rate of females and males showed a marked downward and irregular trend with an increase in age in the recommended, but no surgery group. Univariate analysis indicated that the surgery group had a higher 120-month CSS in females in most stages and males, compared with the no surgery group. RAI-131 therapy was associated with an improved 80-month CSS in T4/N1b/M1 females (P<0.0183) and males (P<0.0011). There was no CSS difference in females or males between the T1-3N0 and T1-3N1a patients. There was no statistical difference between the two subgroups. ConclusionsSurgical treatment should be recommended for elderly DTC patients because surgery can lead to a better CSS. High-risk patients achieve a higher benefit-to-risk ratio with RAI-131 therapy. To avoid the adverse effects associated with RAI-131 therapy, a multidisciplinary discussion should be arranged for intermediate- and low-risk patients.

cancer biology↗

DE NOVO SEQUENCING AND ANALYSIS OF THE RANA CHENSINENSIS TRANSCRIPTOME TO DISCOVER PUTATIVE GENES ASSOCIATED WITH POLYUNSATURATED FATTY ACIDS

Rana chensinensis (R. chensinensis) is an important wild animal found in China, and a precious animal in Chinese herbal medicine. R. chensinensis is rich in polyunsaturated fatty acids (PUFAS). However, information regarding the genes of R. chensinensis related to the synthesis of PUFAs is limited. To identify these genes, we performed Illumina sequencing of R. chensinensis RNA from the skin and Oviductus Ranae. The Illumina Hiseq 2000 platform was used for sequencing, and the I-Sanger cloud platform was used for transcriptome de novo sequencing and information analysis to generate a database. Through the database generated by the transcriptome and the pathway map, we found the pathway for the biosynthesis of R. chensinensis PUFAs. The Pearson coefficient method was used to analyze the correlation of gene expression levels between samples, and the similarity of gene expression in different tissues and the characteristics in their respective tissues were found. Twelve differentially expressed genes of PUFA in skin and Oviductus Ranae were screened by gene differential expression analysis. The 12 unigenes expression levels of qRT-PCR were used to verify the results of gene expression levels consistent with transcriptome analysis. Based on the sequencing, key genes involved in biosynthesis of unsaturated fatty acids were isolated, which established a biotechnological platform for further research on R. chensinensis.

animal behavior and cognition↗

CircGLCE alleviates intervertebral disc degeneration by regulating apoptosis and matrix degradation through the targeting of miR-587/STAP1

BackgroundIntervertebral disc degeneration (IDD) can induce profound global socioeconomic burdens. Recent studies have suggested that circular RNAs might have crucial functions in the progression of IDD. The purpose of this study was to identify a specific circular RNA and to investigate its regulatory mechanism in IDD. MethodsCircGLCE was selected after microarray analyses and was further analysed by RT-qPCR and FISH. After silencing CircGLCE, its function was assessed with RT-qPCR, immunofluorescence analysis and flow cytometry. Based on Sanger sequencing, miR-587 was identified as a direct target of CircGLCE, and it was further examined with RNA pulldown assays, RT-qPCR, dual luciferase assays and FISH. After silencing CircGLCE or miR-587, western blotting, immunofluorescence analysis, and flow cytometry were conducted. STAP1 was assessed by RT-qPCR and luciferase assay, and experiments with silenced and overexpressed miR-587 were performed. A rescue experiment was also included. In an IDD rat model, the in vivo effects of overexpressing CircGLCE on IDD were analysed with imaging techniques, TUNEL staining, FISH, western blotting, H&E staining and immunohistochemistry. ResultsCircGLCE was found to stably exist in the cytoplasm of nucleus pulposus (NP) cells. It was downregulated in IDD. Knockdown of CircGLCE promoted apoptosis and induced the expression of matrix-degrading enzymes in NP cells. CircGLCE served as a miR-587 sponge in NP cells. Inhibiting miR-587 counteracted the IDD-enhancing effect caused by silencing CircGLCE. STAP1 served as the miRNA target that mediated the functions of miR-587. Overexpressing CircGLCE alleviated IDD in vivo. ConclusionsCircGLCE attenuates IDD by regulating the apoptosis of NP cells and by regulating ECM degradation through the targeting of miR-587/STAP1. CircGLCE may be a potential therapeutic target for IDD treatments.

molecular biology↗

A dataset of speed-resolved blood perfusion and oxygen saturation in human skin response to thermal stimulation

The functional status of vessels can be determined by assessing blood perfusion. By integrating diffuse reflectance spectroscopy (DRS) and laser Doppler Flowmetry (LDF), the speed-resolved blood perfusion and blood oxygen saturation can be measured simultaneously by Enhanced Perfusion and Oxygen Saturation (EPOS). The dataset presented in this descriptor contains EPOS data recorded from a forearm point exposed to different levels of thermal stimulation, the classical LDF at control points, the R-R time series and data regarding characteristics of subjects. All data were recorded from 60 recruited healthy subjects. Half of the subjects received different levels of thermal stimulation, and half of them were blank controls. We believe that this dataset will lead to the development of local blood perfusion methods that can be used to index vessel function assessments. This publicly available dataset will be beneficial to the microcirculation evaluation.

bioengineering↗

Mechanosensitive activation of mTORC1 mediates ventilator induced lung injury during the acute respiratory distress syndrome

Acute respiratory distress syndrome (ARDS) is a highly lethal condition that impairs lung function and causes respiratory failure. Mechanical ventilation maintains gas exchange in patients with ARDS, but exposes lung cells to physical forces that exacerbate lung injury. Our data demonstrate that mTOR complex 1 (mTORC1) is a mechanosensor in lung epithelial cells and that activation of this pathway during mechanical ventilation exacerbates lung injury. We found that mTORC1 is activated in lung epithelial cells following volutrauma and atelectrauma in mice and humanized in vitro models of the lung microenvironment. mTORC1 is also activated in lung tissue of mechanically ventilated patients with ARDS. Deletion of Tsc2, a negative regulator of mTORC1, in epithelial cells exacerbates physiologic lung dysfunction during mechanical ventilation. Conversely, treatment with rapamycin at the time mechanical ventilation is initiated prevents physiologic lung injury (i.e. decreased compliance) without altering lung inflammation or barrier permeability. mTORC1 inhibition mitigates physiologic lung injury by preventing surfactant dysfunction during mechanical ventilation. Our data demonstrate that in contrast to canonical mTORC1 activation under favorable growth conditions, activation of mTORC1 during mechanical ventilation exacerbates lung injury and inhibition of this pathway may be a novel therapeutic target to mitigate ventilator induced lung injury during ARDS.

molecular biology↗

A Novel Non-hypermucoviscous ST11 Hypervirulent Carbapenem-resistant Klebsiella pneumoniae Lacking Classical Virulence Factors

BackgroundHypervirulent Klebsiella pneumoniae lacking classical virulence factors is uncommon, and the virulence mechanisms of this organism are not understood. MethodsFollowing a retrospective study of carbapenem-resistant K. pneumoniae based on core genome multilocus sequence typing (cgMLST), isolates that caused high mortality were investigated with a genome-wide association study (GWAS), proteome analysis and an animal model. ResultsThe sublineage of sequence type 11 (ST11) K. pneumoniae, which belongs to complex type 3176 (CT3176) and K-locus 47 (KL47), was highlighted due to the high mortality of infected patients. GWAS analysis showed that ampR was associated with the CT3176 isolates. In a mouse model, the mortality of ampR-carrying isolates was comparable to that of the typical hypervirulent isolate GM2. Even during the first 24 hours of infection, the bacterial load and pathological changes of the ampR-carrying isolates in the lungs were more severe than those of GM2. The ampR complement mutant was able to enhance the virulence of the KL47 isolate but not the virulence of KL1. Proteome analysis showed that the expression of WcaJ in the ampR+ isolates was significantly higher than that in the ampR- isolates, and this result was also confirmed by transcription tests and capsule staining. It is suggested that the enhancement of the initial stage of capsule synthesis may be the cause of the high virulence of these non-hypermucoviscous ST11 carbapenem-resistant K. pneumoniae isolates. ConclusionsNon-hypermucoviscous ST11 hypervirulent carbapenem-resistant K. pneumoniae warrants continued surveillance and investigation.

microbiology↗

Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureum Schum.)

Elephant grass (Pennisetum purpureum Schum., AABB, 2n=4x=28), which is characterized as robust growth and high biomass, and widely distributed in tropical and subtropical areas globally, is an important forage, biofuels and industrial plant. We sequenced its allopolyploid genome and assembled 2.07 Gb (96.88%) into A and B sub-genomes of 14 chromosomes with scaffold N50 of 8.47 Mb. A total of 38,453 and 36,981 genes were annotated in A and B sub-genomes, respectively. A phylogenetic analysis with species in Pennisetum identified that the speciation of the allotetraploid occurred approximately 15 MYA after the divergence between S.italica and P. glaucum. Double whole-genome duplication (WGD) and polyploidization events resulted in large scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional differentiation between sub-genomes; A sub-genome contributed more to plant growth, development and photosynthesis whereas B sub-genome primarily offered functions of effective transportation and resistance to stimulation. The results uncovered enhanced cellulose and lignin biosynthesis pathways with 645 and 666 genes expanded in A and B sub-genomes, respectively. Our findings provided deep insights into the speciation and genetic basis of fast growth and high biomass accumulation in the species. The genetic, genomic, and transcriptomic resources generated in this study will pave the way for further domestication and selection of these economical species and making them more adaptive to industrial utilization.

genomics↗

mTOR-driven widespread exon skipping renders multifaceted gene regulation and proteome complexity

The mammalian target of rapamycin (mTOR) pathway is crucial in cell proliferation. Previously, we reported transcriptome-wide 3’-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon-skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: alternative splicing (AS) in the 5’-UTR controls translation efficiency while AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biochemistry↗

CoolMPS™: Advanced massively parallel sequencing using antibodies specific to each natural nucleobase

Massively parallel sequencing (MPS) on DNA nanoarrays provides billions of reads at relatively low cost and enables a multitude of genomic applications. Further improvement in read length, sequence quality and cost reduction will enable more affordable and accurate comprehensive health monitoring tests. Currently the most efficient MPS uses dye-labeled reversibly terminated nucleotides (RTs) that are expensive to make and challenging to incorporate. Furthermore, a part of the dye-linker (scar) remains on the nucleobase after cleavage and interferes with subsequent sequencing cycles. We describe here the development of a novel MPS chemistry (CoolMPS) utilizing unlabeled RTs and four natural nucleobase-specific fluorescently labeled antibodies with fast (30 sec) binding. We implemented CoolMPS on MGIs PCR-free DNBSEQ MPS platform using arrays of 200nm DNA nanoballs (DNBs) generated by rolling circle replication and demonstrate 3-fold improvement in signal intensity and elimination of scar interference. Single-end 100-400 base and pair-end 2x150 base reads with high quality were readily generated with low out-of-phase incorporation. Furthermore, DNBs with less than 50 template copies were successfully sequenced by strong-signal CoolMPS with 3-times higher accuracy than in standard MPS. CoolMPS chemistry based on natural nucleobases has potential to provide longer, more accurate and less expensive MPS reads, including highly accurate "4-color sequencing" on the most efficient dye-crosstalk-free 2-color imagers with an estimated sequencing error rate of 0.00058% (one error in 170,000 base calls) in a proof-of-concept demonstration.

genomics↗

Endosidin20 targets cellulose synthase catalytic domain to inhibit cellulose biosynthesis

Cellulose is synthesized by rosette structured cellulose synthase (CESA) complexes (CSCs), each of which is composed of multiple units of CESAs in three different isoforms. CSCs rely on vesicle trafficking for delivery to the plasma membrane where they catalyze cellulose synthesis. Although the rosette structured CSCs were observed decades ago, it remains unclear what amino acids in plant CESA that directly participate in cellulose catalytic synthesis. It is also not clear how the catalytic activity of CSCs influences their efficient transport at the subcellular level. Here we report characterization of the small molecule Endosidin20 (ES20) and present evidence that it represents a new CESA inhibitor. We show data from chemical genetic analyses, biochemical assays, structural modeling, and molecular docking to support our conclusion that ES20 targets the catalytic site of Arabidopsis CESA6. Further, chemical genetic analysis reveals important amino acids that potentially form the catalytic site of plant CESA6. Using high spatiotemporal resolution live-cell imaging, we found that inhibition of CSC catalytic activity by inhibitor treatment, or by creating missense mutation at amino acids in the predicted catalytic site, causes reduced efficiency in CSC transport to the plasma membrane. Our results show that the catalytic activity of plant CSCs is integrated with subcellular trafficking dynamics. One sentence summaryEndosidin20 targets cellulose synthase at the catalytic site to inhibit cellulose synthesis and the inhibition of catalytic activity reduces cellulose synthase complex delivery to the plasma membrane.

plant biology↗