bioRxiv Science⌕ Search

Biology subjects

Wang, C.

Publications and source records attributed to Wang, C..

At least 991 records · Page 55Linked to original sources

Response patterns and mechanisms of plants to water stress

Plants are key to the functionality of many ecosystem processes. The duration and intensity of water stress are anticipated to increase in the future; however, an elucidation of the responses of plants to water stress remains incomplete. For this study, we present a global meta-analysis derived from 1301 paired observations from 84 studies to evaluate the response patterns and mechanisms of plants to water stress. The results revealed that while water stress inhibited plant growth and photosynthesis, reactive oxygen species (ROS), plasma membrane permeability, enzymatic antioxidants, and non-enzymatic antioxidants increased. These responses generally increased with the intensity of water stress but were mitigated with experimental duration. Our findings suggested that the overproduction of ROS was the primary mechanism of plants in response to water stress and that plants tend to acclimate to water stress over time to some extent. Our synthesis provides a framework for understanding the responses and mechanisms of plants under drought conditions. One senence summaryThe overproduction of ROS was the primary mechanism of plants in response to water stress and that plants tend to acclimate to water stress over time to some extent.

plant biology↗

Sapphire Nanopores for Low-Noise DNA Sensing

Silicon-supported (SiS) solid-state nanopores have broad applications in single-molecule biosensing and diagnostics, but their high capacitive noise has seriously limited both their sensing accuracy and recording speed. Nanopores on insulating glass have demonstrated reduced capacitance and noise, but it remains challenging to bulk-etch amorphous glass to create membranes reproducibly and uniformly. Here a new approach is reported to form triangular sapphire-supported (SaS) nanopore membranes by batch-processing-compatible anisotropic wet etching of sapphire, with membrane dimension demonstrated from ~200 μm to 5 μm. A SaS nanopore in 68 μm-wide silicon nitride membrane has 130 times smaller capacitance (10 pF) compared to a SiS nanopore (~4 μm SiN membrane, ~1.3 nF), despite a 100 times larger membrane. It has a current noise of 18 pA over 100 kHz bandwidth, much smaller than that from our SiS nanopore (46 pA) and comparable with the best reported low-noise nanopores. Further, the SaS nanopore displays a higher signal-to-noise ratio (SNR, 21 versus 11 for SiS nanopore) in DNA sensing, although the SNR can be further improved using thinner membranes and smaller pores. The SaS nanopore presents a simple platform in both fabrication and structure that is particularly suitable for low-noise and high-speed molecular diagnostics.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

To construct a superior microbial cell factory for chemical synthesis, a major challenge is to fully exploit cell potential via identifying and engineering beneficial gene targets in the sophisticated metabolic networks. Here, we develop an approach that integrates CRISPR interference (CRISPRi) to readily modulate genes expression and omics analyses to identify potential targets in multiple cellular processes, enabling systematical discovery of beneficial chromosomal gene targets that can be engineered to optimize free fatty acids (FFAs) production in Escherichia coli. We identify 56 beneficial genes via synergistic CRISPRi-Omics strategy, including 46 novel targets functioning in cell structure and division, and signaling transduction that efficiently facilitate FFAs production. Upon repressing ihfA and overexpressing aidB and tesA in E. coli, the recombinant strain LihfA-OaidB results in a FFAs titer of 21.6 g L-1 in fed-batch fermentation, which, to our best knowledge, is the maximum FFAs titer by the recombinant E. coli reported to date.

biochemistry↗

Structural basis of transcription-translation coupling

In bacteria, transcription and translation are coupled processes, in which movement of RNA polymerase (RNAP) synthesizing mRNA is coordinated with movement of the first ribosome translating mRNA. Coupling is modulated by the transcription factors NusG--which is thought to bridge RNAP and ribosome--and NusA. Here, we report cryo-EM structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P-site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A; previously termed "expressome"). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling. One Sentence SummaryCryo-EM defines states that mediate NusG- and NusA-dependent transcription-translation coupling in bacteria

molecular biology↗

The Pathogenicity of 2019 Novel Coronavirus in hACE2 Transgenic Mice

Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the Corona Virus Disease 2019 (COVID-19) cases in China has become a public health emergency of international concern (PHEIC). Based on angiotensin converting enzyme 2 (ACE2) as cell entry receptor of SARS-CoV, we used the hACE2 transgenic mice infected with SARS-CoV-2 to study the pathogenicity of the virus. Weight loss and virus replication in lung were observed in hACE2 mice infected with SARS-CoV-2. The typical histopathology was interstitial pneumonia with infiltration of significant lymphocytes and monocytes in alveolar interstitium, and accumulation of macrophages in alveolar cavities. Viral antigens were observed in the bronchial epithelial cells, alveolar macrophages and alveolar epithelia. The phenomenon was not found in wild type mice with SARS-CoV-2 infection. The pathogenicity of SARS-CoV-2 in hACE2 mice was clarified and the Kochs postulates were fulfilled as well, and the mouse model may facilitate the development of therapeutics and vaccines against SARS-CoV-2.

microbiology↗

Microbial trend analysis for common dynamic trend, group comparison and classification in longitudinal microbiome study

MotivationThe human microbiome is inherently dynamic and its dynamic nature plays a critical role in maintaining health and driving disease. With an increasing number of longitudinal microbiome studies, scientists are eager to learn the comprehensive characterization of microbial dynamics and their implications to the health and disease-related phenotypes. However, due to the challenging structure of longitudinal microbiome data, few analytic methods are available to characterize the microbial dynamics over time. ResultsWe propose a microbial trend analysis (MTA) framework for the high-dimensional and phylogenetically-based longitudinal microbiome data. In particular, MTA can perform three tasks: 1) capture the common microbial dynamic trends for a group of subjects on the community level and identify the dominant taxa; 2) examine whether or not the microbial overall dynamic trends are significantly different in groups; 3) classify an individual subject based on its longitudinal microbial profiling. Our extensive simulations demonstrate that the proposed MTA framework is robust and powerful in hypothesis testing, taxon identification, and subject classification. Our real data analyses further illustrate the utility of MTA through a longitudinal study in mice. ConclusionsThe proposed MTA framework is an attractive and effective tool in investigating dynamic microbial pattern from longitudinal microbiome studies.

bioinformatics↗

Machine learning approach reveals heterogeneous responses to FAK and Rho GTPases inhibition on smooth muscle spheroid formation

Atherosclerosis and vascular injury are characterized by neointima formation caused by the aberrant accumulation and proliferation of vascular smooth muscle cells (VSMCs) within the vessel wall. Understanding how to control VSMCs would advance the effort to treat vascular disease. However, the response to treatments aimed at VSMCs is often different among patients with the same disease condition, suggesting patient-specific heterogeneity in VSMCs. Here, we present an experimental and computational method called HETEROID (Heterogeneous Spheroid), which examines the heterogeneity of the responses to drug treatments at the single-spheroid level by combining a VSMC spheroid model and machine learning (ML) analysis. First, we established a VSMC spheroid model that mimics neointima formation induced by atherosclerosis and vascular injury. We found that FAK-Rac/Rho, but not Cdc42, pathways regulate the VSMC spheroid formation through N-cadherin. Then, to identify the morphological subpopulations of drug-perturbed spheroids, we used an ML framework that combines deep learning-based spheroid segmentation and morphological clustering analysis. Our ML approach reveals that FAK, Rac, Rho, and Cdc42 inhibitors differentially affect the spheroid morphology, suggesting there exist multiple distinct pathways governing VSMC spheroid formation. Overall, our HETEROID pipeline enables detailed quantitative characterization of morphological changes in neointima formation, that occurs in vivo, by single-spheroid analysis of various drug treatments.

cell biology↗

The Efficiency, Efficacy, and Retention of Motor Training in Chronic Stroke

In motor skill learning, the greater the dose of training, the greater the efficacy of training, the lower the efficiency of training, and the better the long-term retention. Whether such principles apply to motor training after stroke is unclear. Here, we developed novel mixed-effects models of the change in the quality of arm movements during and following training fitted to data from a recent randomized controlled trial of the effect of the dose of training in chronic stroke. Analysis of the models learning and retention rates demonstrated an increase in efficacy of training with greater doses, a decrease in efficiency of training with both additional doses and additional bouts of training, and fast initial decay following training. Two additional effects modulated retention: a positive "self-training" effect, and an un-expected negative effect of dose. Our results suggest that for patients with sufficient arm use post-training, self-training will further improve use, but additional therapy may be in vain.

neuroscience↗

Polyamine Metabolism Regulates the T Cell Epigenome Through Hypusination

We report here a central role for polyamines in T cell differentiation and function. Deficiency in ornithine decarboxylase (ODC), a critical enzyme for polyamine synthesis, resulted in a profound failure of CD4+ T cells to adopt correct subset specification, underscored by ectopic expression of multiple cytokines and lineage-defining transcription factors across TH1, TH2, TH17, and Treg polarizing conditions, and enhanced colitogenic potential. T cells deficient in deoxyhypusine synthase (DHPS) or deoxyhypusine hydroxylase (DOHH), which sequentially utilize polyamines to generate hypusine, phenocopied Odc-deficient T cells, and mice in which T cells lacked Dhps or Dohh developed colitis. Polyamine-hypusine pathway enzyme deficiency caused widespread chromatin and transcriptional dysregulation accompanied by alterations in histone methylation, histone acetylation, and TCA cycle metabolites. Epigenetic modulation by 2-hydroxyglutarate, or histone acetyltransferase inhibition, restored CD4+ T cell subset specification. Thus, polyamine synthesis via hypusine is critical for maintaining the epigenome to focus TH cell subset fidelity.

immunology↗

Dose-dependent effects of netarsudil, a Rho-kinase inhibitor, on the distal outflow tract

PurposeTo characterize the effects of netarsudil on the aqueous humor outflow tract distal to the trabecular meshwork (TM). We hypothesized that netarsudil increases outflow facility in eyes with and without circumferential ab interno trabeculectomy (AIT) that removes the TM. Methods64 porcine anterior segment cultures were randomly assigned to groups with (n=32) and without circumferential AIT (n=32). Cultures were exposed to 0.1, 1, and 10 M netarsudil (N= 8 eyes per concentration). For each concentration, IOP and vessel diameters were compared to their respective pretreatment baselines. Outflow tract vessel diameters were assessed by spectral-domain optical coherence tomography (SDOCT) and rendered in 4D (XYZ time-series). ResultsNetarsudil at 1 M reduced IOP in both eyes with TM (-0.60{+/-}0.24 mmHg, p = 0.01) and in eyes without TM (-1.79{+/-}0.42 mmHg, p<0.01). At this concentration, vessels of the distal outflow tract dilated by 72%. However, at 0.1 M netarsudil elevated IOP in eyes with TM (1.59{+/-}0.36 mmHg, p<0.001) as well as in eyes without TM (0.23{+/-}0.32 mmHg, p<0.001). Vessels of the distal outflow tract constricted by 31%. Similarly, netarsudil at a concentration of 10 M elevated IOP both in eyes with TM (1.91{+/-}0.193, p<0.001) and in eyes without TM (3.65{+/-}0.86 mmHg, p<0.001). At this concentration, outflow tract vessels constricted by 27%. ConclusionIn the porcine anterior segment culture, the dose-dependent IOP changes caused by netarsudil matched the diameter changes of distal outflow tract vessels. Hyper- and hypotensive properties of netarsudil persisted after TM removal.

physiology↗

3D-Reconstruction of the Human Conventional Outflow System by Ribbon Scanning Confocal Microscopy

PurposeRisk for glaucoma is driven by the microanatomy and function of the anterior segment. We performed a computation-intense, high-resolution, full-thickness ribbon-scanning confocal microscopy (RSCM) of the outflow tract of two human eyes. We hypothesized this would reveal important species differences when compared to existing data of porcine eyes, an animal that does not spontaneously develop glaucoma. MethodsAfter perfusing two human octogenarian eyes with lectin-fluorophore conjugate and optical clearance with benzyl alcohol benzyl benzoate (BABB), anterior segments were scanned by RSCM and reconstructed in 3D for whole-specimen rendering. Morphometric analyses of the outflow tract were performed for the trabecular meshwork (TM), limbal, and perilimbal outflow structures and compared to existing porcine data. ResultsRSCM provided high-resolution data for IMARIS-based surface reconstruction of outflow tract structures in 3D. Different from porcine eyes with an abundance of highly interconnected, narrow, and short collector channels (CCs), human eyes demonstrated fewer CCs which had a 1.5x greater cross-sectional area (CSA) and 2.6x greater length. Proximal CC openings at the level of Schlemms canal (SC) had a 1.3x larger CSA than distal openings into the scleral vascular plexus (SVP). CCs were 10.2x smaller in volume than the receiving SVP vessels. Axenfeld loops, projections of the long ciliary nerve, were also visualized. ConclusionIn this high-resolution, volumetric RSCM analysis, human eyes had far fewer outflow tract vessels than porcine eyes. Human CCs spanned several clock-hours and were larger than in porcine eyes. These species differences may point to factors downstream of the TM that increase our vulnerability to glaucoma. Grant informationNational Eye Institute K08EY022737 (NAL); Initiative to Cure Glaucoma of the Eye and Ear Foundation of Pittsburgh (NAL); Wiegand Fellowship of the Eye and Ear Foundation of Pittsburgh (YD); P30-EY08098 (NAL); Department grant by Research to Prevent Blindness (NAL); an unrestricted fellowship grant from the Xiangya Hospital of Central South University (SC).

physiology↗

Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm

The recent outbreak of pneumonia in Wuhan, China caused by the 2019 Novel Coronavirus (2019-nCoV) emphasizes the importance of detecting novel viruses and predicting their risks of infecting people. In this report, we introduced the VHP (Virus Host Prediction) to predict the potential hosts of viruses using deep learning algorithm. Our prediction suggests that 2019-nCoV has close infectivity with other human coronaviruses, especially the severe acute respiratory syndrome coronavirus (SARS-CoV), Bat SARS-like Coronaviruses and the Middle East respiratory syndrome coronavirus (MERS-CoV). Based on our prediction, compared to the Coronaviruses infecting other vertebrates, bat coronaviruses are assigned with more similar infectivity patterns with 2019-nCoVs. Furthermore, by comparing the infectivity patterns of all viruses hosted on vertebrates, we found mink viruses show a closer infectivity pattern to 2019-nCov. These consequences of infectivity pattern analysis illustrate that bat and mink may be two candidate reservoirs of 2019-nCov.These results warn us to beware of 2019-nCoV and guide us to further explore the properties and reservoir of it. One Sentence SummaryIt is of great value to identify whether a newly discovered virus has the risk of infecting human. Guo et al. proposed a virus host prediction method based on deep learning to detect what kind of host a virus can infect with DNA sequence as input. Applied to the Wuhan 2019 Novel Coronavirus, our prediction demonstrated that several vertebrate-infectious coronaviruses have strong potential to infect human. This method will be helpful in future viral analysis and early prevention and control of viral pathogens.

systems biology↗

In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity

Cellular metabolism, a key regulator of immune responses, is difficult to study with current technologies in individual cells Here, we present Compass, an algorithm to characterize the metabolic state of cells based on single-cell RNA-Seq and flux balance analysis. We applied Compass to associate metabolic states with functional variability (pathogenic potential) amongst Th17 cells and recovered a metabolic switch between glycolysis and fatty acid oxidation, akin to known differences between Th17 and Treg cells, as well as novel targets in amino-acid pathways, which we tested through targeted metabolic assays. Compass further predicted a particular glycolytic reaction (phosphoglycerate mutase -- PGAM) that promotes an anti-inflammatory Th17 phenotype, contrary to the common understanding of glycolysis as pro-inflammatory. We demonstrate that PGAM inhibition leads non-pathogenic Th17 cells to adopt a pro-inflammatory transcriptome and induce autoimmunity in vivo. Compass is broadly applicable for characterizing metabolic states of cells and relating metabolic heterogeneity to other cellular phenotypes.

genomics↗

Novel culture method to diagnose fungal infections with biopsy tissues

Biopsy tissue is a difficult sample to gain for the identification of potential pathogen in the clinical laboratory. At present, there are no effective culture methods for small-sized biopsy tissue. In this study, we propose a novel tissue biopsy culture method based on Myco/F lytic liquid culture system, namely, tissue was grinded before injected into culture bottles. More types and numbers of fungi are cultivated using this culture system than sputum or BALF culture. A few of mycobacteria were also detected with ground tissues. The method may be a promising alternative to or supplement for the traditional plate culture in clinical practice.

microbiology↗

Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway

Cellular metabolism can orchestrate immune cell function. We previously demonstrated that lipid biosynthesis represents one such gatekeeper to Th17 cell functional state. Utilizing Compass, a transcriptome-based algorithm for prediction of metabolic flux, we constructed a comprehensive metabolic circuitry for Th17 cell function and identified the polyamine pathway as a candidate metabolic node, the flux of which regulates the inflammatory function of T cells. Testing this prediction, we found that expression and activities of enzymes of the polyamine pathway were enhanced in pathogenic Th17 cells and suppressed in regulatory T cells. Perturbation of the polyamine pathway in Th17 cells suppressed canonical Th17 cell cytokines and promoted the expression of Foxp3, accompanied by dramatic shift in transcriptome and epigenome, transitioning Th17 cells into a Treg-like state. Genetic and chemical perturbation of the polyamine pathway resulted in attenuation of tissue inflammation in an autoimmune disease model of central nervous system, with changes in T cell effector phenotype.

immunology↗

IRESbase: a Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites

Internal Ribosome Entry Sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA, with no 5' cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidences will be useful for further studies. In this study, we present a comprehensive database of IRESs (IRESbase) by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNA information. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses. As our database collected only IRES of minimal length with functional evidences, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and lncRNAs, 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequences. The IRESbase is available at http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php.

bioinformatics↗

Therapy-induced lipid uptake and remodeling underpin ferroptosis hypersensitivity in prostate cancer

BackgroundMetabolic reprograming, non-mutational epigenetic changes, increased cell plasticity and multidrug tolerance are early hallmarks of therapy resistance in cancer. In this temporary, therapy-tolerant state, cancer cells are highly sensitive to ferroptosis, a form of regulated cell death that is caused by oxidative stress through excess levels of iron-dependent peroxidation of polyunsaturated fatty acids (PUFA). However, mechanisms underpinning therapy-induced ferroptosis hypersensitivity remain to be elucidated. MethodsWe used quantitative single cell imaging of fluorescent metabolic probes, transcriptomics, proteomics and lipidomics to perform a longitudinal analysis of the adaptive response to androgen receptor-targeted therapies (androgen deprivation and enzalutamide) in prostate cancer (PCa). ResultsWe discovered that cessation of cell proliferation and a robust reduction in bioenergetic processes were associated with multidrug tolerance and a strong accumulation of lipids. The gain in lipid biomass was fueled by enhanced lipid uptake through cargo non-selective (macropinocytosis, tunneling nanotubes) and cargo-selective mechanisms (lipid transporters), whereas de novo lipid synthesis was strongly reduced. Enzalutamide induced extensive lipid remodeling of all major phospholipid classes at the expense of storage lipids, leading to increased desaturation and acyl chain length of membrane lipids. The rise in membrane PUFA levels enhanced membrane fluidity and lipid peroxidation, causing hypersensitivity to glutathione peroxidase (GPX4) inhibition and ferroptosis. Combination treatments against AR and fatty acid desaturation, lipase activities or growth medium supplementation with antioxidants or PUFAs altered GPX4 dependence. Despite multidrug tolerance, PCa cells displayed an enhanced sensitivity to inhibition of lysosomal processing of exogenous lipids, highlighting an increased dependence on lipid uptake in the therapy-tolerant state. ConclusionsOur work provides mechanistic insight into processes of lipid metabolism that underpin the acquisition of therapy-induced GPX4 dependence and ferroptosis hypersensitivity to standard of care therapies in PCa. It demonstrated novel strategies to suppress the therapy-tolerant state that may have potential to delay and combat resistance to androgen receptor-targeted therapies, a currently unmet clinical challenge of advanced PCa. Since enhanced GPX4 dependence is an adaptive phenotype shared by several types of cancer in response to different therapies, our work might have universal implications for our understanding of metabolic events that underpin resistance to cancer therapies.

cancer biology↗

LocusFocus: A web-based colocalization tool for the annotation and functional follow-up of GWAS

Genome-wide association studies (GWAS) have primarily identified trait-associated loci in the non-coding genome. Colocalization analyses of SNP-level associations from GWAS with expression quantitative trait loci (eQTL) evidence enable the generation of hypotheses about responsible mechanism, genes and tissues of origin to guide functional characterization. Here, we present a web-based colocalization browsing and testing tool named LocusFocus (https://locusfocus.research.sickkids.ca). LocusFocus formally tests colocalization using our established Simple Sum method to identify the most relevant genes and tissues for a particular GWAS locus in the presence of high linkage disequilibrium and/or allelic heterogeneity. Full documentation and source code for LocusFocus are publicly available.

genomics↗