Biology subjects

Cai, G.

Publications and source records attributed to Cai, G..

51 records · Page 3Linked to original sources

bioRxiv2022

Nucleotide resolution genetic mapping in pigs by publicly accessible whole genome imputation

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in the genetic improvement animals. Despite recent advances in high throughput genotyping technologies, resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2,259 whole genome sequenced animals representing 44 pig breeds. We optimized the imputation procedure to achieve an average concordance rate in excess of 97%, non-reference concordance rate 91%, and r2 0.89. We demonstrated that genotype imputation using this resource can dramatically improve resolution of genetic mapping. Finally, we developed a public web server (swimgeno.org) to allow the pig genetics community to fully utilize this resource. We expect the resource and server to significantly facilitate genetic mapping and accelerate genetic improvement in pigs.

genomics↗

bioRxiv2022

Monitoring of urban ecological environment including air quality using satellite imagery

Rapid urbanisation has highlighted problems in the urban ecological environment and stimulated research on the evaluation of urban environments. In previous studies, key factors such as greenness, wetness, and temperature were extracted from satellite images to assess the urban ecological environment. Although air pollution has become increasingly serious as urbanisation proceeds, information on air pollution is not included in existing models. The Sentinel-5P satellite launched by the European Space Agency in 2017 is a reliable data source for monitoring air quality. By making full use of images from Landsat 8, Sentinel-2A, and Sentinel-5P, this work attempts to construct a new remote sensing monitoring index for urban ecology by adding air quality information to the existing remote sensing ecological index. The proposed index was tested in the Beijing metropolitan area using satellite data from 2020. The results obtained using the proposed index differ greatly in the central urban region and near large bodies of water from those obtained using the existing remote sensing monitoring model, indicating that air quality plays a significant role in evaluating the urban ecological environment. Because the model constructed in this study integrates information on vegetation, soil, humidity, heat, and air quality, it can comprehensively and objectively reflect the quality of the urban ecological environment. Consequently, the proposed remote sensing index provides a new approach to effectively monitoring the urban ecological environment.

ecology↗

bioRxiv2021

A portable and high-integrated 3D microfluidic chip for bacterial quantification and antibiotic susceptibility testing

On-site single-cell antibiotic susceptibility testing (sc-AST) provides unprecedented technical potential to improve the treatment of bacterial infections and study heterogeneous resistance to antibiotics. Herein, we developed a portable and high-integrated 3D polydimethylsiloxane (PDMS) chip to perform fast and on-site bacteria quantification and sc-AST. The 3D arrangement of the chambers significantly improved the integration of reaction units ([~]10000/cm2) and widened the dynamic range to 5 orders of magnitude. A capillary valve-based flow distributor was adopted for flow equidistribution in 64 parallel channels and uniform sample loading in as short as 2 s. The degassed PDMS enabled this device to independently dispense the sample into 3D chamber array with almost 100% efficiency. The quantification of Escherichia coli (E. coli) strains with various activity was accomplished in 0.5-2 h, shortened by 20 h in comparison to the traditional plate counting. The functionality of our platform was demonstrated with several effective antibiotics by determining minimum inhibitory concentrations at single-cell level. Furthermore, we utilized the lyophilization of test reagents and needle-mediated reagents rehydration to realize one-step on-site sc-AST. The results indicate that the proposed sc-AST platform is portable, highly sensitive, fast, accurate and user-friendly, thus it has the potential to facilitate precise therapy in time and monitor the treatment. Meanwhile, it could serve as an approach for investigating the mechanisms of heteroresistance at single-cell resolution.

microbiology↗

bioRxiv2021

BMI-CNV: A Bayesian framework for multiple genotyping platforms detection of copy number variation

Whole-exome sequencing (WES) enables detection of Copy number variations (CNVs) with high resolution in protein-coding regions. However, variations in the intergenic or intragenic regions are excluded from studies. Fortunately, samples have been previously sequenced by other genotyping platforms, such as SNP array. Moreover, conventional single sample-based methods suffer from high false discovery rate due to prominent data noise. Therefore, methods for integrating multiple genotyping platforms and samples are highly demanded for improved CNV detection. We developed BMI-CNV, a Bayesian Multi-sample and Integrative CNV (BMI-CNV) profiling method with data sequenced by both WES and microarray. For the multi-sample integration, we identify the shared CNVs regions across samples using a Bayesian probit stick-breaking process model coupled with a Gaussian Mixture model estimation. With extensive simulations, BMI-CNV outperformed existing methods with remarkably improved accuracy. By applying to the matched 1000 genomes project and HapMap project data, we showed that BMI-CNV accurately detected common variants. We further applied it to The Research of International Cancer of Lung (TRICL) consortium with matched WES and OncoArray data and identified lung cancer risk associated genes in 17q11.2, 1p36.12, 8q23.1 and 5q22.2 regions, which may provide new insights into the etiology of lung cancer.

genetics↗

bioRxiv2021

Rapid and Visible RPA-Cas12a fluorescence Assay for Accurate Detection of Zoonotic Dermatophytes

BackgroundDermatophytosis is an infectious disease of global significance caused by several fungal species, which affects the hair, nails, or superficial layers of the skin. The most common zoonotic dermatophytes are Microsporum canis, Nannizzia gypsea and Trichophyton mentagrophytes. Woods lamp examination, microscopic identification and fungal culture are the main conventional diagnostic methods used in clinics. Less common methods are dermatophyte PCR and biopsy/histopathology. However, these methods also have limitations for providing both accuracy and timely on-site detection. The recent development of CRISPR-based diagnostic platform provides the possibility of a rapid, accurate, and portable diagnostic tool, which has huge potential for clinical applications. ObjectivesThe purpose of this study is to establish a molecular method for rapid and accurate diagnosis of clinical dermatophytes, which can accelerate clinical diagnostic testing and help timely treatment. MethodsIn this paper, we design a Cas12a-based assay combined with recombinase polymerase amplification (RPA) to differentiate three main zoonotic dermatophytes. The limit of detection (LOD) is determined by using standard strains. A total of 25 clinical samples (hair and scurf) are identified to evaluate the sensitivity and specificity of this assay. ResultsThe RPA-Cas12a method showed high sensitivity and specificity (100% and 100%, respectively). The results could be observed directly by naked-eyes, and all tested samples were consistent with fungal culture and sequencing results. ConclusionsCompared with other methods, the RPA-Cas12a-fluorescence assay requires less time (30 minutes) and less complicated equipment, and visible changes can be clearly observed, which is suitable for on-site clinical diagnosis.

microbiology↗

bioRxiv2021

A phosphorylation of RIPK3 kinase initiates an intracellular apoptotic pathway that promotes corpus luteum regression

Receptor-interacting serine/threonine-protein kinase 3 (RIPK3) normally signals to necroptosis by phosphorylating MLKL. We report here that when the cellular RIPK3 chaperone Hsp90/CDC37 level is low, RIPK3 also signals to apoptosis. The apoptotic function of RIPK3 requires phosphorylation of the serine 165/threonine 166 sites on its kinase activation loop, resulting in inactivation of RIPK3 kinase activity while gaining the ability to recruit RIPK1, FADD, and caspase-8 to form a cytosolic caspase-activating complex, thereby triggering apoptosis. We found that PGF2 induces RIPK3 expression in luteal granulosa cells in the ovary to cause luteal regression through this RIPK3-mediated apoptosis pathway. Mice carrying homozygous phosphorylation-resistant RIPK3 S165A/T166A knockin mutations failed to respond to PGF2 but retained pro-necroptotic function, whereas mice with phospho-mimicking S165D/T166E homozygous knockin mutation underwent spontaneous apoptosis in multiple RIPK3-expressing tissues and died shortly after birth. Thus, RIPK3 signals to either necroptosis or apoptosis depending on its serine 165/threonine 166 phosphorylation status.

cell biology↗

bioRxiv2020

Casein Kinase 1G2 Suppresses Necroptosis-Promoted Testis Aging by Inhibiting Receptor-Interacting Kinase 3

Casein kinases are a large family of intracellular serine/threonine kinases that control a variety of cellular signaling functions. Here we report that a member of casein kinase 1 family, casein kinase 1G2, CSNK1G2, binds and inhibits the activation of receptor-interacting kinase 3, RIP3, thereby attenuating RIP3-mediated necroptosis. The binding of CSNK1G2 to RIP3 is triggered by auto-phosphorylation at serine 211/threonine 215 sites in its C-terminal domain. CSNK1G2-knockout mice showed significantly enhanced necroptosis response and pre-maturing aging of their testis, a phenotype that was rescued by either double knockout of the RIP3 gene or feeding the animal with a RIP1 kinase inhibitor-containing diet. Moreover, CSNK1G2 is also co-expressed with RIP3 in human testis, and the necroptosis activation marker phospho-MLKL was observed in the testis of old (>80) but not young men, indicating that the testis-aging program carried out by the RIP3-mediated and CSNK1G2-attenuated necroptosis is evolutionarily conserved between mice and men.

cell biology↗

bioRxiv2020

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection

Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e., boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we therefore proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic correlation (i.e., LD). To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presents high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. We also theoretically demonstrated the correlation structure of CNV data, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. This new segmentation algorithm has a wide scope of application with next-generation sequencing data analysis and single-cell sequencing analysis. Author SummaryCopy number variants (CNVs) refers to gains or losses of the DNA segments in comparison to a reference genome. CNVs have garnered extensive interests in recent years as they play an important role susceptibility to disorders and diseases such as autism, schizophrenia and cancer [1-7]. Although innovation in modern technology is promoting the discoveries related to CNVs, the methodology for CNV detection is still lagging, which limits the novel discoveries regarding the role of CNVs in complex diseases. In this study, we are proposing a novel segmentation algorithm, LDcnv, to accurately locate the breakpoints or boundaries of CNVs in the human genome. Instead of utilizing an independent assumption of the signal intensities as has been used in traditional segmentation algorithms, LDcnv models the correlation structure in the genome in a change-point CNV detection model, which allows for accurate and fast computation with a whole genome scan. Our study showed strong theoretical evidence of the existence of correlation structure in real CNV data, and we believe that taking this evidence into consideration will improve the power of CNV detection. Extensive simulation studies have demonstrated the advantage of the LDcnv algorithm in stability, robustness and accuracy over existing methods. We also used high-quality CNV profiles to further support the superior performance of the LDcnv algorithm over existing methods. The development of the LDcnv algorithm provides great insights for new directions in developing CNV detection tools.

genetics↗

bioRxiv2020

Mitochondrial Genome Sequence of Phytophthora sansomeana and Comparative Analysis of Phytophthora Mitochondrial Genomes

Phytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthetase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3 truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.

microbiology↗

bioRxiv2020

SCANNER: A Web Server for Annotation, Visualization and Sharing of Single Cell RNA-seq Data

MotivationIn recent years, efficient scRNA-seq methods have been developed, enabling the transcriptome profiling of single cells massively in parallel. Meanwhile, its high dimensionality brought challenges in data modeling, analysis, visualization and interpretation. Available analysis tools require extensive knowledge and training of data properties, statistical modeling and computational skills. It is challenging for biologists to efficiently view, browse and interpret the data. ResultsHere we developed SCANNER, as a public webserver resource to equip the biologists and bioinformatician to share and analyze scRNA-seq data in a comprehensive and collaborative manner. It is effort-less and host-free without requirement on software setup or coding skills, and enables a user-friendly way to compare the activation status of gene sets on single cell basis. Also, it is equipped with multiple data interfaces for easy data sharing and currently provide a database for studying the smoking effect on single cell gene expression in lung. Using SCANNER, we have identified larger proportions of cancer-associated fibroblasts cells and activeness of fibroblast growth related genes in melanoma tissues in females compared to males. Moreover, we found ACE2 is mainly expressed in pneumocytes, secretory cells and ciliated cells with disparity in gene expression by smoking behavior. Availability and implementationSCANNER is available at https://www.thecailab.com/scanner/. Supplementary informationSupplementary data are available online. ContactGCAI@mailbox.sc.edu or XIAOF@mailbox.sc.ecu Key PointsO_LISCANNER provides a new web server resource for promoting scRNA-seq data analysis C_LIO_LISCANNER enables comprehensive and dynamic analysis and visualization, novel functional annotation and activeness inference, online databases and easy data sharing. C_LIO_LISCANNER bridges the data analysis and the biological experiment units. C_LI

bioinformatics↗

bioRxiv2019

Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms

Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome surveys have not been conducted in hotel environments; thus, the composition and associated environmental factors are not clear. We presented the first continental-scale microbiome study of hotel rooms (n = 68) spanning large geographic regions. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified, but fungal taxa showed a local distribution compared with bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with high compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for [~]80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbial dynamics and 16 indoor and outdoor environmental characteristics. Fungal {beta}-diversity and quantity showed concordant variation and were associated with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea and visible mold, while -diversity decreased with heavy traffic (95% CI: -127.05 to -0.25) and wall-to-wall carpet (95% CI: -47.60 to -3.82). Bacterial {beta}-diversity was associated with latitude, quality of the interior and floor type, while -diversity decreased with recent decoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI: -136.71 to -5.12). ImportanceThis is the first microbiome study to characterize microbial composition and associated environmental characteristics. In this study, we found concordant variation between microbial {beta}-diversity and absolute quantity and discordant variation between {beta}-diversity/quantity and -diversity. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

microbiology↗

bioRxiv2019

Direct synthesis of EM-visible gold nanoparticles on genetically encoded tags for single-molecule visualization in cells

Single-molecule visualization in cells with genetically encoded tags for electron microscopy (EM) has been a long-awaited but unimplemented tool for cell biologists. Here, we report an approach for directly synthesizing EM-visible gold nanoparticles (AuNPs) on cysteine-rich tags for single-molecule visualization in cells. We first uncovered an auto-nucleation suppression mechanism that allows specific synthesis of AuNPs on isolated cysteine-rich tags. We next exploited this mechanism to develop an approach for single-molecule detection of proteins in prokaryotic cells and achieved an unprecedented labeling efficiency. We then expanded it to more complicated eukaryotic cells and successfully detected the proteins targeted to various organelles, including the membranes of endoplasmic reticulum (ER) and nuclear envelope, ER lumen, nuclear pores, spindle pole bodies, and mitochondrial matrix. Thus, our implementation of genetically encoded tags for EM should allow cell biologists to address an enormous range of biological questions at single-molecule level in diverse cellular ultrastructural contexts without using antibodies.

biophysics↗

bioRxiv2018

RNA-seq analyses of molecular abundance (RoMA) for detecting differential gene expression

MotivationVarious methods have been proposed, each with its own limitations. Some naive normal-based tests have low testing power with invalid normal distribution assumptions for RNA-seq read counts, whereas count-based methods lack a biologically meaningful interpretation and have limited capability for integration with other analysis packages for mRNA abundance. In this study, we propose an improved method, RoMA, to accurately detect differential expression and unlock the integration with upstream and downstream analyses on mRNA abundance in RNA-seq studies.\n\nResultsRoMA incorporates information from both mRNA abundance and raw counts. Studies on simulated data and two real datasets showed that RoMA provides an accurate quantification of mRNA abundance and a data adjustment-tolerant DE analysis with high AUC, low FDR, and an efficient control of type I error rate. This study provides a valid strategy for mRNA abundance modeling and data analysis integration for RNA-seq studies, which will greatly facilitate the identification and interpretation of DE genes.\n\nAvailability and implementationRoMA is available at https://github.com/GuoshuaiCai/RoMA.\n\nContactGCAI@mailbox.sc.edu or Michael.L.Whitfield@Dartmouth.edu

bioinformatics↗

bioRxiv2018

Did a novel virus contribute to late blight epidemics?

Phytophthora infestans is the causal agent of potato and tomato late blight. In this study, we characterized a novel RNA virus, Phytophthora infestans RNA virus 2 (PiRV-2). The PiRV-2 genome is 11,170 nt and lacks a polyA tail. It contains a single large open reading frame (ORF) with short 5- and 3-untranslated regions. The ORF is predicted to encode a polyprotein of 3710 aa (calculated molecular weight 410.94 kDa). This virus lacks significant similarity to any other known viruses, even in the conserved RNA-dependent RNA polymerase region. Comparing isogenic strains with or without the virus demonstrated that the virus stimulated sporangia production in P. infestans and appeared to enhance its virulence. Transcriptome analysis revealed that it achieved sporulation stimulation likely through down-regulation of ammonium and amino acid intake in P. infestans. This virus was faithfully transmitted through asexual reproduction. Survey of PiRV-2 presence in a P. infestans collection found it in most strains in the US-8 lineage, a very successful clonal lineage of P. infestans in North America. We suggest that PiRV-2 may have contributed to its success, raising the intriguing possibility that a potentially hypervirulent virus may contribute to late blight epidemics.\n\nAuthor SummaryPotato late blight, the notorious plant disease behind the Irish Potato Famine, continues to pose a serious threat to potato and tomato production worldwide. While most studies on late blight epidemics focuses on pathogen virulence, host resistance, environmental factors and fungicide resistance, we present evidence in this study that a virus infecting the causal agent, Phytophthora infestans, may have played a role. We characterized a novel RNA virus, Phytophthora infestans RNA virus 2 (PiRV-2) and examined its effects on its host. By comparing identical P. infestans strains except with or without the virus, we found that PiRV-2 stimulated sporulation of P. infestans (a critical factor in late blight epidemics) and increased its virulence. We also profiled gene expression in these strains and identified potential molecular mechanisms through which PiRV-2 asserted its sporulation stimulation effect. In a survey of PiRV-2 presence in a P. infestans collection, we found PiRV-2 in most isolates of the US-8 clonal lineage, a very successfull ineage that dominated potato fields in North America for several decades. We suggest that PiRV-2 may have contributed to its success. Our findings raise the intriguing possibility that a potentially hypervirulent virus may contribute to late blight epidemics.

pathology↗

bioRxiv2018

Generation of a novel growth-enhanced and reduced environmental impact transgenic pig strain

In pig production, insufficient feed digestion causes excessive nutrients such as phosphorus and nitrogen, which are then released to the environment. To address the issue of environmental emissions, we have established transgenic pigs harboring a single-copy quad-cistronic transgene and simultaneously expressing three microbial enzymes, {beta}-glucanase, xylanase, and phytase in the salivary glands. All the transgenic enzymes were successfully expressed, and the digestion of non-starch polysaccharides (NSPs) and phytate in the feedstuff was enhanced. Fecal nitrogen and phosphate outputs were reduced by 23%-46%, and growth rate improved by 23.4% (gilts) and 24.4% (boars) when the pigs were fed on a corn and soybean-based diet and high-NSP diet. The transgenic pigs showed a 11.5%- 14.5% improvement in feed conversion rate compared to the age-matched wild-type littermates. These findings indicate that transgenic pigs are promising resources for improving feed efficiency and reducing nutrient emissions to the environment.

biochemistry↗