Biology subjects

Zhang, R.

Publications and source records attributed to Zhang, R..

At least 433 records · Page 24Linked to original sources

bioRxiv2022

Keystone species determine the productivity of synthetic microbial biofilm communities

Microbes typically reside in multi-species communities, whose interactions have considerable impacts on the robustness and functionality of such communities. To manage microbial communities, it is essential to understand the factors driving their assemblage and maintenance. Even though the community composition could be easily assessed, interspecies interactions during community establishment remain poorly understood. Here, we combined co-occurrence network analysis with quantitative PCR to examine the importance of each species within synthetic communities (SynComs) of pellicle biofilms. Genome-scale metabolic models and in vitro experiments indicated that the biomass of SynComs was primarily affected by keystone species that are acting either as metabolic facilitators or as competitors. Our study sets an example of how to construct a model SynCom and investigate interspecies interactions.

microbiology↗

bioRxiv2022

Single cell profiling of γδ hepatosplenic T-cell lymphoma unravels tumor cell heterogeneity associated with disease progression

Hepatosplenic T-cell lymphoma (HSTCL), mostly derived from {gamma}{delta} T cells, is a rare but very aggressive lymphoma with poor outcomes. The molecular pathogenesis driving HSTCL is largely unknown while only limited treatment options are available. In this study, by performing paired single cell RNA-seq and T cell receptor (TCR) sequencing on biopsies from a HSTCL patient pre- and post-chemotherapy treatments, we characterized unique gene expressing signatures of malignant {gamma}{delta} T cells, with a set of marker genes were newly identified in HSTCL (AREG, PLEKHA5, VCAM1 etc.). Although the malignant {gamma}{delta} T cells were expanded from a single TCR clonotype according to their TCR identities, they evolved into two transcriptional distinct tumor subtypes during the disease progression. The Tumor_1 subtype was dominant in pre-treatment samples with highly aggressive phenotypes. While the Tumor_2 had relative mild cancer hallmark signatures but expressed genes associated with tumor survival signal and drug resistance (IL32, TOX2, AIF1, AKAP12 etc.), and finally became the main tumor subtype post-treatment. We further dissected the tumor microenvironment of the HSTCL and noticed that CD8 memory T cells were clonal expanded post-treatment. In addition, we discovered dynamically rewiring cell-cell interaction networks during the treatment. The tumor cells had reduced communications with the microenvironment post-treatment. Our study reveals heterogenous and dynamic tumor and microenvironment underlying pathogenesis of HSTCL and may contribute to identify novel targets for diagnosis and cure of HSTCL in the future.

cancer biology↗

bioRxiv2022

Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (the CLiP Mutant Library Background)

The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more sensitive to heat than CC-1690. Furthermore, CC-5325 had an intact cell wall with comparable integrity to that in CC-1690, though appears to have reduced thickness. Finally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC160 did. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.

plant biology↗

bioRxiv2022

Ccdc38 is required for sperm flagellum biogenesis and male fertility in mouse

Sperm flagellum is essential for male fertility, defects in flagellum biogenesis are associated with male infertility. Deficiency of CCDC42 is associated with malformation of the mouse sperm flagella. Here, we find that the testis-specific expressed protein CCDC38 (coiled-coil domain containing 38) interacts with CCDC42 and localizes on manchette and sperm tail during spermiogenesis. Inactivation of CCDC38 in male mice results in distorted manchette, multiple morphological abnormalities of the flagella (MMAF) of spermatozoa, and eventually male sterility. Furthermore, we find that CCDC38 interacts with intra-flagellar transport protein 88 (IFT88) as well as the outer dense fibrous 2 (ODF2), and its depletion reduces the transportation of ODF2 to flagellum. Altogether, our results uncover the essential role of CCDC38 during sperm flagellum biogenesis, and suggesting the defects of these genes might be associated with male infertility in human being. Summary statementWe demonstrated that CCDC38, localizes on manchette and sperm tail, is crucial for male fertility.

developmental biology↗

bioRxiv2022

Novel Methods for Elucidating Modality Importance in Multimodal Electrophysiology Classifiers

Multimodal classification is increasingly common in biomedical informatics studies. Many such studies use deep learning classifiers with raw data, which makes explainability difficult. As such, only a few studies have applied explainability methods, and new methods are needed. In this study, we propose sleep stage classification as a testbed for method development and train a convolutional neural network with electroencephalogram (EEG), electrooculogram, and electromyogram data. We then present a global approach that is uniquely adapted for electrophysiology analysis. We further present two local approaches that can identify subject-level differences in explanations that would be obscured by global methods and that can provide insight into the effects of clinical and demographic variables upon the patterns learned by the classifier. We find that EEG is globally the most important modality for all sleep stages, except non-rapid eye movement stage 1 and that local subject-level differences in importance arise. We further show that sex, followed by medication and age had significant effects upon the patterns learned by the classifier. Our novel methods enhance explainability for the growing field of multimodal classification, provide avenues for the advancement of personalized medicine, and yield novel insights into the effects of demographic and clinical variables upon classifiers.

bioinformatics↗

bioRxiv2021

TACAN is a novel regulator of PKD2

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in membrane receptor PKD1 or cation channel PKD2. TACAN (also named TMEM120A), recently reported as an ion channel in neuron cells for mechano and pain sensing, is also distributed in diverse non-neuronal tissues such as kidney, heart and intestine, suggesting its involvement in other functions. In this study, we found that TACAN is in complex with PKD2 in native renal cell lines. Using the two-electrode voltage clamp in Xenopus oocytes we found that TACAN inhibited the channel activity of PKD2 gain-of-function mutant F604P. The first and last transmembrane domains of TACAN were found to interact with the PKD2 C-and N-terminal portions, respectively. We showed that the TACAN N-terminus acted as a blocking peptide and that TACAN inhibits the PKD2 function through the PKD2/TACAN binding. By patch clamping in mammalian cells, we found that TACAN inhibits both the single channel conductance and open probability of PKD2 and mutant F604P. PKD2 co-expressed with TACAN, but not PKD2 alone, exhibited pressure sensitivity. Furthermore, we also found that TACAN aggravates PKD2-dependent tail curvature and pronephric cysts in larval zebrafish, in support of the in vitro inhibitory effects of TACAN. In summary, this study revealed that TACAN acts as a PKD2 inhibitor and mediates mechano sensitivity of the PKD2/TACAN channel complex.

physiology↗

bioRxiv2021

High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effect

CRISPR-Cas13 systems have recently been employed for targeted RNA degradation in various organisms. However, collateral degradation of bystander RNAs has imposed a major barrier for their in vivo applications. We designed a dual-fluorescent reporter system for detecting collateral effects and screening Cas13 variants in mammalian cells. Among over 200 engineered variants, several Cas13 variants (including Cas13d and Cas13X) exhibit efficient on-target activity but markedly reduced collateral activity. Furthermore, transcriptome-wide off-targets and cell growth arrest induced by Cas13 are absent for these variants. Importantly, high-fidelity Cas13 variants show comparable RNA knockdown activity with wild-type Cas13 but no detectable collateral damage in transgenic mice and adeno-associated virus-mediated somatic cell targeting. Thus, high-fidelity Cas13 variants with minimal collateral effect are now available for targeted degradation of RNAs in basic research and therapeutic applications.

molecular biology↗

bioRxiv2021

Evolution of Enterococcus faecium to A Combination of Daptomycin and Fosfomycin Reveals Distinct and Diverse Adaptive Strategies

Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) are an important public health threat. VREfm have become increasingly resistant to the front-line antibiotic, daptomycin (DAP). As such, the use of DAP combination therapies (like fosfomycin [FOS]), has received increased attention. Antibiotic combinations could extend the efficacy of current available antibiotics and potentially delay the onset of further resistance. We investigated the potential for E. faecium HOU503, a clinical VREfm isolate that is DAP and FOS susceptible, to develop resistance to a DAP-FOS combination. Of particular interest was whether the genetic drivers for DAP-FOS resistance might be epistatic and, thus, potentially decrease the efficacy of a combinatorial approach in either inhibiting VREfm or in delaying the onset of resistance. We show that resistance to DAP-FOS could be achieved by independent mutations to proteins responsible for cell wall synthesis for FOS and in altering membrane dynamics for DAP. However, we did not observe genetic drivers that exhibited substantial cross-drug epistasis that could undermine DAP-FOS combination. Of interest was that FOS resistance in HOU503 was largely mediated by changes in phosphoenolpyruvate (PEP) flux as a result of mutations in pyruvate kinase (pyk). Increasing PEP flux could be a readily accessible mechanism for FOS resistance in many pathogens. Importantly, we show that HOU503 were able to develop DAP resistance through a variety of biochemical mechanisms and were able to employ different adaptive strategies. Finally, we showed that the addition of FOS can prolong the efficacy of DAP, significantly extending the timeline to resistance in vitro. ImportanceWhile the discovery of antibiotics was one of the greatest health care advances in history, its success is being challenged by the emergence of multidrug-resistant pathogens, including vancomycin-resistant enterococci (VRE). Daptomycin (DAP), a lipopeptide antibiotic that targets cell membrane, is currently prescribed as a frontline drug to treat VRE infections. However, emergence of daptomycin-resistant VRE is concerning. Consequently, DAP-Fosfomycin (FOS) combination (DF) has been proposed as a potential method to maintain DAP efficacy. Here, we provide evidence that DF successfully delayed the emergence of resistance in vitro. Genetic data indicates that resistance was acquired independently, with little evidence of significant cross-drug epistasis that could undermine a combinatorial approach. We also uncovered a novel FOS resistance mechanism, through changes in phosphoenolpyruvate (PEP) flux, that may potentially be shared with other bacterial species. Additionally, we also have evidence showing that E. faecium was able to employ different resistance mechanisms.

evolutionary biology↗

bioRxiv2021

Reduced sera neutralization to Omicron SARS-CoV-2 by bothinactivated and protein subunit vaccines and the convalescents

Omicron variant continues to spread all over the world. There are lots of scientific questions remaining to be answered for such a devastating variant. There are a dozen of vaccines already in clinical use. The very urgent scientific question would be whether or not these vaccines can protect Omicron variant. Here, we tested the sera from both convalescents and vaccine recipients receiving either inactivated or protein subunits vaccines (CoronaVac from Sinovac, or BBIBP-CoV from Sinopharm, or ZF2001 from Zhifei longcom) for the binding antibody titers (ELISA) and neutralization antibodies titers (pseudovirus neutralization assay). We showed that Omicron do have severe immune escape in convalescents, with 15 of 16 were negative in neutralization. By contrast, in vaccinees who received three jabs of inactivated or protein subunit vaccine, the neutralizing activity was much better preserved. Especially in the ZF2001 group with an extended period of the second and third jab (4-6 months) remains 100% positive in Omicron neutralization, with only 3.1-folds reduction in neutralizing antibody (NAb) titer. In this case, we proposed that, the multi-boost strategy with an extended interval between the second and third jab for immune maturation would be beneficial for NAb against devastating variants such as Omicron.

immunology↗

bioRxiv2021

Semi-supervised single-cell cross-modality translation using Polarbear

The emergence of single-cell co-assays enables us to learn to translate between single-cell modalities, potentially offering valuable insights from datasets where only one modality is available. However, the sparsity of single-cell measurements and the limited number of cells measured in typical co-assay datasets impedes the power of cross-modality translation. Here, we propose Polarbear, a semi-supervised translation framework to predict cross-modality profiles that is trained using a combination of co-assay data and traditional "single-assay" data. Polarbear uses single-assay and co-assay data to train an autoencoder for each modality and then uses just the co-assay data to train a translator between the embedded representations learned by the autoencoders. With this approach, Polarbear is able to translate between modalities with improved accuracy relative to state-of-the-art translation techniques. As an added benefit of the training procedure, we show that Polarbear also produces a matching of cells across modalities.

bioinformatics↗

bioRxiv2021

Fast anther dehiscence state recognition system establishing by deep learning to screen heat tolerant cotton

Cotton is one of the most economically important crops in the world. The fertility of male reproductive organs is a key determinant of cotton yield. The anther dehiscence or indehiscence directly determine the probability of fertilization in cotton. Thus, the rapid and accurate identification of cotton anther dehiscence status is important for judging anther growth status and promoting genetic breeding research. The development of computer vision technology and the advent of big data have prompted the application of deep learning techniques to agricultural phenotype research. Therefore, two deep learning models (Faster R-CNN and YOLOv5) were proposed to detect the number and dehiscence status of anthers. The single-stage model based on YOLOv5 has higher recognition efficiency and the ability to deploy to the mobile end. Breeding researchers can apply this model to terminals to achieve a more intuitive understanding of cotton anther dehiscence status. Moreover, three improvement strategies of Faster R-CNN model were proposed, the improved model has higher detection accuracy than YOLOv5 model. In addition, the percentage of dehiscent anther of randomly selected 30 cotton varieties were observed from cotton population under normal temperature and high temperature (HT) conditions through the integrated Faster R-CNN model and manual observation. The result showed HT varying decreased the percentage of dehiscent anther in different cotton lines, consistent with the manual method. Thus, this system can help us to rapid and accurate identification of HT-tolerant cotton. One sentence summaryThe deep learning technique was applied to identify the anther dehiscence state for the first time to quickly screen heat tolerant cotton varieties and help to explore key genetic improvement genes.

bioengineering↗

bioRxiv2021

Fast and sensitive GCaMP calcium indicators for imaging neural populations

Calcium imaging with protein-based indicators is widely used to follow neural activity in intact nervous systems. The popular GCaMP indicators are based on the calcium-binding protein calmodulin and the RS20 peptide. These sensors report neural activity at timescales much slower than electrical signaling, limited by their biophysical properties and trade-offs between sensitivity and speed. We used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators. The resulting jGCaMP8 sensors, based on calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (rise times, 2 ms) and still feature the highest sensitivity for neural activity reported for any protein-based sensor. jGCaMP8 sensors will allow tracking of larger populations of neurons on timescales relevant to neural computation.

neuroscience↗

bioRxiv2021

Diversity, function and evolution of aquatic vertebrate genomes

Aquatic vertebrates consist of jawed fish (cartilaginous fish and bony fish), aquatic mammals, reptiles and amphibians. Here, we present a comprehensive analysis of 630 aquatic vertebrate genomes to generate a standardized compendium of genomic data. We demonstrate its value by assessing their genome features as well as illuminating gene families related to the transition from water to land, such as Hox genes and olfactory receptor genes. We found that LINEs are the major transposable element (TE) type in cartilaginous fish and aquatic mammals, while DNA transposons are the dominate type in bony fish. To our surprise, TE types are not fixed in amphibians, the first group that transitioned to living on land. These results illustrate the value of a unified resource for comparative genomic analyses of aquatic vertebrates. Our data and strategy are likely to support all evolutionary and ecological research on vertebrates.

genomics↗

bioRxiv2021

Quorum sensing signal autoinducer-2 inhibits sporulation of Bacillus by interacting with RapC and functions across species

Collective behavior of bacteria is regulated by quorum sensing (QS). Bacterial cells sense the density of the population and induce corresponding traits and developmental processes. Autoinducer-2 (AI-2) is a common QS signal that regulates behavior of both Gram-positive and Gram-negative bacteria. In spite of the plethora of processes described to be influenced by AI-2 in diverse Gram-negative bacteria, the AI-2-regulated processes in Bacilli are relatively unexplored. Previously, we demonstrated that AI-2 regulates root colonization of Bacillus velezensis SQR9, a well-studied plant beneficial rhizobacterium. Here, we describe a novel function for AI-2 in B. velezensis SQR9 related to development of dormant spores. AI-2 inhibited the initiation of spore development throught the phosphatase RapC and the DNA binding regulator ComA. Using mutant strains and protein-protein interaction studies, we demonstrate that AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA. We further demonstrate that ComA is essential for Spo0A-regulated sporulation in B. velezensis SQR9. Finally, the AI-2 molecule could be shared cross species for inhibiting Bacillus sporulation. Our study revealed a novel function and regulation mechanism of AI-2 in sporulation inhibition of Bacilli that overall suggests sporulation to be a population-level decision process in Bacilli rather than just a individual cell behavior. Author summaryQuorum sensing (QS) regulates many bacterial social behavior. Bacteria cells could moniter and respond cell density by sensing the self produced QS signals. While most QS signals are unique for either Gram-positive or Gram-negative bacteria, autoinducer-2 (AI-2) is a QS signal that could produced by both bacteria groups. However, knowledge of the mechanism of AI-2 affecting bacterial behavior is poorly understood. Here, we found AI-2 inhibite Bacillus velezensis SQR9 sporulation, a generally known bacterial individual behavior. We further revealed the mechanism of AI-2 influencing sporulation of B. velezensis SQR9 was dependent on RapC and ComA. AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA, and then inhibited the Spo0A-regulated sporulation. Interestingly, we show B. velezensis SQR9 could also sense the AI-2 produced by other bacteria and reduce their own sporulation. Taken together we discovered the novel function of AI-2 in sporulation, which will expand the significance of QS signal that they regulate not only social behavior but also individual behavior of bacteria.

microbiology↗

bioRxiv2021

Double-edged role of resource competition in gene expression noise and control

Despite extensive investigation demonstrating that resource competition can significantly alter the circuits deterministic behaviors, a fundamental issue is how resource competition contributes to the gene expression noise and how the noise can be controlled. Utilizing a two-gene circuit as a prototypical system, we uncover a surprising double-edged role of resource competition in gene expression noise: the competition decreases noise through a resource constraint but generates its own type of noise which we name as "resource competitive noise." Utilization of orthogonal resources enables retaining the noise reduction conferred by resource constraint while removing the added resource competitive noise. The noise reduction effects are studied using three negative feedback controller types: negatively competitive regulation (NCR), local, and global controllers, each having four placement architectures in the protein biosynthesis pathway (mRNA or protein inhibition on transcription or translation). Our results show that both local and NCR controllers with mRNA-mediated inhibition are efficacious at reducing noise, with NCR controllers demonstrating a superior noise-reduction capability. We also find that combining negative feedback controllers with orthogonal resources can improve the local controllers. This work provides deep insights into the origin of stochasticity in gene circuits with resource competition and guidance for developing effective noise control strategies.

synthetic biology↗

bioRxiv2021

Direct precise measurement of the stall torque of the flagellar motor in E. coli

The flagellar motor drives the rotation of flagellar filaments, propeling the swimming of flagellated bacteria. The maximum torque the motor generates, the stall torque, is a key characteristics of the motor function. Direct measurements of the stall torque carried out three decades ago suffered from large experimental uncertainties, and subsequently there were only indirect measurements. Here, we applied magnetic tweezer to directly measure the stall torque in E. coli. We precisely calibrated the torsional stiffness of the magnetic tweezer, and performed motor resurrection experiments at stall, accomplishing a precise determination of the stall torque per torque-generating unit (stator unit). From our measurements, each stator passes 2 protons per step, indicating a tight coupling between motor rotation and proton flux.

biophysics↗

bioRxiv2021

The mitochondrial deubiquitinase USP30 regulates AKT/mTOR signaling

Mitophagy is an intracellular mechanism to maintain mitochondrial health by removing dysfunctional mitochondria. The E3 ligase Parkin ubiquitinates the membrane proteins on targeted mitochondria to initiate mitophagy, and USP30 antagonizes this Parkin-dependent mitophagy. AKT/mTOR signaling is a master regulator of cell proliferation, differentiation, survival, and growth. Although mounting evidence showed mitophagy and AKT/mTOR signaling interact with each other during mitophagy, the specific mechanisms between Parkin/USP30 and AKT/mTOR signaling have not been elucidated. This research artificially expressed Parkin and USP30 in Hela cells and compared AKT/mTOR and apoptosis signals between Hela cells, HeLa Parkin cells, and Hela Parkin USP30 cells during mitophagy. The studys results suggest that Parkin promotes AKT degradation via ubiquitination, which induces cell apoptosis during mitochondrial stress. On the contrary, USP30 protects AKT via deubiquitination. These findings provide new insights into Parkin and USP30s role in cell apoptosis and physiological and pathological functions of USP30 beyond mitophagy.

pharmacology and toxicology↗

bioRxiv2021

Bicolor angelfish (Centropyge bicolor) provides the first chromosome-level genome of the Pomacanthidae family

The Bicolor Angelfish, Centropyge bicolor, is a tropical coral reef fish. It is named for its striking two-color body. However, a lack of high-quality genomic data means little is known about the genome of this species. Here, we present a chromosome-level C. bicolor genome constructed using Hi-C data. The assembled genome is 650 Mbp in size, with a scaffold N50 value of 4.4 Mbp, and a contig N50 value of 114 Kbp. Protein-coding genes numbering 21,774 were annotated. Our analysis will help others to choose the most appropriate de novo genome sequencing strategy based on resources and target applications. To the best of our knowledge, this is the first chromosome-level genome for the Pomacanthidae family, which might contribute to further studies exploring coral reef fish evolution, diversity and conservation.

genomics↗