Biology subjects

Tong, C.

Publications and source records attributed to Tong, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Binary Ethyleneimine inactivated- Encephalomyocarditis virus as an experimental vaccine candidate showed strong neutralization responses.

A novel Encephalomyocarditis virus (EMCV) of the group 3 cluster (EMCV-3) was first reported in 2002 to be responsible for the deaths of orang-utans in an outbreak in the Singapore Zoo. After this first outbreak, sporadic infections among the primate population caused by EMCV-3 continued to be reported, suggesting that the virus remains prevalent in Singapore. To prevent future infections, we constructed an experimental vaccine using binary ethylenimine (BE) to inactivate the EMCV-3 virus. The immunological performance of the BE-inactivated (BEI) virus was analysed in mice and the neutralising titre of the immune sera measured against the wild-type EMCV-3. The BEI virus showed a strong immunological response in BALB/c mice at 1: 40,960 titre, suggesting that it can be used as a promising experimental vaccine candidate to prevent EMCV-3 infections.

microbiology↗

bioRxiv2023

Cell-type specific optogenetic fMRI on basal forebrain reveals functional network basis of behavioral preference

The basal forebrain (BF) is a complex structure that plays key roles in regulating various brain functions. However, it remains unclear how cholinergic and non-cholinergic BF neurons modulate large-scale functional networks and their relevance in intrinsic and extrinsic behaviors. With optimized awake mouse optogenetic fMRI approach, we revealed optogenetic stimulations of four BF neuron types evoked distinct cell-type specific whole-brain BOLD activations, which could attribute to BF-originated low dimensional structural networks. Additionally, optogenetic activation of VGLUT2, ChAT and PV neurons in BF modulated the preference of locomotion, exploration and grooming, respectively. Furthermore, we uncovered the functional network basis of the above BF-modulated behavioral preference, through a decoding model linking the BF-modulated BOLD activations, low dimensional structural networks, and behavioral preference. To summarize, we decoded functional network basis of differential behavioral preference with cell-type specific optogenetic fMRI on BF, and provided an avenue for investigating mouse behaviors from a whole-brain view.

neuroscience↗

bioRxiv2023

Insulin determines the effects of TGF-beta on HNF4alpha transcription and epithelial-to-mesenchymal transition in hepatocytes

To date, epithelial-to-mesenchymal transition (EMT) has been observed in cultured hepatocytes, but not in vivo. TGF-{beta} is supposed to initiate EMT in hepatocytes by inhibiting HNF4 through the SMAD2/3 complex. We report that TGF-{beta} does not directly inhibit HNF4, but contributes to its transcriptional regulation by SMAD2/3 recruiting acetyltransferase CBP/p300 to the HNF4 promoter. The recruitment of CBP/p300 is indispensable for C/EBPa binding, another essential requirement for constitutive HNF4 expression in hepatocytes. In contrast to the observed induction of HNF4, SMAD2/3 inhibits C/EBP transcription. Therefore, long-term TGF-{beta} incubation results in C/EBP depletion, which abrogates HNF4 expression. Intriguingly, SMAD2/3 inhibitory binding to the C/EBP promoter is abolished by insulin. Thus, maintaining a high insulin concentration in culture medium ensures constitutive HNF4 and thereby prevents TGF-{beta}-induced hepatocyte EMT. Furthermore, insulin inhibits TGF-{beta}-induced SMAD2/3 binding to the promoters of core EMT transcription factors e.g., SNAI1. SNAI1 transcription requires both SMAD2/3 and FOXO1 in nuclei. Insulin inhibits SNAI1 transcription through impeding SMAD2/3 binding to its promoter and inducing FOXO1 phosphorylation. Hence, insulin is the key factor that prevents TGF-{beta}-induced EMT in hepatocytes.

cell biology↗

bioRxiv2022

Instantaneous antidepressant effect of lateral habenula deep brain stimulation in rats studied with functional magnetic resonance imaging

The available treatments for depression have substantial limitations, including low response rates and substantial lag time before a response is achieved. We applied deep brain stimulation (DBS) to the lateral habenula (LHb) of two rat models of depression (Wistar Kyoto rats and lipopolysaccharide-treated rats) and observed an immediate (within seconds to minutes) alleviation of depressive-like symptoms with a high response rate. Simultaneous functional magnetic resonance imaging (fMRI) conducted on the same sets of depressive rats used in behavioral tests revealed DBS-induced activation of multiple regions in afferent and efferent circuitry of the LHb. The activation levels of brain regions connected to the medial LHb (M-LHb) was correlated with the extent of behavioral improvements. Rats with more medial stimulation sites in the LHb exhibited greater antidepressant effects than those with more lateral stimulation sites. These results indicated that the antidromic activation of the limbic system and orthodromic activation of the monoaminergic systems connected to the M-LHb played a critical role in the rapid antidepressant effects of LHb-DBS. This study indicates that M-LHb-DBS might act as a valuable, rapid-acting antidepressant therapeutic strategy for treatment-resistant depression and demonstrates the potential of using fMRI activation of specific brain regions as biomarkers to predict and evaluate antidepressant efficacy.

neuroscience↗

bioRxiv2022

A systematically optimized awake mouse fMRI paradigm

Functional magnetic resonance imaging (fMRI) has been increasingly utilized in mice. Due to the non-negligible effects of anesthetics on mouse fMRI, it is becoming more common to perform fMRI in the awake mice. However, high stress level and head motion in awake mouse fMRI remain to be fully addressed, which limits its practical applications. Therefore, here we presented a systematically optimized awake mouse fMRI paradigm as a practical and open-source solution. First, we designed a soundproof habituation chamber in which multiple mice can be habituated simultaneously and independently. Then, combining corticosterone, body weight and behavioral measurements, we systematically evaluated the potential factors that may contribute to animals stress level for awake imaging. Among many factors, we found that the restraining setup allowing forelimbs freely moving and head tilted at 30-degree was optimal for minimizing stress level. Importantly, we implemented multiband simultaneous multi-slice imaging to enable ultrafast fMRI acquisition in awake mice. Compared to conventional single-band EPI, faster acquisition enabled by multiband imaging were more robust to head motion and yielded higher statistical power. Thus, more robust resting-state functional connectivity was detected using multiband acquisition in awake mouse fMRI, compared to conventional single-band acquisition. In conclusion, we presented an awake mouse fMRI paradigm that is highly optimized in both awake mice habituation and fMRI acquisition, and such paradigm minimized animals stress level and provided more resistance to head motion and higher statistical power.

neuroscience↗

bioRxiv2022

Myosin-Binding Protein C Stabilizes, But Is Not the Sole Determinant of SRX Myosin in Cardiac Muscle

The myosin Super Relaxed (SRX) state is central to striated muscle metabolic and functional regulation. In skeletal muscle, SRX myosin are predominantly colocalized with Myosin-Binding Protein C (MyBP-C) in the C-zone, proximal to the sarcomere center. To define how MyBP-C and its specific domains contribute to stabilizing the SRX state in cardiac muscle, we took advantage of transgenic MyBP-C null mice and those expressing MyBP-C with a 271 residue N-terminal truncation. Utilizing super-resolution microscopy, we determined the lifetime and sub-sarcomeric location of individual fluorescent-ATP turnover events within isolated cardiac myofibrils. The proportion of SRX myosin was highest in the C-zone (71{+/-}6%) and lower in the D-zone (45{+/-}10%) which lies farther from the sarcomere center and lacks MyBP-C, suggesting a possible role for MyBP-C in stabilizing the SRX state within the C-zone. However, myofibrils from MyBP-C null mice demonstrated an ~40% SRX reduction, not only within the now MyBP-C-free C-zone (49{+/-}9% SRX), but also within the D-zone (22{+/-}5% SRX). These data suggest that the influence of MyBP-C on the SRX state is not limited to the C-zone, but extends along the thick filament. Interestingly, myofibrils with N-terminal truncated MyBP-C had an SRX content and spatial gradient similar to the MyBP-C null, indicating that the N terminus of cardiac MyBP-C is necessary for MyBP-Cs role in establishing SRX along the entire thick filament. Given that SRX myosin are enriched in the C-zone, even in the absence of MyBP-C or its N-terminus, an inherent bias must exist in the structure of the thick filament to stabilize the SRX state. One candidate may be a differential in the super repeats of titin that interact with MyBP-C and myosin and which template the thick filament.

physiology↗

bioRxiv2022

Convergent genomic signatures of adaptation to an extreme environment in cyprinoid fishes

Cyprinoids are a worldwide distributed and diverse group of freshwater fish with more than 3,000 species. Although primarily freshwater, some cyprinoid species had convergently evolved to thrive in extreme environments and underlying genetic mechanisms remain unclear. Here, we leveraged 32 cyprinoid fish genomes to identify common genomic changes associated with convergent adaptation to highly saline and alkaline water in two East Asian cyprinoid fish species, Gymnocypris przwalskii and Leuciscus waleckii, representing two independent extremophile fish lineages. We found that genome-wide rate of nonsynonymous substitution and signal of intensified selection is higher in extremophile relative to non-extremophile fish taxa. We further tested gene-wide molecular convergence and found hundreds of genes tended to experience convergent shifts in selections in extremophile fish taxa, including convergent acceleration and positive selection. These genes were associated with several key functions, such as nervous system development, reproduction, ion transport and immune response, and included genes that previously have been implicated for saline or alkaline tolerance in fish. Additionally, comparative transcriptomic analyses defined the convergent roles of differentially expressed genes under selection in extremophile fish taxa during convergent adaptation. Taken together, our work provides insights into the genomic basis of convergent adaptation to extreme environments in fish.

evolutionary biology↗

bioRxiv2022

Constitutive, calcium-independent endoplasmic reticulum-plasma membrane contact site oscillations and its implications in store-operated calcium entry

The endoplasmic reticulum and plasma membrane (ER-PM) contact site dynamics plays a central role for store-operated calcium entry (SOCE). ER localized calcium sensor STIM1 translocates to the contact sites, interacts with Orai and mediates calcium influx from the extracellular environment. Different species of phosphoinositides (PIPs) have been reported to be involved in contact site dynamics as well as STIM1 translocation. However, most of the studies were based on loss-of-function experiments or conditions that generate massive calcium store depletion. The kinetics of ER-PM contact site dynamics during physiological stimuli -induced calcium oscillations are not well understood. Using total internal reflection fluorescence microscopy (TIRFM), we investigated the relationship between dynamics of STIM1 as well as cortical ER (cER) proteins and calcium oscillations in rat basophilic leukemia (RBL) mast cells. Surprisingly, a significant percentage of cells displayed cyclic STIM1 and cER dynamics that were calcium-independent. Using specific lipid sensors, we showed that cyclic ER-PM contact site assembly was in phase with PI(4)P oscillation, but preceded phases of PI(4,5)P2 or PI(3,4,5)P3 oscillation. Optogenetic recruitment of the phosphoinositide 5-phosphatase from INPP5E, which decreased PI(4,5)P2 and increased PI(4)P levels on the plasma membrane, stimulated the translocation of STIM1 and inhibited calcium oscillations. Interestingly, prolonged stable translocation of STIM1 to the plasma membrane had an inhibitory effect on calcium oscillations. Collectively, our findings suggest that ER-PM contact sites formation is PI(4)P-dependent. In addition, reversibility of ER-PM contact sites dynamics and intermediate strength of ER-PM contact are needed for calcium oscillation.

cell biology↗

bioRxiv2021

Integrated resource for functional and structural connectivity of the marmoset brain

Comprehensive integration of structural and functional connectivity data is required to model brain functions accurately. While resources for studying the structural connectivity of non-human primate brains already exist, their integration with functional connectivity data has remained unavailable. Here we present a comprehensive resource that integrates the most extensive awake marmoset resting-state fMRI data available to date (39 marmoset monkeys, 710 runs, 12117 mins) with previously published cellular-level neuronal tracing (52 marmoset monkeys, 143 injections) and multi-resolution diffusion MRI datasets. The combination of these data allowed us to (1) map the fine-detailed functional brain networks and cortical parcellations; (2) develop a deep-learning-based parcellation generator that preserves the topographical organization of functional connectivity and reflects individual variabilities, and (3) investigate the structural basis underlying functional connectivity by computational modeling. This resource will enable modeling structure-function relationships and facilitate future comparative and translational studies of primate brains.

neuroscience↗

bioRxiv2021

Automated skull stripping in mouse fMRI analysis using 3D U-Net

Skull stripping is an initial and critical step in the pipeline of mouse fMRI analysis. Manual labeling of the brain usually suffers from intra- and inter-rater variability and is highly time-consuming. Hence, an automatic and efficient skull-stripping method is in high demand for mouse fMRI studies. In this study, we investigated a 3D U-Net based method for automatic brain extraction in mouse fMRI studies. Two U-Net models were separately trained on T2-weighted anatomical images and T2*-weighted functional images. The trained models were tested on both interior and exterior datasets. The 3D U-Net models yielded a higher accuracy in brain extraction from both T2-weighted images (Dice > 0.984, Jaccard index > 0.968 and Hausdorff distance < 7.7) and T2*-weighted images (Dice > 0.964, Jaccard index > 0.931 and Hausdorff distance < 3.3), compared with the two widely used mouse skull-stripping methods (RATS and SHERM). The resting-state fMRI results using automatic segmentation with the 3D U-Net models are identical to those obtained by manual segmentation for both the seed-based and group independent component analysis. These results demonstrate that the 3D U-Net based method can replace manual brain extraction in mouse fMRI analysis.

neuroscience↗

bioRxiv2021

Critical Assessment of Metagenome Interpretation - the second round of challenges

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from [~]1,700 novel and known microbial genomes, as well as [~]600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results. Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.

bioinformatics↗

bioRxiv2021

Single Cell Raman-Deuterium Isotope Probing for Drug Resistance of Elizabethkingia spp.

Nosocomial infection associated with Elizabethkingia spp. is an emerging clinical concern characterized by multi-drug resistance and severe clinical consequences particularly in immunocompromised individuals and infants. Efficient control of this infection demands quick and reliable methods to determine the right drugs for the treatment. In this study, E. meningoseptica ATCC 13253 and four clinical isolates of Elizabethkingia spp. obtained from China, were subjected to single cell Raman spectroscopy analysis coupling with deuterium probing (single cell Raman-DIP). The results demonstrated that single cell Raman-DIP could generate an antimicrobial susceptibility testing result for Elizabethkingia spp. colonies within 4 hours based on their metabolisms variations at single cell level, and the drug resistant spectra of Elizabethkingia spp. determined by single cell Raman-DIP were consistent with the classical MIC method. Meanwhile single cell Raman spectroscopy (single cell RS) was applied to analyze Raman spectra of Elizabethkingia spp., which were revealed that their ratios of nucleic acid/protein were lower than other gram-negative pathogens and isolates from different origins could be distinguished by their Raman fingerprint. The in vitro results confirmed that minocycline and levofloxacin are first-line antimicrobials for Elizabethkingia spp. infection.

microbiology↗

bioRxiv2021

Genome-wide, genic, and site-specific changes associated with the convergent evolution of sociality in spiders

The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.

evolutionary biology↗

bioRxiv2020

Genomic signature of shifts in selection and alkaline adaptation in highland fish

Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed primarily related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species and four alkaline intolerant species. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of shared genes associated with ion transport, apoptosis, immune response and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude. Significance StatementLittle is known about how wild fish responds to extreme alkaline stress besides hypoxia at high altitude. Comparative genomics has begun to elucidate the genomic basis of alkaline adaptation in lowland fish, such as killifish, but insight from highland fish has lagged behind. The common role of adaptive molecular evolution during alkaline adaptation in highland and lowland fish has rarely been discussed. We address this question by comparing 15 fish omics data. We find numbers of shared orthologs exhibited consistent patterns of molecular evolution in alkaline tolerant species relative to intolerant species. We further identify remarkably consistent signatures of rapidly evolving and positive selection in a substantial shared core of genes in both highland and lowland alkaline tolerant species.

evolutionary biology↗

bioRxiv2020

Geminin is required for Hox gene regulation to pattern the developing limb

Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5 Hox transcription factor expression is essential for proper limb bud patterning and elaboration of distinct limb skeletal elements. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5 Hox gene expression expanded into more proximal and anterior regions of the embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior SHH signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the HOXD13 target Shh, and the SHH target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of GLI3, a SHH pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb. SummaryThis work identifies a new role for Geminin in mouse limb development. Geminin is a nuclear protein that regulates gene expression to control several other aspects of vertebrate development.

developmental biology↗

bioRxiv2019

Comparative genomics identifies rapidly evolving ion transport genes in a saline-alkaline lake-dwelling Schizothoracine fish

Tibetan Plateau imposes extremely inhospitable environment on most wildlife. Besides the harsh aquatic environment including hypoxia and chronic cold, high salinity and alkalinity is an increasing threat to Tibetan endemic fishes. Previous genome-wide studies identified key genes contributed to highland fish adaptation to hypoxia and long-term cold, while our understanding of saline and alkaline adaptation in Tibetan fish remains limited. In this study, we performed a comparative genomics analysis in a saline lake-dwelling highland fish Gymnocypris przewalskii, aimed to identify candidate genes that contributed to saline and alkaline adaptation. We found elevated genome-wide rate of molecular evolution in G. przewalskii relative to lowland teleost fish species. In addition, we found nine genes encoding biological macromolecules associated with ion transport functions underwent accelerated evolution in G. przewalskii, which broadly expressed across kidney, gill, liver, spleen, brain and muscle tissues. Moreover, we found putative evidence of ion transport under selection were interacted by co-expression in G. przewalskii adaptation to high salinity and alkalinity environment of Lake Qinghai. Taken together, our comparative genomics study identified a set of rapidly evolving ion transport genes and transcriptomic signatures in Schizothoracine fish adaptation to saline and alkaline environment on the Tibetan Plateau.

genomics↗

bioRxiv2019

Transcriptomic signature of rapidly evolving immune genes in a highland fish

Recent genome-wide studies have begun to elucidate the genomic basis of hypoxia, long-term cold and high saline and alkaline adaptation in highland fish, and a number of key genes contributed to its highland adaptation were identified. An increasing number of studies indicated that immune genes of Tibetan endemic fish species underwent positive selection towards functional shift, while the insight into immune gene repertoire of Tibetan highland fishes from genome-wide studies has largely lagged behind. In this study, we performed one of the first comparative genomics study in particular focusing on the signatures of immune genes in a highland fish, Gymnocypris przewalskii based on immune-relevant tissue transcriptome assemblies. We identified seven putative rapidly evolving immune genes with elevated molecular evolutionary rate (dN/dS) relative to lowland fish species. Using tissue-transcriptome data, we found most of rapidly evolving immune genes were broadly expressed in head-kidney, spleen, gills and skin tissues, which significantly enriched for complement activation and inflammatory response processes. In addition, we found a set of complement activation related genes underwent accelerated evolution and showed consistently repressed expression patterns in response to parasite Ichthyophthirius multifiliis infection. Moreover, we detected a number of immune genes involved in adaptive immune system exhibited distinct signature of upregulated expression patterns after parasite infection. Taken together, this study provided putative transcriptomic signatures of rapidly evolving immune genes, and will gain the insight into Schizothoracine fish adaptation to high-altitude extreme aquatic environments including diversified pathogen challenge.

genomics↗

bioRxiv2019

Genomic signature of ongoing alkaline adaptation in a Schizothoracine fish (Cyprinidae) inhabiting soda lake on the Tibetan Plateau

Comparative genomics has elucidate the molecular footprints of adaptations to extreme environments at high altitude including hypoxia, but insight into the genomic basis of saline and alkaline adaptation in highland fish has rarely been provided. The increasing of water salinization is a growing threat to Tibetan endemic fish species. Here we performed one of the first comparative genomics studies and began to characterize genomic signature of alkaline adaptation in a Schizothoracine fish inhabiting soda lake on the Tibetan Plateau. We found that expansions of lineage-specific genes associated with ion transport and transmembrane functions, genome-wide elevated rate of molecular evolution in Schizothoracine fishes relative to other lowland teleost fish species. In addition, we found specific changes in the rate of molecular evolution between G. p. kelukehuensis and other teleost fishes for ion transport-related genes. Furthermore, we identified a set of genes associated with ion transport and energy metabolism underwent positive selection. Using tissue-transcriptomics, we found that most REGs and PSGs in G. p. kelukehuensis were broadly expressed across three tissues and significantly enriched for ion transport functions. Finally, we identified a set of ion transport-related genes with evidences for both selection and co-expressed which contributed to alkaline tolerance in G. p. kelukehuensis. Altogether, our study identified putative genomic signature and potential candidate genes contributed to ongoing alkaline adaptation in Schizothoracine fish.

genomics↗