Biology subjects

Fang, C.

Publications and source records attributed to Fang, C..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model

Deciphering the universal gene regulatory mechanisms in diverse organisms holds great potential to advance our knowledge of fundamental life process and facilitate research on clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms, resulting in limited collection and integration of complex features on various cell types across species. Recent breakthroughs in single-cell sequencing and advancements in deep learning techniques present an unprecedented opportunity to tackle this challenge. In this study, we developed GeneCompass, the first knowledge-informed, cross-species foundation model pre-trained on an extensive dataset of over 120 million single-cell transcriptomes from human and mouse. During pre-training, GeneCompass effectively integrates four types of biological prior knowledge to enhance the understanding of gene regulatory mechanisms in a self-supervised manner. Fine-tuning towards multiple downstream tasks, GeneCompass outperforms competing state-of-the-art models in multiple tasks on single species and unlocks new realms of cross-species biological investigation. Overall, GeneCompass marks a milestone in advancing knowledge of universal gene regulatory mechanisms and accelerating the discovery of key cell fate regulators and candidate targets for drug development.

bioinformatics↗

bioRxiv2023

SoyDNGP: A Web-Accessible Deep Learning Framework for Genomic Prediction in Soybean Breeding

Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. Addressing this biological complexity requires innovative and accurate tools for trait prediction. In response to this challenge, we have developed SoyDNGP, a Convolutional Neural Networks (CNN)-based model that offers significant advancements in the field of soybean trait prediction. Compared to existing methods, such as DeepGS and DNNGP, SoyDNGP boasts a distinct advantage due to its lower parameter volume and superior predictive accuracy. Through rigorous performance comparison, including prediction accuracy and model complexity, SoyDNGP consistently outperformed its counterparts. Furthermore, it effectively predicted complex traits with remarkable precision, demonstrating robust performance across different sample sizes and trait complexities. We also tested the versatility of SoyDNGP across multiple crop species, including Cotton, Maize, Rice, and Tomato. Our results showed its consistent and comparable performance, emphasizing SoyDNGPs potential as a versatile tool for genomic prediction across a broad range of crops. To enhance its accessibility to users without extensive programming experience, we have designed a user-friendly web server, available at http://xtlab.hzau.edu.cn/SoyDNGP. The server provides two primary features: Trait Lookup, offering users the ability to access pre-existing trait predictions for over 500 soybean accessions, and Trait Prediction, allowing for the upload of VCF files for trait estimation. By providing a high-performing, accessible tool for trait prediction and genomic analysis, SoyDNGP opens up new possibilities in the quest for efficient and optimized soybean breeding.

plant biology↗

bioRxiv2023

High-resolution structure of mouse radial spoke and its in-situ structure in ependymal cilia revealed by cryo-EM and cryo-ET

Radial spokes (RS) transmit mechanochemical signals between the central pair (CP) and axonemal dynein arms to coordinate ciliary motility. However, the high-resolution structure of mammalian RS remains missing. Here, we present the high-resolution cryo-EM structure of mouse RS head-neck complex in both monomer and dimer forms and reveal the intrinsic dynamics of the dimer. We also map the genetic mutations related to primary ciliary dyskinesia and asthenospermia on the head-neck complex. Moreover, we present the unprecedented cryo-ET and sub-tomogram averaging map of mouse ependymal cilia, whose beating creates unidirectional cerebrospinal fluid flow, and build the models for RS1-3, IDAs, and N-DRC. Strikingly, our cryo-ET map reveals the lack of IDA-b/c/e and the absence of tektin filaments within the A-tubule of doublet microtubules in ependymal cilia compared with mammalian respiratory cilia and sperm flagella. This tissue-specific feature may represent an evolutionary choice driven by the functional requirements on ependymal cilia. Our findings reveal the RS head-neck assembly mechanism, shed light on the coordinated rigid and elastic RS-CP interaction modes beneficial for the regulation of asymmetric ciliary beating, and also facilitate understandings on the etiology of ciliary dyskinesia-related ciliopathies.

biophysics↗

bioRxiv2023

Deciphering the rule of antigen-antibody amino acid interaction

Antigenic drift is the biggest challenge for mutagenic RNA virus vaccine development. The most fundamental but neglected thing is to determine the immune escape mutation map (IEMM) of 20 amino acids to reveal the rule of the viral immune escape. We use universal protein tags as a linear epitope model to determine the relationship between the epitope mutation and immune escape. To describe and draw amino acid interaction maps, mutations of protein tags are classified into four types: IEM (immune escape mutation), ADERM (antibody-dependent enhancement risk mutation), EQM (equivalent mutation), and IVM (invalid mutation). To make up for the data limitation, the amino acid interaction pairs determined by 3D structure through literature search are simultaneously used to form a more systematic and universal antigen-antibody interaction maps. The results are: (i) one residue interacts with multiple amino acids in antigen-antibody interaction; (ii) Most amino acid replacements are IVM and EQM. (iii) Once aromatic amino acids replace non-aromatic amino acids, the mutation is often inactive. (iv) Substituting residues with the same physical and chemical properties easily lead to IEM. Therefore, this study had important theoretical significance for future research on antigenic drift, antibody rescue and vaccine renewal design. ImportanceWe typed the antigenic epitope mutations into IEM, ADERM, EQM, and IVM types to describe and quantify the results of antigenic mutations. According to the results, the antigen-antibody interaction rule was summarized as one-to-many interaction rule. To sum up, the Epitope mutation rules were defined as IVM and EQM predomination rule, aryl mutation escape rule and homogeneous mutation escape rule.

immunology↗

bioRxiv2023

TERT accelerates BRAF mutant-induced thyroid cancer dedifferentiation and progression by regulating ribosome biogenesis

TERT reactivation occurs frequently in human malignancies. While BRAF activating mutation widely existed in cancers at various stages, TERT reactivation mainly occurs in advanced tumors. However, in vivo evidence for TERT role in cancer progression and the underlying mechanism is currently lacking. In this study, we induced TERT and/or BRAF V600E expression in mouse thyroid epithelium. TERT overexpression alone had no evident effect on tumor initiation. BRAFVE expression itself induced mediocre papillary thyroid cancer (PTC). Notably, the co-expression of BRAFVE and TERT resulted in aggressive poorly differentiated thyroid carcinoma (PDTC). Spatial transcriptome revealed that tumors from co-mutant mice were highly heterogeneous and dedifferentiation process significantly correlated with ribosomal pathways. Mechanistically, TERT boosted ribosomal RNA expression and protein synthesis. CX-5461, a rRNA transcription inhibitor, effectively blocked proliferation and induced redifferentiation. Thus, TERT promotes thyroid cancer progression by inducing dedifferentiation, and ribosome biogenesis inhibition represents a potential treatment strategy for TERT-reactivated cancers. Highlights[tpltrtarr] TERT accelerated thyroid cancer dedifferentiation and metastasis in vivo [tpltrtarr]TERT regulated rRNA metabolism and MTORC1/ S6K/RPS6 activities [tpltrtarr]CX-5461 inhibited the progression of TERT-reactivated melanoma and thyroid cancer [tpltrtarr]Inhibition of rRNA induced redifferentiation of advanced thyroid cancer with TERT activation

cancer biology↗

bioRxiv2022

Central extended amygdala neurons in the development of activity-based anorexia

Anorexia nervosa (AN) is a serious psychiatric disease characterized by restricted eating, fear of gaining weight, as well as excessive exercise, and also is often comorbid with emotional disorders such as anxiety and depression. However, the etiology of AN is unknown and the neural mechanism that leads to AN remains to be determined. Here, we show that a specific subpopulation of neurons, marked by the expression of protein kinase C-delta (PKC-{delta}), in two nuclei of the central extended amygdala (EAc)-- central nucleus (CeA) and oval region of bed nucleus of stria terminalis (ovBNST)--regulates development of activity-based anorexia (ABA), the current best animal model of AN. Specifically, simultaneous dual ablation of CeAPKC-{delta} and ovBNSTPKC-{delta} neurons prevents the key phenotypes of ABA: increases in wheel activity, decreases in food intake, and life-threatening body weight loss. However, ablating PKC-{delta} neurons in CeA or ovBNST alone is not sufficient to prevent ABA. Correspondingly, activation of PKC-{delta} neurons in one type of nuclei continues to suppress food intake even when PKC-{delta} neurons in the other nuclei are silenced. Consistent with their role in suppressing food intake when activated, these PKC-{delta} neurons show increased activity with ABA development. Together, our study illuminates how neurons in the amygdala regulate ABA development and supports the complex and heterogenous etiology of AN.

neuroscience↗

bioRxiv2022

Why is Babesia not killed by artemisinin like Plasmodium?

Babesia spp. are intraerythrocytic apicomplexan organisms digesting hemoglobin similar to intraerythrocytic Plasmodium spp. However, unlike Plasmodium spp., Babesia spp. are not sensitive to artemisinin, The difference between Babesia genomes and Plasmodium genomes revealed that smaller Babesia genomes lack numerous genes, especially haem synthesis-related genes. Single-cell sequencing analysis showed that different groups of B. microti with expressed pentose phosphate pathway (PPP)-related, DNA replication-related, antioxidation-related, glycolysis-related, and glutathione-related genes were not as sensitive to artemether as P. yoelii 17XNL. Especially, PPP-related, DNA replication-related, and glutathione-related genes were inactively expressed compared with P. yoelii 17XNL. Adding iron supply in vivo can promote the reproduction of B. microti. These results suggest that Babesia spp. lack a similar mechanism to that in malaria parasites, by which haem or iron in hemoglobin is utilized, but it likely leads to their insensitivity to artemisinin in turn. Author summaryBabesia and Plasmodium are similar in many ways, from morphology to life history. In particular, both ingest and break down hemoglobin. However, compared with Plasmodium, Babesia cannot form hemozoin with less pathogenicity and insensitivity to artemisinin. Recent studies suggest that artemisinin can kill malaria parasites through free-radical and iron-capture effects, indicating that iron and haem play a key role in the sensitivity of malaria parasites to artemisinin. The Babesia genome is smaller and does not contain haem synthesis-related genes, indicating low requirements and utilization of haem and iron (HI). Moreover, we found that the expression of PPP-related and DNA replication-related genes is not active, distinctly different from malaria parasites. However, adding iron supply in vivo can increase the infection rate of B. microti. Therefore, we hypothesized that Babesia lacks mechanisms for the efficient utilization of HI, resulting in low requirements for HI, and therefore insensitivity to artemisinin.

evolutionary biology↗

bioRxiv2022

Systematic comparison and rational design of theophylline riboswitches for efficient gene repression

Riboswitches are promising regulatory tools in synthetic biology. To date, 25 theophylline riboswitches have been developed for gene expression regulation in bacteria. However, no one has systematically evaluated their regulatory effects. To facilitate rational selection of theophylline riboswitches, we examined 25 theophylline riboswitches in Escherichia coli and surprised to find that none of the five repressive riboswitches were more than 2-fold effective. To solve this problem, we rationally designed a transcriptional repressive riboswitch and demonstrated its effect not only in various bacterial strains but also in different growth media or different temperatures. By introducing two copies of theophylline riboswitches and a RepA protein degradation tag coding sequence at the 5-end of a reporter gene, we successfully constructed a dual gene expression regulatory system with up to 150-fold potency, namely the R2-RepA system. R2-RepA system is only 218 bp in length, expression of any protein could be repressed efficiently by simply inserting this system upstream of the target protein-coding sequence. This study represented a crucial step toward harnessing theophylline riboswitches and expanding the synthetic biology toolbox.

synthetic biology↗

bioRxiv2022

Neural learning rules for generating flexible predictions and computing the successor representation

The predictive nature of the hippocampus is thought to be useful for memory-guided cognitive behaviors. Inspired by the reinforcement learning literature, this notion has been formalized as a predictive map called the successor representation (SR). The SR captures a number of observations about hippocampal activity. However, the algorithm does not provide a neural mechanism for how such representations arise. Here, we show the dynamics of a recurrent neural network naturally calculate the SR when the synaptic weights match the transition probability matrix. Interestingly, the predictive horizon can be flexibly modulated simply by changing the network gain. We derive simple, biologically plausible learning rules to learn the SR in a recurrent network. We test our model with realistic inputs and match hippocampal data recorded during random foraging. Taken together, our results suggest that the SR is more accessible in neural circuits than previously thought and can support a broad range of cognitive functions.

neuroscience↗

bioRxiv2022

Multiple omic investigations of freeze tolerance adaptation in the aquatic ectothermic vertebrate, the Amur sleeper

Freeze tolerance is an amazing overwintering strategy that enables ectotherms to occupy new niches and survive in cold climates. However, the genetic basis underpinning this ecologically relevant adaptation is largely unknown. Amur sleeper is the only known freeze-tolerant fish species that can overwinter with its entire body frozen in ice. Here, we sequenced the chromosome-level genome of the Amur sleeper and performed comparative genomic, transcriptomic, and metabolomic analyses to investigate this remarkable adaptation. Phylogenetic analyses showed that the Amur sleeper diverged from its close relative with no cold hardiness about 15.07 million years ago and revealed two unusual population expansions during the glacial epochs. Integrative omics data identified a synchronous regulation of genes and metabolites involved in hypometabolism and cellular stress response, and several related genes showed strong evidence of accelerated evolution and positive selection. Potential evolutionary innovations that might aid in freezing survival were found to be associated with the dynamic rearrangement of the cytoskeleton to maintain cell viability, redistribution of water and cryoprotectants to limit cell volume reduction, and inhibition in nerve activity to facilitate dormancy, demonstrating a coordinated evolution for this complex adaptation. Overall, our work provides valuable resources and opportunities to unveil the genetic basis of freeze tolerance adaptation in ectothermic vertebrates.

evolutionary biology↗

bioRxiv2022

Semi-automated protocol to quantify and characterize fluorescent, 3D vascular images

The microvasculature facilitates gas exchange, provides nutrients to cells, and regulates blood flow in response to stimuli. Vascular abnormalities are an indicator of pathology for various conditions, such as compromised vessel integrity in small vessel disease and angiogenesis in tumors. Traditional immunohistochemistry enables visualization of tissue cross-sections containing exogenously labeled vasculature. Although this approach can be utilized to quantify vascular changes within small fields-of-view, it is not a practical way to study the vasculature on the scale of whole organs. Three-dimensional (3D) imaging presents a more appropriate method to visualize the vascular architecture in tissue. Here we describe the complete protocol that we use to characterize the vasculature of different organs in mice encompassing the methods to fluorescently label vessels, optically clear tissue, collect 3D vascular images, and quantify these vascular images with a semi-automated approach. To validate the automated segmentation of vascular images, one user manually segmented fifty random regions of interest across different vascular images. The automated segmentation results had an average sensitivity of 80{+/-}8% and an average specificity of 90{+/-}5% when compared to manual segmentation. Applying this procedure of image analysis presents a method to reliably quantify and characterize vascular networks in a timely fashion. This procedure is also applicable to other methods of tissue clearing and vascular labels that generate 3D images of microvasculature.

bioengineering↗

bioRxiv2021

Diverse operant control of different motor cortex populations during learning

During motor learning, as well as during neuroprosthetic learning, animals learn to control motor cortex activity in order to generate behavior. Two different population of motor cortex neurons, intra-telencephalic (IT) and pyramidal tract (PT) neurons, convey the resulting cortical signals within and outside the telencephalon. Although a large amount of evidence demonstrates contrasting functional organization among both populations, it is unclear whether the brain can equally learn to control the activity of either class of motor cortex neurons. To answer this question, we used a Calcium imaging based brain-machine interface (CaBMI) and trained different groups of mice to modulate the activity of either IT or PT neurons in order to receive a reward. We found that animals learn to control PT neuron activity faster and better than IT neuron activity. Moreover, our findings show that the advantage of PT neurons is the result of characteristics inherent to this population as well as their local circuitry and cortical depth location. Taken together, our results suggest that motor cortex is optimized to control the activity of pyramidal track neurons, embedded deep in cortex, and relaying motor commands outside of the telencephalon.

neuroscience↗

bioRxiv2021

The Hox gene Antennapedia regulates wing development through 20-hydroxyecdysone in insect

A long-standing view in the field of evo-devo is that insect forewings develop without any Hox gene input. The Hox gene Antennapedia (Antp), despite being expressed in the thoracic segments of insects, has no effect on wing development. This view has been obtained from studies in two main model species, Drosophila and Tribolium. Here, we show that partial loss of function of Antp resulted in reduced and malformed adult wings in Bombyx, Drosophila, and Tribolium. Antp mediates wing growth in Bombyx by directly regulating the ecdysteriod biosynthesis enzyme gene (shade) in the wing tissue, which leads to local production of the growth hormone 20E. In turn, 20E signaling also up-regulates Antp. Additional targets of Antp are wing cuticular protein genes CPG24, CPH28, and CPG9, essential for wing development. We propose, thus, that insect wing development occurs in an Antp-dependent manner.

developmental biology↗

bioRxiv2021

High-resolution single-molecule long-fragment rRNA gene amplicon sequencing for uncultured bacterial and fungal communities

Although several large-scale environmental microbial projects have been initiated in the past two decades, understanding of the role of complex microbiotas is still constrained by problems of detecting and identifying unknown microorganisms1-6.Currently, hypervariable regions of rRNA genes as well as internal transcribed spacer regions are broadly used to identify bacteria and fungi within complex communities7,8, but taxonomic and phylogenetic resolution is hampered by insufficient sequencing length9-11. Direct sequencing of full length rRNA genes is currently limited by read length using second generation sequencing or sacrificed quality and throughput by using single molecule sequencing. We developed a novel method to sequence and assemble nearly full length rRNA genes using second generation sequencing.Benchmarking was performed on mock bacterial and fungal communities as well as two forest soil samples. The majority of rRNA gene sequences of all species in the mock community samples were successfully recovered with identities above 99.5% compared to the reference sequences. For soil samples we obtained exquisite coverage with identification of a large number of putative new species, as well as high abundance correlation between replicates. This approach provides a cost-effective method for obtaining extensive and accurate information on complex environmental microbial communities.

microbiology↗

bioRxiv2021

A recombinant selective drug-resistant M. bovis BCG enhances the bactericidal activity of a second-line tuberculosis regimen

Drug-resistant tuberculosis (DR-TB) results from infection by Mycobacterium tuberculosis strains resistant to at least rifampin or isoniazid. To improve the treatment outcome in DR-TB, therapeutic vaccines are considered an ideal choice as they can enhance pathogen clearance and minimize disease sequelae. To date, there is no therapeutic vaccine reported to be effective when combined with a chemotherapy regimen against DR-TB. The only available TB vaccine, the M. bovis BCG (BCG) is susceptible to several anti-TB drugs hence not a perfect option for therapeutic vaccination. Herein, we developed a recombinant BCG (RdrBCG) overexpressing Ag85B and Rv2628 with resistance to selected anti-TB drugs. When administered three times adjunct to a second-line anti-TB regimen in a classical murine model of DR-TB, the RdrBCG lowered lung M. tuberculosis colony-forming units by 1 log10. Furthermore, vaccination with the RdrBCG adjunct to TB chemotherapy minimized lung tissue pathology in mice. Most importantly, the RdrBCG maintained the exogenously inserted genes and showed almost the same virulence as its parent BCG Tice strain in severe combined immune-deficient mice. All these suggested that the RdrBCG was stable, safe and effective. Hence, the "recombinant" plus "drug-resistant" BCG strategy could be a useful concept for developing therapeutic vaccines against DR-TB.

microbiology↗

bioRxiv2021

SARS-CoV-2 RBD-Tetanus toxoid conjugate vaccine induces a strong neutralizing immunity in preclinical studies

Controlling the global COVID-19 pandemic depends, among other measures, on developing preventive vaccines at an unprecedented pace. Vaccines approved for use and those in development intend to use neutralizing antibodies to block viral sites binding to the hosts cellular receptors. Virus infection is mediated by the spike glycoprotein trimer on the virion surface via its receptor binding domain (RBD). Antibody response to this domain is an important outcome of the immunization and correlates well with viral neutralization. Here we show that macromolecular constructs with recombinant RBD conjugated to tetanus toxoid induce a potent immune response in laboratory animals. Some advantages of the immunization with the viral antigen coupled to tetanus toxoid have become evident such as predominant IgG immune response due to affinity maturation and long-term specific B-memory cells. This paper demonstrates that subunit conjugate vaccines can be an alternative for COVID-19, paving the way for other viral conjugate vaccines based on the use of small viral proteins involved in the infection process.

immunology↗

bioRxiv2020

Deciphering the mystery of influenza virus A antigenic drift and immune escape

The biggest challenge of influenza A virus vaccine development is the constant mutation of the virus, especially the antigenic drift. Therefore, we suggest establishing a research system for upgrading of current influenza A vaccines. The most fundamental but neglected thing is to determine the immune escape mutation (IEM) map (IEMM) of 20 amino acids in linear epitope to reveal the precise mechanism of the viral immune escape. Based on this assumption, we primarily divided IEM of HA-tag linear epitope into four types according to antibody affinity by ELISA. Our aim is to attract scholars to establish of IEMM library to deal with influenza A virus mutations in the future.

immunology↗

bioRxiv2020

Hybrid capture-based sequencing enables unbiased recovery of SAR-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants

BackgroundIn response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples. MethodsEighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization. ResultsBy examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period. ConclusionsThe hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.

genomics↗