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Gao, C.

Publications and source records attributed to Gao, C..

At least 163 records · Page 9Linked to original sources

Detection of Chemotherapy-Resistant Pancreatic Cancer Using a Glycan Biomarker

Background and AimsA subset of pancreatic ductal adenocarcinomas (PDACs) is highly resistant to systemic chemotherapy, but no markers are available in clinical settings to identify this subset. We hypothesized that chemotherapy-resistant PDACs express a glycan biomarker called sTRA. Methods. We tested this marker to identify treatment-resistant PDAC in multiple systems: sets of cell lines, organoids, and isogenic cell lines; primary tumors; and blood plasma from cohorts of human subjects. Results. Among a panel of 27 cell lines, high levels of cell-surface sTRA identified higher resistance to seven chemotherapeutics used against PDAC. Using primary tumors from two different cohorts, patients who were positive for a gene-expression classifier for sTRA received no statistically significant benefit from adjuvant chemotherapy, in contrast to those negative for the signature. In another cohort, using direct measurements of sTRA in tissue microarrays by quantitative immunofluorescence, patients who were high in sTRA again had no statistically significant benefit from adjuvant chemotherapy. Further, a blood-plasma test for the sTRA glycan identified the PDACs that showed rapid relapse following neoadjuvant chemotherapy. This blood test performed with 96% specificity and 56% sensitivity in a blinded cohort using samples collected before the start of treatment. Conclusion. These findings establish that tissue or plasma sTRA can identify PDACs that are resistant to neoadjuvant or adjuvant chemotherapy. This capability could help apply systemic treatments more precisely and facilitate biomarker-guided trials targeting resistant PDAC.

cancer biology↗

GuidingNet: revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization

The DNA methyltransferases (DNMTs) (DNMT3A, DNMT3B, and DNMT3L) are primarily responsible for the establishment of genomic locus-specific DNA methylation patterns, which play an important role in gene regulation and animal development. However, this important protein familys binding mechanism, i.e., how and where the DNMTs bind to genome, is still missing in most tissues and cell lines. This motivates us to explore DNMTs and TFs cooperation and develop a network regularized logistic regression model, GuidingNet, to predict DNMTs genome-wide binding by integrating gene expression, chromatin accessibility, sequence, and protein-protein interaction data. GuidingNet accurately predicted methylation experimental data validated DNMTs binding, outperformed single data source based method and sparsity regularized methods, and performed well in within and across tissue prediction for several DNMTs in both human and mouse. Importantly, GuidingNet can reveal transcription co-factors assisting DNMTs for methylation establishment. This provides biological understanding in the DNMTs binding specificity in different tissues and demonstrate the advantage of network regularization. In addition, GuidingNet achieves good performance for chromatin regulators binding other than DNMTs and serves as a useful method for studying chromatin regulator binding and function. The GuidingNet is freely available at https://github.com/AMSSwanglab/GuidingNet. Author summaryDNA methyltransferases (DNMTs) are in charge of the addition of methyl groups to cytosine residues by binding to DNA specific region. However, DNMTs do not have DNA binding domains to recognize specific DNA sequences and an urging question is how DNMTs recognize their binding sites in the genome in different tissues. Here, we propose a network regularized logistic regression model, GuidingNet, for predicting DNMT genome-wide binding by integrating gene expression, chromatin accessibility, sequence, and protein-protein interaction data. The main contribution is to hypothesize that DNMTs interact with transcription factors and are guided by the TF network to bind to DNA, and methylate DNA GuidingNet captures the mechanism of DNMT binding in different tissue contexts and predict DNMTs binding well.

bioinformatics↗

Novel non-transposable-element regulation patterns of KZFP family reveal new drivers of its rapid evolution

One striking feature of the large KRAB-containing zinc finger protein (KZFP) family is its rapid expansion and divergence since its formation about 400 million years ago. However, the evolutionary characteristics of KRAB domains, C2H2 zinc fingers and the full protein of KZFPs have not been fully analyzed. As for the drivers of the rapid evolution, its partly due to their coevolution with transposable elements (TEs). But their diverse functions besides inhibiting TEs suggest other reasons exist. Here we address these two issues by the systematic analysis of the divergence time and diversification pattern of KZFPs at three aspects and the functional analysis of the potential target genes besides TEs. We found that old-zinc-finger-containing KZFPs tend to have varied and disordered KRAB domains, indicating there are two ways of the evolution of KZFPs, including the variation of KRAB domains and the diversification of zinc fingers. Among them, the divergence of zinc fingers mainly contributes to the rapid evolution of KZFPs. Thus, we mainly focused on the functional requirements of the evolution of zinc fingers. Different from the classical regulation pattern of this family, we found and experimentally confirmed that KZFPs tend to bind to non-TE regions and can positively regulate target genes. Although most young genes tend to be with a low expression level, young-zinc-finger-containing KZFPs tend to be highly expressed in early embryonic development or early mesoderm differentiation, indicating their particular evolutionarily novel functional roles in these two processes. We further validated a young KZFP, ZNF611, can bind to non-TE region of STK38 gene and positively regulates its expression in ESCs. The emergence of new sequence in STK38 promoter may drive the evolution of zinc fingers in ZNF611. Finally, we proposed a two-way evolution model of KZFP family.

evolutionary biology↗

Role of short-chain fatty acids in the gut-brain axis in schizophrenia: contribution to immune activation and pathophysiology in humans and mice

ObjectiveGut microbiota dysbiosis and aberrant gut-brain functional modules including short-chain fatty acid (SCFA) production and long-lasting immune activation (IA) are presented in schizophrenia. Given the key roles of gut microbiota and SCFA in shaping immunity, we propose that dysbiosis-induced SCFA upregulation could contribute to IA and behavioral symptoms in schizophrenia. DesignGut microbiota, SCFA, and IA biomarkers were compared between schizophrenic patients and healthy controls. The roles of SCFA in schizophrenia-related IA were analyzed in cultured peripheral blood mononuclear cells (PBMCs) and a mouse model of schizophrenia. The effects of SCFAs on schizophrenia-related phenotypes were analyzed in both human and mouse. ResultsBoth microbial-derived SCFA and SCFA-producing bacteria were elevated in the guts of schizophrenic patients, and this increased SCFA production in gut was associated with IA in schizophrenia. The microbiome signature underpinning schizophrenia-related IA includes increased diversity and increased SCFA-producing bacteria and inflammation-associated bacteria. The impact of SCFAs on immune responses of cultured PBMC depend on the diagnosis and IA status of donors. Small-molecule serum filtrates from immune-activated schizophrenic patients increased the inflammatory response of PBMCs from healthy volunteers, which can be enhanced and attenuated by SCFAs supplementation and inhibition of SCFA signaling, respectively. Chronically elevated SCFAs in adolescence induced neuroinflammation and schizophrenia-like behaviors in adult mice. Moreover, chronically elevated SCFAs in adult mice prenatally exposed to IA potentiated their expression of schizophrenia-like behaviors. Conclusionmicrobiota-derived SCFAs are important mediators of dysregulated gut-brain axis and participant in pathogenesis via enhance IA in schizophrenia. SummaryO_ST_ABSSignificance of this studyC_ST_ABSO_LIWhat is already known about this subject? [tpltrtarr]Schizophrenia pathogenesis goes beyond the brain since increasing peripheral abnormalities are revealed including gut microbiota dysbiosis, GI dysfunction, and systemic immune activation (IA). [tpltrtarr]Systemic IA/inflammation contributes to the neuroinflammation and brain impairment underlying schizophrenia, and adjunctive immunotherapy can improve psychotic symptoms. [tpltrtarr]Short-chain fatty acids (SCFA) mediate the microbiota-gut-brain communication and modulate several pathways involved in schizophrenia, including pathways of immunity and neurotransmitters. C_LIO_LIWhat are the new findings? [tpltrtarr]Patients with schizophrenia displayed increased rates of IA and increased SCFA production compared with healthy controls, and increased SCFA is associated with IA in patients. [tpltrtarr]A unique microbiota signature including enriched SCFA-producing bacterial species can distinguish patients with IA from other patients and controls. [tpltrtarr]Small molecules in the serum of immune-activated patients with schizophrenia enhance LPS-induced immune response of cultured peripheral blood mononuclear cell (PBMCs), which is partially mediated by SCFA signaling. [tpltrtarr]SCFA intake upregulates both peripheral and brain inflammation and potentiates the expression of schizophrenia-like behaviors in mice prenatally exposed to IA. C_LIO_LIHow might it impact on clinical practice in the foreseeable future? [tpltrtarr]Interference of SCFA signaling or targeted destruction of SCFA-producing bacteria may provide a new approach for the prevention and treatment of schizophrenia. [tpltrtarr]Immune activation status of patients should be an important condition considered when selecting immunotherapy for future precision psychiatric therapy. C_LI

neuroscience↗

Jointly Defining Cell Types from Multiple Single-Cell Datasets Using LIGER

High-throughput single-cell sequencing technologies hold tremendous potential for defining cell types in an unbiased fashion using gene expression and epigenomic state. A key challenge in realizing this potential is integrating single-cell datasets from multiple protocols, biological contexts, and data modalities into a joint definition of cellular identity. We previously developed an approach called Linked Inference of Genomic Experimental Relationships (LIGER) that uses integrative nonnegative matrix factorization to address this challenge. Here, we provide a step-by-step protocol for using LIGER to jointly define cell types from multiple single-cell datasets. The main steps of the protocol include data preprocessing and normalization, joint factorization, quantile normalization and joint clustering, and visualization. We describe how to jointly define cell types from single-cell RNA-seq and single-nucleus ATAC-seq data, but similar steps apply across a wide range of other settings and data types, including cross-species analysis, single-nucleus DNA methylation, and spatial transcriptomics. Our protocol contains examples of expected results, describes common pitfalls, and relies only on our freely available, open-source R implementation of LIGER. We also provide Rmarkdown tutorials showing the outputs from each individual code segment. The analysis process can be performed in 1 - 4 h depending on dataset size and assumes no specialized bioinformatics training.

bioinformatics↗

Swine Promyelocytic Leukemia Isoform II Inhibits Pseudorabies Virus Infection by Suppressing Viral Gene Transcription in PML-NBs

Promyelocytic leukaemia nuclear bodies (PML-NBs) possess an important intrinsic antiviral activity against -herpesvirus infection. PML is the structural backbone of NBs, comprising different isoforms. However, the contribution of each isoform to -herpesvirus restriction is not well understood. Here, we report the role of PML-NBs and swine PML (sPML) isoforms in pseudorabies virus (PRV) infection in its natural host swine cells. We found that sPML-NBs exhibit an anti-PRV activity in the context of increasing the expression level of endogenous sPML. Of four sPML isoforms cloned and examined, only isoform sPML-II/IIa, not sPML-I and IVa, expressed in a sPML knockout cells inhibits PRV infection. Both the unique 7b region of sPML-II and sumoylation-dependent normal formation of PML-NBs are required. 7b possesses a transcriptional repression activity and suppresses viral gene transcription during PRV infection with the cysteine residue 589 and 599 being critically involved. We conclude that sPML-NBs inhibit PRV infection by repressing viral gene transcription through the 7b region of sPML-II. IMPORTANCEPML-NBs are nuclear sites that mediate the antiviral restriction of -herpesvirus gene expression and replication. However, the contrition of each PML isoform to this activity of PML-NBs is not well characterized. Using PRV and its natural host swine cells as a system, we have discovered that the unique C-terminus of sPML isoform II is required for PML-NBs to inhibit PRV infection by directly engaging in repression of viral gene transcription. Our study not only confirms in swine cells that PML-NBs have an anti-viral function, but also presents a mechanism to suggest that PML-NBs inhibit viral infection in an isoform specific manner.

immunology↗

Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning

Recent experimental advances have enabled high-throughput single-cell measurement of gene expression, chromatin accessibility and DNA methylation. We previously used integrative non-negative matrix factorization (iNMF) to jointly learn interpretable low-dimensional representations from multiple single-cell datasets using dataset-specific and shared metagene factors. These factors provide a principled, quantitative definition of cellular identity and how it varies across biological contexts. However, datasets exceeding 1 million cells are now widely available, creating computational barriers to scientific discovery. For instance, it is no longer feasible to analyze large datasets using standard pipelines on a personal computer with limited memory capacity. Moreover, there is a need for an algorithm capable of iteratively refining the definition of cellular identity as efforts to create a comprehensive human cell atlas continually sequence new cells. To address these challenges, we developed an online learning algorithm for integrating large and continually arriving single-cell datasets. We extended previous online learning approaches for NMF to minimize the expected cost of a surrogate function for the iNMF objective. We also derived a novel hierarchical alternating least squares algorithm for iNMF and incorporated it into an efficient online algorithm. Our online approach accesses the training data as mini-batches, decoupling memory usage from dataset size and allowing on-the-fly incorporation of new datasets as they are generated. The online implementation of iNMF converges much more quickly using a fraction of the memory required for the batch implementation, without sacrificing solution quality. Our new approach processes 1.3 million single cells from the entire mouse embryo on a laptop in 25 minutes using less than 500 MB of RAM. We also analyze large datasets without downloading them to disk by streaming them over the internet on demand. Furthermore, we construct a single-cell multi-omic cell atlas of the mouse motor cortex by iteratively incorporating eight single-cell RNA-seq, single-nucleus RNA-seq, single-nucleus ATAC-seq, and single-nucleus DNA methylation datasets generated by the BRAIN Initiative Cell Census Network. Our approach obviates the need to recompute results each time additional cells are sequenced, dramatically increases convergence speed, and allows processing of datasets too large to fit in memory or on disk. Most importantly, it facilitates continual refinement of cell identity as new single-cell datasets from different biological contexts and data modalities are generated.

bioinformatics↗

Map3k2-Regulated Intestinal Stromal Cells (MRISC) Define a Distinct Sub-cryptic Stem Cell Niche for Damage Induced Wnt Agonist R-spondin1 Production

Intestinal stem cell propagation and differentiation are essential for rapid repair of tissue damage in the gut. While intestinal stromal cells were recently identified as key mediators of this process, the cellular and molecular mechanisms by which this diverse population induces tissue repair remains poorly understood. Here we show that Map3k2 has a colon stromal cell specific function critically required for maintenance of Lgr5+ intestinal stem cells and protection against acute intestinal damage. This Map3k2-specific function is mediated by enhancing Wnt agonist R-spondin1 production. We further reveal a unique novel cell population, named Map3k2-regulated intestinal stromal cells (MRISC), as the primary cellular source of R-spondin1 following intestinal injury. Together, our data identify a novel intestinal stem cell niche organized by MRISC, which specifically dependent on the Map3k2-signaling pathway to augment the production of Wnt agonist R-spondin1 and promote regeneration of the acutely damaged intestine.\n\nHighlightsO_LIMap3k2 protects mice from DSS-induced colitis by promoting intestinal stem cell regeneration.\nC_LIO_LIMap3k2-MAPK pathway cross-talks with Wnt signaling pathway via upregulation of R-spondin1.\nC_LIO_LIMap3k2-Regulated Intestinal Stromal Cells (MRISC) marked by co-expression of CD90, CD34 and CD81 defines a novel colonic stem cell niche.\nC_LI

cell biology↗

Peroxiredoxin promotes longevity and H2O2-resistance in yeast through redox-modification of PKA

Peroxiredoxins are H2O2 scavenging enzymes that also carry H2O2 signaling and chaperone functions. In yeast, the major cytosolic peroxiredoxin, Tsa1 is required for both promoting resistance to H2O2 and extending lifespan upon caloric restriction. We show here that Tsa1 effects both these functions not by scavenging H2O2, but by repressing the nutrient signaling Ras-cAMP-PKA pathway at the level of the protein kinase A (PKA) enzyme. Tsa1 stimulates sulfenylation of cysteines in the PKA catalytic subunit by H2O2 and a significant proportion of the catalytic subunits are glutathionylated on two cysteine residues. Redox modification of the conserved Cys243 inhibits the phosphorylation of a conserved Thr241 in the kinase activation loop and enzyme activity, and preventing Thr241 phosphorylation can overcome the H2O2 sensitivity of Tsa1-deficient cells. Results support a model of aging where nutrient signaling pathways constitute hubs integrating information from multiple aging-related conduits, including a peroxiredoxin-dependent response to H2O2.

biochemistry↗

Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis

Aberrant chromatin structure is a hallmark in cancer cells and has long been used for clinical diagnosis of cancer. However, underlying higher-order chromatin folding during malignant transformation remains elusive, due to the lack of molecular scale resolution. Using optimized stochastic optical reconstruction microscopy (STORM) for pathological tissue (PathSTORM), we uncovered a gradual decompaction and fragmented higher-order chromatin folding throughout all stages of carcinogenesis in multiple tumor types, even prior to the tumor formation. Our integrated imaging, genomic, and transcriptomic analyses reveal the functional consequences in enhanced formation of transcription factories, spatial juxtaposition with relaxed nanosized chromatin domains and impaired genomic stability. We also demonstrate the potential of imaging higher-order chromatin decompaction to detect high-risk precursors that cannot be distinguished by conventional pathology. Taken together, our findings reveal the gradual decompaction and fragmentation of higher-order chromatin structure as an enabling characteristic in early carcinogenesis to facilitate malignant transformation, which may improve cancer diagnosis, risk stratification, and prevention.\n\nSIGNIFICANCEGenomic DNA is folded into a higher-order structure that regulates transcription and maintains genomic stability. Although much progress has been made on understanding biochemical characteristics of epigenetic modifications in cancer, the higher-order folding of chromatin structure remains largely unknown. Using optimized super-resolution microscopy, we uncover de-compacted and fragmented chromatin folding in tumor initiation and stepwise progression in multiple tumor types, even prior to the presence of tumor cells. This study underlines the significance of unfolding higher-order chromatin structure as an enabling characteristic to promote tumorigenesis, which may facilitate the development and evaluation of new preventive strategies. The potential of imaging higher-order chromatin folding to improve cancer detection and risk stratification is demonstrated by detecting high-risk precursors that cannot be distinguished by conventional pathology.

cancer biology↗

Is asthma associated with exposure to smoke from a coal mine fire?

In 2014, a fire at the Hazelwood open cut coal mine (Victoria, Australia) burned for about 6 weeks. Residents of the adjacent town of Morwell were exposed to high levels of fine particulate matter (PM2.5) during this period. Three and a half years after the event, this study aimed to investigate the long-term impact of short-term exposure to coal mine fire smoke on asthma.\n\nA cross-sectional analysis was undertaken on a group of exposed participants with asthma from Morwell (n=165) and a group of unexposed participants with asthma from the control town of Sale (n=64). Town exposure status was determined by modelled PM2.5 data for the mine fire period. Respiratory symptoms were assessed with a validated respiratory health questionnaire and symptom severity score. Asthma control was assessed with an asthma control questionnaire. Lung function testing included spirometry, bronchodilator response, and fraction of exhaled nitric oxide.\n\nThere was no evidence that exposed Morwell participants had more severe asthma symptoms, worse lung function, or more eosinophilic airway inflammation compared to unexposed Sale participants. However there was some evidence that Morwell participants had more uncontrolled than well-controlled asthma, compared to the participants from Sale (adjusted relative risk ratio 2.71 95%CI: 1.02, 7.21, p=0.046).\n\nThree and a half years after exposure, coal mine fire smoke does not appear to be associated with more severe asthma symptoms or worse lung function, but may be associated with poorer asthma control.\n\nSummary take home messageIn people with asthma, short-term coal mine fire smoke exposure does not appear to have long-term impact on severity of asthma symptoms, lung function or eosinophilic airway inflammation, but may affect asthma control.

epidemiology↗

Discovery of functional alternatively spliced PKM transcripts in human cancers

The association of pyruvate kinase muscle type (PKM) with survival of cancer patients is controversial. Here, we focus on different transcripts of PKM and investigate the association between their mRNA expression and the clinical survival of the patients in 25 different cancers. We find that the transcript encoding PKM2, and three other functional transcripts are prognostic in multiple cancers. Our integrative analysis shows that the functions of these four transcripts are highly conservative in different cancers. Next, we validate the prognostic effect of these transcripts in an independent kidney renal clear-cell carcinoma (KIRC) cohort and identify a prognostic signature which could distinguish high- and low-risk KIRC patients. Finally, we reveal the functional role of alternatively spliced PKM transcripts in KIRC, and discover the protein products of different transcripts of PKM. Our analysis demonstrated that alternatively spliced transcripts of not only PKM but also other genes should be considered in cancer studies, since it may enable the discovery and targeting of the right protein product for development of the efficient treatment strategies.

systems biology↗

Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica

Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. Despite its enormous industrial, cultural and medicinal values, the chloroplast (cp) and mitochondrial (mt) genomes are not available for Camellia sinensis var. assamica. In this study, we de novo assembled the cp genome sequence of C. sinensis var. assamica into a circular contig of 157,100 bp in length with an overall GC content of 37.29%, comprising a large single-copy region (LSC, 86,649 bp) and a small single-copy region (SSC, 18,285 bp) separated by a pair of inverted repeats (IRs, 26,083 bp). We annotated a total of 141 cp genes, of which 87 are protein-coding genes, 46 are tRNA genes, and eight are rRNA genes. We also de novo assembled the mt genome of C. sinensis var. assamica into two complete circular scaffolds (702,253 bp and 178,082 bp) with overall GC contents of 45.63% and 45.81%, respectively. We annotated a total of 71 mt genes, including 44 protein-coding genes, 24 tRNAs, and 3 rRNAs. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are [~]4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an invaluable resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

genomics↗

Urinary AQP5 is independently associated with eGFR decline in patients with type 2 diabetes and nephropathy

AQP5 has been shown to be upregulated in kidney biopsies from patients with diabetic nephropathy. Here we investigate whether urinary baseline AQP5 is independently associated with eGFR decline in patients with type 2 diabetes and nephropathy. Baseline urine samples (n=997) from patients with type 2 diabetes and nephropathy recruited in the Sun-MACRO randomized placebo controlled double blind clinical trial were used for AQP5 measurement, using human AQP5-specific enzyme linked immunosorbent kits. Pearson correlation and multiple linear regression between AQP5 with eGFR slope (calculated by [&ge;]3 serum creatinine during followup) was performed, and association with fast renal function decline, defined as eGFR slope less than 3.0 mL/min/1.73m2/year, was determined by logistic regression. Followup eGFR data over 1.4 years from n=700 were available for analysis. AQP5 was undetectable in 138 patients. Tertiles of AQP5 were 0.4 [0 - 2.2], 7.3 [5.9 - 9.1], and 16.0 [13.0 - 21.6] (ng/mL), respectively (p<0.01). Patients in the highest tertile of AQP5 had significantly higher total cholesterol, lower baseline eGFR, and higher levels of albuminuria compared to the lowest tertile. AQP5 was inversely correlated with eGFR slope (Pearson r = -0.12, p<0.001), and independent of clinical risk factors age, sex, race, and baseline SBP, DBP, HbA1c, Tot. Cholesterol, eGFR, and UACR ({beta} = -0.05, p<0.004). Furthermore, AQP5 was significantly associated with fast eGFR decline (OR = 1.03 (95%CI 1.003 - 1.06), p<0.03). Our data suggest that baseline AQP5 is independently associated with the progression of eGFR decline in patients with type 2 diabetes and nephropathy.

physiology↗

Susceptibility of Spotted Doves (Streptopelia chinensis) to Experimental Infection with the SFTS Phlebovirus

BackgroundSevere fever with thrombocytopenia syndrome virus (SFTSV), an emerging human pathogen naturally transmitted by ticks, has spread widely during the last few years. Although SFTSV has been detected in wild birds, the natural reservoir and amplifying hosts for the virus have not been well-studied.\n\nMethodology/Principle FindingsHere we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14 (hereafter JS2010), a Chinese lineage strain and JS2014-16 (JS2014) from a Japanese lineage, which represent the main viral genotypes currently circulating in East Asia. We determined that spotted doves were susceptible to SFTSV and the severity of the viremia was dose-dependent. When challenged with 107 and 105 PFU, all doves developed viremia which peaked 3-5 days post-infection (dpi). A subset (25-62.5%) of the birds challenged at 103 PFU, developed viremia. Virulence of SFTSV in spotted doves appeared to be strain-dependent. Infection with the strain of JS2014 led to a death rate of 12.5% and higher viremia titers in experimentally inoculated birds. The doves inoculated with the JS2010 strain survived infection with relatively lower virus titers in the blood.\n\nConclusions/SignificanceOur results suggest that spotted doves, one of the most abundant bird species in China, could be a competent amplifying host of SFTSV, the strain of the Japanese lineage in particular, with higher viremia titers and play an important role in the transmission of SFTSV. Our observations shed light on the ecology of SFTSV which could benefit the implementation of future surveillance and control programs.\n\nAuthor SummarySevere fever with thrombocytopenia syndrome virus (SFTSV), an emerging human pathogen naturally transmitted by ticks. Our recent study have showed that some species of migratory birds, such as swan geese and spotted doves, could be parasitized by H. longicornis, and antibodies against the virus could also be determined in these birds, which showed that migratory birds could be infected by SFTSV naturally. Other studies have reported that migratory bird routes and the distribution of H. longicornis in East Asia overlap with the geographic distribution of SFTSV. Migratory birds are known to be carriers and transmitters of infectious agents, like the causative agents of influenza, West Nile encephalitis, and Lyme disease. Wild birds often travel long distances carrying various parasites, including ticks, which may be infected with viruses and bacteria. It is therefore reasonable to hypothesize that migratory birds may have played an important role in dispersing H. longicornis-borne SFTSV in both scenarios, either the birds are infected directly with the virus or the birds are carriers of parasitic ticks that are infected with the virus. Here we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14 (hereafter JS2010), a Chinese lineage strain and JS2014-16 (JS2014) from a Japanese lineage, which represent the main viral genotypes currently circulating in East Asia. We determined that spotted doves were susceptible to SFTSV and the severity of the viremia was dose-dependent.\n\nInterestingly, virulence of SFTSV in spotted doves appeared to be strain-dependent. Infection with the strain of JS2014 led to a death rate of 12.5% and higher viremia titers in experimentally inoculated birds. The doves inoculated with the JS2010 strain survived infection with relatively lower virus titers in the blood. These findings provide novel insights for understanding the rapid spread of the virus in a short time span, especially the SFTSV strains from the Japanese lineage (genotype E), which presented cross ocean transmission.

microbiology↗

Molecular basis of Cul3 ubiquitin ligase subversion by vaccinia virus protein A55

BTB-Kelch proteins are substrate-specific adaptors for cullin-3 (Cul3) RING-box based E3 ubiquitin ligases, which mediate protein ubiquitylation leading to proteasomal degradation. Vaccinia virus encodes three BTB-Kelch proteins, namely A55, C2 and F3. Viruses lacking A55 or C2 demonstrate altered cytopathic effect in cultured cells and altered pathology in vivo. Previous studies show that the ectromelia virus orthologue of A55, EVM150, interacts with Cul3 in cells. We show that A55 binds directly to Cul3 via its N-terminal BTB-BACK domain, and together they form a 2:2 complex in solution. The crystal structure of the A55/Cul3 complex was solved to 2.8 [A] resolution. The overall conformation and binding interfaces resemble those of the cellular BTB-BACK/Cul3 complex structures, despite low sequence similarity of A55 to cellular BTB-BACK proteins. Surprisingly, despite this structural similarity the affinity of Cul3 for A55 is significantly higher than for reported cellular BTB-BACK proteins. Detailed analysis of the binding interface suggests that I48 from A55 at the BTB/Cul3 interface is important for this high-affinity interaction and mutation at this site reduced the affinity by several orders of magnitude. I48 is conserved only in close orthologues of A55 from poxviruses, but not in C2, F3, or other poxvirus or cellular BTB-Kelch proteins. The high affinity interaction between A55 and Cul3 suggests that, in addition to directing the Cul3-RING E3 ligase complex to degrade cellular/viral target proteins that are normally unaffected, A55 may also sequester Cul3 from cellular adaptor proteins and thus protect substrates of these cellular adaptors from ubiquitination and degradation.

biochemistry↗

Metagenomic characterization of the viral community of the South Scotia Ridge

Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous genetic diversity. While their great influence on the marine ecosystems is widely acknowledged, current information about their diversity remains scarce. Aviral metagenomic analysis of two surfaces and one bottom water sample was conducted from sites on the South Scotia Ridge (SSR) near the Antarctic Peninsula, during the austral summer 2016. The taxonomic composition and diversity of the viral communities were investigated and a functional assessment of the sequences was determined. Phylotypic analysis showed that most viruses belonging to the order Caudovirales, in particular, the family Podoviridae (41.92-48.7%), which is similar to the viral communities from the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many of the sequences associated with Caudovirales and NCLDV were novel and distinct from known complete phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found in SSR area and complete and partial Pgvv-like were obtained which may have an influence on host-virus interactions in the area during summer. Our study expands the existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.\n\nImportanceIn this study, we used high-throughput sequencing and bioinformatics analysis to analyze the viral community structure and biodiversity of SSR in the open sea near the Antarctic Peninsula. The results showed that the SSR viromes are novel, oceanic-related viromes and a high proportion of sequence reads was classified as unknown. Among known virus counterparts, members of the order Caudovirales were most abundant which is consistent with viromes from the Pacific Ocean. In addition, phylogenetic analyses based on the viral marker genes (TerL and MCP) illustrate the high diversity among Caudovirales and NCLDV. Combining deep sequencing and a random subsampling assembly approach, a new Pgvv-like group was also found in this region, which may a signification factor regulating virus-host interactions.

microbiology↗

Genome-wide characterization, evolutionary analysis of WRKY genes in Cucurbitaceae species and assessment of its roles in resisting to powdery mildew disease

The WRKY proteins constitute a large family of transcription factors that have been known to play a wide range of regulatory roles in multiple biological processes. Over the past few years, many reports have focused on analysis of evolution and biological function of WRKY genes at the whole genome level in different plant species. However, little information is known about WRKY genes in melon (Cucumis melo L.). In the present study, a total of 56 putative WRKY genes were identified in melon, which were randomly distributed on their respective chromosomes. A multiple sequence alignment and phylogenetic analysis using melon, cucumber and watermelon predicted WRKY domains indicated that melon WRKY proteins could be classified into three main groups (I-III). Our analysis indicated that no recent duplication events of WRKY genes were detected in melon, and strong purifying selection was observed among the 85 orthologous pairs of Cucurbitaceae species. Expression profiles of CmWRKY derived from RNA-seq data and quantitative RT-PCR (qRT-PCR) analyses showed distinct expression patterns in various tissues, and the expression of 16 CmWRKY were altered following powdery mildew infection in melon. Besides, we also found that a total of 24 WRKY genes were co-expressed with 11 VQ family genes in melon. Our comparative genomic analysis provides a foundation for future functional dissection and understanding the evolution of WRKY genes in cucurbitaceae species, and will promote powdery mildew resistance study in melon.

plant biology↗