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Bao, Y.-J.

Publications and source records attributed to Bao, Y.-J..

4 recordsLinked to original sources

Group A Streptococcus remains viable inside fibrin clots and gains access to human plasminogen for subsequent fibrinolysis and dissemination

Group A Streptococcus (GAS) is a Gram-positive bacterial pathogen that causes a wide spectrum of illnesses ranging from pharyngitis and rheumatic fever to more invasive and severe diseases such as necrotizing fasciitis and toxic shock syndrome. Invasive outcomes of GAS infections often result from entry of the bacteria via an open wound into tissue and blood systems. The coagulation cascade serves as an innate defense mechanism that initiates fibrin clots to sequester bacteria and restrict its growth and prevent dissemination into deeper tissues. GAS, especially skin-tropic bacterial strains, utilize the specific virulence factors Plasminogen binding M-protein (PAM) and streptokinase (SK) to manipulate hemostasis and ultimately activate human plasminogen to cause fibrinolysis and escape from the fibrin clot. A major unresolved question regarding this process is to understand the temporal dynamics of how GAS that is enmeshed in a fibrin clot accesses host plasminogen for dissolution of the clot and eventual dissemination. Using fluorescently labeled plasminogen and fibrinogen, we established conditions to observe the process of fibrin clot dissolution by GAS (an AP53 CovR+S-strain) that is sequestered in a fibrin clot using real-time imaging microscopy. We hypothesized that initiation of fibrinolysis by GAS inside a fibrin clot would be determined by the rate of hPg access into the fibrin clot where bacteria are trapped. Our live imaging studies show that GAS trapped inside a fibrin clot, has limited access to hPg; however, at 4.25 h post incubation, when sufficient hPg is accessible to the bacterium, fibrinolysis quickly occurs. If hPg is bound to the bacterial surface prior to being trapped inside a clot, dissolution and bacterial dissemination occurs at a much faster rate of 2.5 h post incubation. During the time which bacteria are trapped in the clot without access to hPg, we did not observe any growth of GAS; however, we demonstrate that the bacteria continue to remain viable inside the fibrin clot. We performed RNA-seq analysis of GAS and the isogenic GAS SK-deficient mutant to understand SK-dependent transcriptional changes during the lag-phase of the GAS bacteria inside the fibrin clot. We observed a dramatic change in the transcription profile of wt GAS inside the fibrin clot over time prior to escape from the fibrin clot (22 gene expression changes at 4h, to 802 gene expression changes at 8h). Furthermore, we also identified gene expression changes that were distinct between wt GAS and the GAS SK-deficient mutant. Our findings reveal for the first time that GAS can engage a latent, growth suspended phase whereby physical structures such as fibrin clots and Neutrophil extracellular traps that immobilize an invading pathogen allow bacteria to remain viable and transcriptionally active for an extended time during host infection. GAS that is trapped in a fibrin clot will therefore enter a state in which the bacteria suspend growth, but remain viable, until sufficient access to hPg allow it to initiate fibrinolysis and escape into surrounding tissues. The viability of GAS while trapped and its readiness to avoid immune defenses allow GAS to act quickly to disseminate when host conditions are more favorable for the bacteria.

microbiology↗

SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes

BackgroundThe gene-specific sweep is a selection process where an advantageous mutation along with the nearby neutral sites in a gene region increases the frequency in the population. It has been demonstrated to play important roles in ecological differentiation or phenotypic divergence in microbial populations. Therefore, identifying gene-specific sweeps in microorganisms will not only provide insights into the evolutionary mechanisms, but also unravel potential genetic markers associated with biological phenotypes. However, current methods were mainly developed for detecting selective sweeps in eukaryotic data of sparse genotypes and are not readily applicable to prokaryotic data. Furthermore, some challenges have not been sufficiently addressed by the methods, such as the low spatial resolution of sweep regions and lack of consideration of the spatial distribution of mutations. ResultsWe proposed a novel gene-centric and spatial-aware approach for identifying gene-specific sweeps in prokaryotes and implemented it in a python tool SweepCluster. Our method searches for gene regions with a high level of spatial clustering of pre-selected polymorphisms in genotype datasets assuming a null distribution model of neutral selection. The pre-selection of polymorphisms is based on their genetic signatures, such as elevated population subdivision, excessive linkage disequilibrium, or significant phenotype association. Performance evaluation using simulation data showed that the accuracy and sensitivity of the clustering algorithm in SweepCluster is above 90%. The application of SweepCluster in two real datasets from the bacteria Streptococcus pyogenes and Streptococcus suis showed that the impact of pre-selection was dramatic and significantly reduced the uninformative signals. We validated our method using the genotype data from Vibrio cyclitrophicus, the only available dataset of gene-specific sweeps in bacteria, and obtained a concordance rate of 78%. We noted that the concordance rate could be underestimated due to distinct reference genomes and clustering strategies. The application to the human genotype datasets showed that SweepCluster is also applicable to eukaryotic data and recovered the known sweep regions in a wide dynamic range of pre-selection parameters. ConclusionsSweepCluster is applicable to a broad category of datasets. It will be valuable for detecting gene-specific sweeps in diverse genotypic data and provide novel insights on adaptive evolution.

bioinformatics↗

The Genetic Variation Landscape of African Swine Fever Virus Reveals Frequent Positive Selection on Amino Acid Replacements

African swine fever virus (ASFV) is a lethal disease agent that causes high mortality in swine population and devastating loss in swine industries. The development of efficacious vaccines has been hindered by the gap in knowledge concerning genetic variation of ASFV and the genetic factors involved in host adaptation and virus-host interactions. In this study, we performed a meta-genetic study of ASFV aiming to profile the variation landscape and identify genetic factors with signatures of positive selection and relevance to host adaptation. Our data reveals a high level of genetic variability of ASFV shaped by both diversifying selection and selective sweep. The selection signatures are widely distributed across the genome with the diversifying selection falling within 29 genes and selection sweep within 25 genes, highlighting strong signals of adaptive evolution of ASFV. Further examination of the sequence properties reveals the link of the selection signatures with virus-host interactions and adaptive flexibility. Specifically, we discovered a site at 157th of the key antigen protein EP402R under diversifying selection, which is located in the cytotoxic T-cell epitope related with the low level of cross-reaction in T-cell response. Importantly, two multigene families MGF360 and MGF505, the host range factors of ASFV, exhibit divergent selection among the paralogous members, conferring sequence pools for genetic diversification and adaptive capability. By integrating the genes with selection signatures into a unified framework of interactions between ASFV and hosts, we showed that the genes are involved in multiple processes of host immune interaction and virus life cycles, and may play crucial roles in circumventing host defense systems and enhancing adaptive fitness. Our findings will allow enhanced understanding of genetic basis of rapid spreading and adaptation of ASFV among the hosts.

evolutionary biology↗

Universal and naked-eye gene detection platform based on CRISPR/Cas12a/13a system

Colorimetric gene detection based on gold nanoparticles (AuNPs) is an attractive detection format due to its simplicity. Here, we report a new design for a colorimetric gene-sensing platform based on the CRISPR/Cas system that has improved specificity, sensitivity, and universality. CRISPR/Cas12a and CRISPR/Cas13a have two distinct catalytic activities and are used for specific target gene recognition. Programmable recognition of DNA by Cas12a/crRNA and RNA by Cas13a/crRNA with a complementary sequence activates the nonspecific trans-ssDNA or -RNA cleavage, respectively, thus degrading the ssDNA or RNA linkers which are designed as a hybridization template for the AuNP-DNA probe pair. Target-induced trans -ssDNA or RNA cleavage leads to a distance-dependent color change for the AuNP-DNA probe pair. In this platform, naked eye detection of transgenic rice, African swine fever virus (ASFV), and a miRNA can be completed within 1 hour. Our colorimetric gene-sensing method shows superior characteristics, such as probe universality, isothermal reaction conditions, on-site detection capability, and sensitivity that is comparable to that of the fluorescent detection; thus, this method represents a robust next generation gene detection platform.

bioengineering↗