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Usutu virus (USUV) is an emerging mosquito-transmitted flavivirus with increasing incidence of human infection and geographic expansion, thus posing a potential threat to public health. In this study, we established a comprehensive spatiotemporal database encompassing USUV infections in vectors, animals, and humans worldwide by an extensive literature search. Based on this database, we characterized the geographic distribution and epidemiological features of USUV infections. By employing boosted regression tree (BRT) models, we projected the distributions of three main vectors (Culex pipiens, Aedes albopictus, and Culiseta longiareolata) and three main hosts (Turdus merula, Passer domesticus, and Ardea cinerea) to obtain the mosquito index and bird index. These indices were further incorporated as predictors into the USUV infection models. Through an ensemble learning model, we achieved a decent model performance, with an area under the curve (AUC) of 0.992. The mosquito index contributed significantly, with relative contributions estimated at 25.51%. Our estimations revealed a potential exposure area for USUV spanning 1.80 million km2 globally with approximately 1.04 billion people at risk. This can guide future surveillance efforts for USUV infections, especially for countries located within high-risk areas and those that have not yet conducted surveillance activities.

Background: California hare coltivirus (CHCV) was isolated in California in 1976 from a hare. Despite its long history, it remained unclear whether CHCV was exclusively distributed in California with limited host ranges. Main body: By next-generation sequencing (NGS), we obtained a complete sequence of CHCV from Ixodes persulcatus collected in 2019 in northeast China. An expanded epidemiological investigation was subsequently performed on ticks belonging to four species (Ix. persulcatus, Haemaphysalis concinna, Devmacentor silvarum, Haemaphysalis longicornis) collected in northeastern China by applying CHCV-specific RT-PCR and sequencing. CHCV RNA-positive results were found in 1.56% of the tick samples. Positive ticks were obtained in three of four sampled locations, with the highest rate observed in Inner Mongolia (2.69%), followed by Heilongjiang (1.94%) and Jilin provinces (0.55%). All positive results were derived from Ix. persulcatus ticks (2.33%), while no positive detection was found in the other tick species, even at the same location. Sequence analysis revealed that the current CHCV showed a high genetic identity (>80% amino acid identity) with the previously reported CHCV in all segments except segment seven (64.59% amino acid identity). Phylogenetic analysis based on RNA-dependent RNA polymerase (RdRp) amino acid sequences demonstrated that both the current and previously reported CHCV strains were grouped phylogenetically into the genus Coltivirus. Both CHCV strains formed a distinct clade, clustering with three human pathogenic coltiviruses (Colorado tick fever virus, Salmon River virus, and Eyach virus), and were distant from the other coltiviruses. Conclusions: We report the identification and characterization of CHCV for the first time in Ix. persulcatus ticks, expanding the currently known geographic scope, host, and genetic heterogeneity in CHCV.

ABSTRACT As an essential component of host defense against infection, necroptosis is a novel highly regulated mode of cell death that is mediated by signaling complexes containing receptor-interacting protein kinase 1 (RIPK1) and RIPK3. Lymphocyte depletion and immunosuppression are typical clinical features of pigs infected with classical swine fever virus (CSFV). Here, we provide the first evidence for the involvement of necroptosis in the necrosis of T lymphocytes in the spleen and peripheral blood of pigs infected in vivo with CSFV. However, it is true for some viruses with non-cytopathic effects, including CSFV, to balance host defense against infection. In vitro, the induction of autophagy by CSFV at a later stage of infection clearly restricts necroptosis. Mechanistic studies revealed that CSFV NS4A protein promoted tripartite motif-containing 25 expression, synergistically induced the occurrence of mitophagy, targeted the autophagic degradation of RIPK3 to block the progression of necroptosis occurrence, and achieved persistent viral infection. Interestingly, we found that RIPK3 was able to specifically localize at the outer mitochondrial membrane, and the autophagy receptor NDP52 was most likely involved in the autophagic degradation of RIPK3 during CSFV infection. Our findings provide evidence supporting that the CSFV-induced autophagy pathway plays an important role in counteracting host cell necrosis, enriching our knowledge of pathogens that may subvert and evade necroptosis this host defense, and shedding new light on understanding the mechanisms of T lymphocyte exhaustion and immunosuppression during CSFV infection. IMPORTANCE CSFV infection in pigs causes persistent high fever, hemorrhagic necrotizing multi-organ inflammation, and high mortality, which seriously threatens the global swine industry. Cell death is an essential immune response of the host against pathogen invasion, and lymphopenia is the most typical clinical feature in the acute phase of CSFV infection, which affects the initial host antiviral immunity. As an “old” virus, CSFV has evolved mechanisms to evade host immune response after a long genetic evolution. Here, we show that necroptosis is a limiting host factor for CSFV infection and that CSFV-induced autophagy can subvert this host defense mechanism to promote its sustained replication. Our findings reveal a complex link between necroptosis and autophagy in the process of cell death, provide evidence supporting the important role for CSFV in counteracting host cell necrosis, and enrich our knowledge of pathogens that may subvert and evade this host defense.

Pseudorabies is a hot infectious disease, which can cause fever, encephalomyelitis, multiple organ failure, paralysis and other symptoms in infected animals. The pathogen of the disease is enveloped DNA virus, and pig is the only natural repository, which has strong resistance to the host and can attack the nervous system of the host. The prevalence of pseudorabies seriously harms the pig industry in China, therefore, it is listed among the diseases that need priority control and purification in China. At present, one of the main prevention and control measures against pseudorabies in pigs is vaccination. However, the virus is prone to mutate to produce new strains, which leads to the decline of the immune effect of the vaccine, and difficult to provide complete protection. Therefore, it is very important to find and develop new drugs as substitutes for the prevention and control of pseudorabies. There are many natural active ingredients in plant extracts, such as polyphenols, polysaccharides, alkaloids, and etc. These ingredients not only have antibacterial activity, antioxidant properties and antitoxin properties, but also have certain therapeutic effects on animal diseases. These active ingredients possess the advantages of multifunction and less side effects, which can effectively guarantee the safety of pig breeding and production. In the study, the active components of plant extracts are briefly summarized, the antiviral effects of different active components of plant extracts on pseudorabies virus are emphatically summarized, and the application prospects are discussed in order to provide references for the research and development of novel plant drugs.

Flow cytometry is a biological technique for counting and sorting out tiny particles suspended in fluid based on flow cytometer through the detection of scattering or coupled fluorescence signals to obtain a series of important biophysical and biochemical related characteristics of suspended particles (usually cells, bacteria and other tiny particles) in a quick, accurate, objective and high-throughput way, and to automatically analyze and sort out specific populations according to the pre-selected parameter range of cells, bacteria and other tiny particles. Flow cytometry is widely used in many scientific fields, especially biotechnology and medicine. Although the application of flow cytometry in agricultural research started relatively late, great progress has been made. With the continuous improvement of the performance of flow cytometer, the continuous development and improvement of labeling methods and detection technologies, the application prospect of flow cytometry will become wider, and it will also play an increasingly important role in the agricultural field. In this review, it introduces the working principle and functional classification of flow cytometer, discusses the application and research progress of flow cytometry in agricultural fields such as crop genome and protoplast analysis, stress resistance research, animal immunity and trace element analysis, sperm quality and sex control, toxin toxicity analysis, pathogenic bacteria and virus analysis, and then looks forward to the development prospect of this research field, providing a new direction for the potential application of flow cytometry in agricultural fields.

The H3N8 influenza virus is known to circulate in wild birds but cross-species transmission to mammalian hosts was also reported. In this case study, the authors report human infection with a reassortment avian influenza A H3N8 virus in a four-year old boy that developed severe symptoms.

Sweet orange ‘Newhall’ (C. sinensis) is a popular fruit in high demand all over the world. Its peel and pulp are rich in a variety of nutrients and are widely used in catering, medicine, food and other industries. Grafting is commonly practiced in citrus production. Different rootstock types directly affect the fruit quality and nutritional flavor of citrus. However, the studies on citrus metabolites by grafting with different rootstocks are very limited, especially for amino acids (AAs). The preliminary test showed that there were significant differences in total amino acid content of two rootstocks (Poncirus trifoliata (CT) and C. junos Siebold ex Tanaka (CJ)) after grafting, and total amino acid content in the peel was higher than flesh. However, the molecular mechanism affecting amino acid differential accumulation remains unclear. Therefore, this study selected peel as the experimental material to reveal the amino acid components and differential accumulation mechanism of sweet orange ‘Newhall’ grafted with different rootstocks through combined transcriptome and metabolome analysis. Metabolome analysis identified 110 amino acids (AAs) and their derivatives in sweet orange ‘Newhall’ peels, with L-valine being the most abundant. L-asparagine was observed to be affected by both developmental periods and rootstock grafting. Weighted gene co-expression network analysis (WGCNA) combined with Redundancy Analysis (RDA) revealed eight hub structural genes and 41 transcription factors (TFs) that significantly influenced amino acid biosynthesis in sweet orange ‘Newhall’ peels. Our findings further highlight the significance of rootstock selection in enhancing the nutritional value of citrus fruits and might contribute to the development of functional citrus foods and nutritional amino acid supplements.

A comprehensive profiling of the vaginal microbial communities and their variability enables an accurate description of the microbiome in women. However, there is a lack of studies available on Chinese women. In the present study, the composition of the vaginal microbiota during pregnancy and the 6-week postpartum period of 454 Chinese women was characterized by sequencing the V3–V4 region of the 16S ribosomal RNA (rRNA) gene. The vaginal microbiome showed variations during pregnancy and the postpartum period based on the abortion history, hypertensive disorders, delivery mode, and maternal age. Co-variation of 22 bacterial taxa, including the Lactobacillus genus and two of its species, may account for the common characteristics of the vaginal microbiome under scenarios of different medical histories and pregnancy outcomes. In contrast, discriminant bacterial species were significantly different between women who had preterm birth (PTB) with and without premature rupture of membranes (PROM), and the community state type (CST) IV-A without any predominant Lactobacillus species in the microbiota was more prevalent during pregnancy in the PROM-PTB cases, suggesting that specific bacterial species could be considered to distinguish between different types of PTB. By providing data on Chinese women, this study will enrich the knowledge of the human microbiome and contribute to a better understanding of the association between the vaginal microbiome and reproductive health.

Mudanjiang phlebovirus (MJPV) is a newly discovered phlebovirus, initially detected from Ixodes persulcatus ticks in China in 2022. In this study, by next-generation sequencing (NGS) on a wide variety of ticks and wild small animals in China, we detected MJPV from I. persulcatus and Meriones meridianus. Additionally, we conducted RT-PCR and sequencing on 1815 adult ticks and 805 wild small mammals collected from eight provinces in China between 2017 and 2021. MJPV RNA-positive results were found in 0.22% (4/1815) of tick samples, as well as in 0.12% (1/805) of rodent samples. All positive detections were obtained from Heilongjiang and Inner Mongolia. Sequencing analysis revealed nucleotide similarities ranging from 98.23% to 99.11%, as well as amino acid similarities ranging from 99.12% to100%, between the current MJPV strain and previously reported strains of MJPV. Phylogenetic tree analysis demonstrated that the previously reported MJPV strain along with our two variants clustered together with other tick-borne phenuiviruses, indicating their close relationship within this viral group. This study represents the first detection of MJPV infection in wild rodents, expanding the known host range for this virus in the endemic regions.

ABSTRACT Campylobacter is the leading bacterial cause of diarrheal illnesses worldwide. Campylobacter jejuni and C. coli are the most common species accounting for campylobacteriosis. Although the proportion of campylobacteriosis caused by C. coli is increasing rapidly in China, the underlying mechanisms of this emergence remain unclear. In this study, we analyzed the whole-genome sequences and associated environments of 1,195 C. coli isolates with human, poultry, or porcine origins from 1980 to 2021. C. coli isolates of human origin were closely related to those from poultry, suggesting that poultry was the main source of C. coli infection in humans. Analysis of antimicrobial resistance determinants indicated that the prevalence of multidrug-resistant C. coli has increased dramatically since the 2010s, coinciding with the shift in abundance from C. jejuni to C. coli in Chinese poultry. Compared with C. jejuni, drug-resistant C. coli strains were better adapted and showed increased proliferation in the poultry production environment, where multiple antimicrobial agents were frequently used. This study provides an empirical basis for the molecular mechanisms that have enabled C. coli to become the dominant Campylobacter species in poultry; we also emphasize the importance of poultry products as sources of campylobacteriosis caused by C. coli in human patients. IMPORTANCE The proportion of campylobacteriosis caused by C. coli is increasing rapidly in China. Coincidentally, the dominant species of Campylobacter occurring in poultry products has shifted from C. jejuni to C. coli. Here, we analyzed the whole-genome sequences of 1,195 C. coli isolates from different origins. The phylogenetic relationship among C. coli isolates suggests that poultry was the main source of C. coli infection in humans. Further analysis indicated that antimicrobial resistance in C. coli strains has increased dramatically since the 2010s, which could facilitate their adaptation in the poultry production environment, where multiple antimicrobial agents are frequently used. Thus, our findings suggest that the judicious use of antimicrobial agents could mitigate the emergence of multidrug-resistant C. coli strains and enhance clinical outcomes by restoring drug sensitivity in Campylobacter.

Abstract Antibody-dependent cellular cytotoxicity (ADCC) responses to viral infection are a form of antibody regulated immune responses mediated through the Fc fragment. Whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggered ADCC responses contributes to COVID-19 disease development is currently not well understood. To understand the potential correlation between ADCC responses and COVID-19 disease development, we analyzed the ADCC activity and neutralizing antibody response in 255 individuals ranging from asymptomatic to fatal infections over 1 year post disease. ADCC was elicited by 10 days post-infection, peaked by 11–20 days, and remained detectable until 400 days post-infection. In general, patients with severe disease had higher ADCC activities. Notably, patients who had severe disease and recovered had higher ADCC activities than patients who had severe disease and deceased. Importantly, ADCC activities were mediated by a diversity of epitopes in SARS-COV-2-infected mice and induced to comparable levels against SARS-CoV-2 variants of concern (VOCs) (B.1.1.7, B.1.351, and P.1) as that against the D614G mutant in human patients and vaccinated mice. Our study indicates anti-SARS-CoV-2 ADCC as a major trait of COVID-19 patients with various conditions, which can be applied to estimate the extra-neutralization level against COVID-19, especially lethal COVID-19.

Abstract Background In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported. Results In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. Conclusions To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.

Listeria monocytogenes is a foodborne human pathogen that affects public health worldwide. Whole-genome sequencing (WGS) can classify L. monocytogenes isolates and identify virulence islands and resistance genes potentially influencing infectivity. Herein, WGS was used to assess 151 L. monocytogenes isolates from 120 cases of clinical infection in Beijing, China, between 2014 and 2018. Most isolates were either serogroup 1/2a,3a or serogroup 1/2b,3b,7, with 25 multilocus sequence typing (MLST) types (STs) represented, of which ST8, ST87, and ST5 were the most common. Core-genome MLST (cgMLST) grouped the 151 isolates into 116 cgMLST types. The discriminatory power of cgMLST was greater than other subtypes, revealing that isolates from the same patient were highly related (only differing at one allele). Eighty-six isolates formed 30 complexes with ≤ 7 cgMLST alleles between neighboring isolates, suggesting possible outbreaks. Compared with isolates in the United States, ST8, ST121, ST619, ST87, and ST155 isolates were grouped into unified clades. All 151 isolates were positive for common virulence-associated loci, and 26 lineage I isolates harbored the pathogenicity island 3 (LIPI-3) locus, while 42 lineage I isolates harbored the complete LIPI-4 locus. Eleven ST619 isolates had both LIPI-3 and LIPI-4. Among the 151 isolates, 13 were resistant to at least one antibiotic, and no multidrug-resistant isolates were identified. Resistance phenotypes correlated with genotypes, apart from two meropenem resistance isolates. The findings provided insight into the nature of L. monocytogenes strains currently causing clinical disease in Beijing, and WGS analysis indicated possible outbreaks.

J paramyxovirus (JPV) is a rodent-borne Jeilongvirus isolated from moribund mice (Mus musculus) with hemorrhagic lung lesions trapped in the 1972 in northern Queensland, Australia. The JPV antibodies have been detected in wild mice, wild rats, pigs, and human populations in Australia. Here, by next-generation sequencing (NGS), we detected JPV from M. musculus in Shandong Province of China. Molecular detection of JPV was performed to survey to survey the infection among 66 species of wild small mammals collected from six eco-climate regions in China by applying JPV specific RT-PCR and sequencing. Altogether, 21 out of 3070 (0.68%) wild small mammals of four species were positive for JPV, including 5.26% (1/19) of Microtus fortis, 3.76% (17/452) of M. musculus, 1.67% (1/60) of Apodemus peninsulae, and 0.48% (2/421) of Apodemus agrarius, which captured three eco-climate regions of China (northeastern China, northern China, and Inner Mongolia-Xinjiang). Sequence analysis revealed the currently identified JPV was clustered with other 14 Jeilongvirus members, and shared 80.2% and 89.2% identity with Australia’s JPV partial RNA polymerase (L) and glycoprotein (G) genes, respectively. Phylogenetic analysis demonstrated the separation of three lineages of the current JPV sequences. Our results show three new hosts (A. agrarius, A. peninsulae, and M. fortis) for JPV, most of which were widely distributed in China, and highlight the potential zoonotic transmission of JPV in humans. The detection of JPV in wild small mammals in China broaden the viral diversity, geographical distribution, and reservoir types of JPV. Future studies should prioritize determining the epidemiological characteristics of JPV, so that potential risks can be mitigated.

Fruit aromas are composed of a complex mixture of volatile organic compounds, which are essential attributes associated with the overall flavor and consumer preference. Muscadine grape (MG; Vitis rotundifolia Michx.) is an aroma-dense fruit crop. However, there is very scarce information on its volatile profiles. In this study, the volatile constituents of five newly introduced MG cultivars, including Alachua, Carlos, Fry, Granny Val, and Noble, were profiled using headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC/MS) combined with multivariate statistical analysis. A total of 44 compounds, including esters, aldehydes, alcohols, fatty acids, terpenes, ketones, and furan, were identified and relatively quantified. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) evidently discriminated against the five MG cultivars based on their volatile profiles. The specific volatiles that contributed the most to this discrimination were highlighted. Geraniol and cinnamyl alcohol were demonstrated to be essential for characterizing the Alachua MG cultivar, whereas ethyl trans-2-butenoate and propyl acetate were shown to be important compounds to characterize the Noble MG cultivar. The results further showed that 2-Ethyl-1-hexanol, (Z)-3-hexenal, and (E)-2-hexenol were closely related to Carlos, Fry, and Granny Val cultivars, respectively. This investigation is the first in-depth exploration of the volatile profiles of the aroma-dense muscadine grape, which is essential for future genetic or biotechnological improvements to attain a cultivar with the desired flavor.

Campylobacter species are zoonotic pathogens and the leading cause of bacterial enteritis worldwide. With the increase of antimicrobial resistance to fluoroquinolones and macrolides, they have been identified by the World Health Organization (WHO) as high-priority antimicrobial-resistant pathogens. There is currently little known about the prevalence and antimicrobial resistance characteristics of Campylobacter species in Beijing. In this study, we performed a 2-year surveillance of Campylobacter in Beijing, China. We used multilocus sequence typing (MLST) and antimicrobial susceptibility testing to analyze 236 Campylobacter isolates recovered from 230 clinical infectious cases in Beijing between 2017 and 2018. The Campylobacter isolation rate in diarrhea patients was 7.81%, with higher isolation rates in male patients than female patients and in autumn compared with other seasons. We identified 125 sequence types (STs) of 23 cloning complexes (CCs) among the 236 isolates, including four new alleles and 19 new STs. The most commonly isolated STs of Campylobacter jejuni were ST-22 and ST-760 (4.50%), and the most commonly isolated ST of Campylobacter coli was ST-9227 (16.67%). We also compared our isolates with clinical Campylobacter isolates from other countries in Asia, CC-353 of Campylobacter coli was found in eight countries, CC-1034 and CC-1287 of Campylobacter coli were found only in China. All C. jejuni isolates were resistant to at least one antimicrobial. C. jejuni showed the highest rate of resistance toward ciprofloxacin (94.50%), followed by tetracycline (93.50%), and nalidixic acid (92.00%), while C. coli showed highest resistance toward ciprofloxacin (94.44%) and tetracycline (94.44%) followed by nalidixic acid (88.89%). The most commonly observed MDR combination of C. jejuni were quinolone, phenicol and tetracycline (11.50%), while the most commonly observed MDR combination of C. coli were macrolide, quinolone, phenicol, tetracycline and lincosamide (30.56%). Surveillance of molecular characterization will provide important information for prevention of Campylobacter infection. This study enhances insight into Campylobacter infections in diarrheal patients, with relevance for treatment regimens in Beijing.

Listeria monocytogenes is an important foodborne pathogen with a significant impact on public health worldwide. A great number of outbreaks caused by L. monocytogenes has been reported, especially in the United States, and European countries. However, listeriosis has not yet been included in notifiable disease in China, and thus information on this infection has been scarce among the Chinese population. In this study, we described a 3-year surveillance of listeriosis in Beijing, China. Fifty-six L. monocytogenes strains isolated from 49 clinical infectious cases (27 pregnancy-associated infections and 22 non-pregnancy-associated infections) were analyzed by serotyping, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and antimicrobial susceptibility testing between 2014 and 2016 in Beijing. The predominant serogroups were 1/2a,3a and 1/2b,3b,7 which accounted for 92% of the overall isolates. Four strains were serogroup 4b,4d,4e, isolated from patients with pregnancy-associated infections. Based on PFGE, these isolates were divided into 32 pulsotypes (PTs) and 3 clusters associated with serogroups. Ten PTs were represented by more than one isolate with PT09 containing the most number of isolates. MLST differentiated the isolates into 18 STs, without new ST designated. The three most common STs were ST8 (18.4%), ST5 (16.3%), and ST87 (12.2%), accounting for 46.9% of the isolates. STs prevalent in other parts of the world were also present in China such as ST1, ST2, ST5, ST8, and ST9 which caused maternal fetal infections or outbreaks. However, the STs and serogroup distribution of clinical L. monocytogenes in Beijing, China was different from those in other countries. Strains of ST1 and ST2 were isolated from patients with pregnancy-associated infection, whereas none of ST155 isolates caused pregnancy-associated cases. Surveillance of molecular characterization will provide important information for prevention of listeriosis. This study also enhances our understanding of genetic diversity of clinical L. monocytogenes in China.

Abstract Heparanase activity is involved in cancer growth and development in humans and single nucleotide polymorphisms (SNPs) in the heparanase gene (HPSE) have been shown to be associated with tumors. In this study, we investigated whether SNPs in HPSE were a risk factor for hepatocellular carcinoma (HCC) by undertaking a comprehensive haplotype-tagging, case-control study. For this, six haplotype-tagging SNPs (htSNPs) in HPSE were genotyped in 400 HCC patients and 480 controls by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. A log-additive model revealed significant correlations between the HPSE polymorphisms rs12331678 and rs12503843 and the risk of HCC in the overall samples (p = 0.0046 and p = 0.0055). When the analysis was stratified based on hepatitis B virus (HBV) carrier status, significant interactions between rs12331678 and rs12503843 and HBV were observed. Conditional logistic regression analysis for the independent effect of one significant SNP suggested that rs12331678 or rs12503843 contributed an independent effect to the significant association with the risk of HCC, respectively. Our findings suggest that the SNPs rs12331678 and rs12503843 are HCC risk factors, although the potential functional roles of these two SNPs remain to be fully elucidated.

Phosphatase and tensin homolog (PTEN), v-akt murine thymoma viral oncogene homolog 1 (AKT1), mouse double minute 2 (MDM2) and p53 play important roles in the development of cancer. We examined whether the single nucleotide polymorphisms (SNPs) in the PTEN, AKT1, MDM2 and p53 genes were related to the risk and severity of nasopharyngeal carcinoma (NPC) in the Chinese population. Seven SNPs [p53 rs1042522, PTEN rs11202592, AKT1 SNP1-5 (rs3803300, rs1130214, rs3730358, rs1130233 and rs2494732)] were genotyped in 593 NPC cases and 480 controls by PCR direct sequencing or PCR-RFLP analysis. Multivariate logistic regression analysis was used to calculate adjusted odds ratios (ORs) and 95% confidence intervals (CIs). None of the polymorphisms alone was associated with the risk or severity of NPC. However, haplotype analyses indicated that a two-SNP core haplotype (SNP4-5, AA) in AKT1 was associated with a significantly increased susceptibility to NPC risk (adjusted OR = 3.87, 95% CI = 1.96-7.65; P

FHL1 is an important tumor-suppressor that is downregulated in multiple tumors by unknown mechanisms. We demonstrated that miR-410 specifically targets the 3'UTR of FHL1. Furthermore, using DNA bisulfite modification and sequencing experiments, we demonstrated that the FHL1 promoter is hypermethylated in cancer cells. FHL1 methylation is increased upon miR-410 expression, suggesting that the regulation of FHL1 by miR-410 occurs by a dual mechanism. Using chromatin immunoprecipitation assays, we observed that miR-410 overexpression results in the increased binding of DNMT3A at the FHL1 promoter, which could explain how miR-410 regulates FHL1 methylation. Importantly, in vitro and in vivo results suggest that miR-410 may have oncogenic properties. Furthermore, both miR-410 and DNMT3A are upregulated in clinical human liver and colorectal tumors cancers. Our results suggest that miR-410 may function as an oncomiR and are consistent with its key function in regulating FHL1 in certain digestive system cancers.

Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis and hemolytic-uremic syndrome in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-Seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. One hundred and sixty eight chromosomal and pO157 genes were differentially expressed (≥2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant Xuzhou21m grew slower than wild type Xuzhou21 and pO157_Sal plasmid complemented strain Xuzhou21c in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-Seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. Through complementation of Xuzhou21m with a plasmid construct carrying the pO157_Sal hha homolog we further showed that the pO157_Sal hha represses the expression of T3SS effectors. These findings demonstrated that the plasmid pO157_Sal affects the transcription of the chromosomal and pO157 plasmid genes and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects the virulence and adaptation of E. coli O157:H7.

MicroRNAs have been implicated in the regulation of gene expression of various biological processes in a post-transcriptional manner under physiological and pathological conditions including host responses to viral infections. The 2009 pandemic H1N1 influenza virus is an emerging reassortant strain of swine, human and bird influenza virus that can cause mild to severe illness and even death. To further understand the molecular pathogenesis of the 2009 pandemic H1N1 influenza virus, we profiled cellular microRNAs of lungs from BALB/c mice infected with wild-type 2009 pandemic influenza virus A/Beijing/501/2009 (H1N1) (hereafter referred to as BJ501) and mouse-adapted influenza virus A/Puerto Rico/8/1934 (H1N1) (hereafter referred to as PR8) for comparison. Microarray analysis showed both the influenza virus BJ501 and PR8 infection induced strain- and temporal-specific microRNA expression patterns and that their infection caused a group of common and distinct differentially expressed microRNAs. Characteristically, more differentially expressed microRNAs were aroused on day 5 post infection than on day 2 and more up-regulated differentially expressed microRNAs were provoked than the down-regulated for both strains of influenza virus. Finally, 47 differentially expressed microRNAs were obtained for the infection of both strains of H1N1 influenza virus with 29 for influenza virus BJ501 and 43 for PR8. Among them, 15 microRNAs had no reported function, while 32 including miR-155 and miR-233 are known to play important roles in cancer, immunity and antiviral activity. Pathway enrichment analyses of the predicted targets revealed that the transforming growth factor-β (TGF-β) signaling pathway was the key cellular pathway associated with the differentially expressed miRNAs during influenza virus PR8 or BJ501 infection. To our knowledge, this is the first report of microRNA expression profiles of the 2009 pandemic H1N1 influenza virus in a mouse model, and our findings might offer novel therapy targets for influenza virus infection.

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a major foodborne pathogen causing hemorrhagic colitis and hemolytic-uremic syndrome. The role of EHEC O157:H7-enterohemolysin (Ehx) in the pathogenesis of infections remains poorly defined. In this study, we used gene deletion and complement methods to confirm its putative functions. Results demonstrated that, in THP-1 cells, EHEC O157:H7-Ehx is associated with greater production of extracellular interleukin (IL)-1β than other cytokines. The data also showed that EHEC O157:H7-Ehx contributed to cytotoxicity in THP-1 cells, causing the release of lactate dehydrogenase (LDH). Although we observed a positive correlation between IL-1β production and cytotoxicity in THP-1 cells infected with different EHEC O157:H7 strains, our immunoblot results showed that the majority of IL-1β in the supernatant was mature IL-1β and not the pro-IL-1β that can be released after cell death. However, EHEC O157:H7-Ehx had no detectable effect on biologically inactive pro-IL-1β at the mRNA or protein synthesis levels. Neither did it affect the expression of apoptosis-associated speck-like protein containing a CARD (ASC), caspase-1, or NOD-like receptor family pyrin domain containing 3 (NLRP3). RNA interference experiments showed that EHEC O157:H7-induced IL-1β production required the involvement of ASC, caspase-1, and NLRP3 expression in THP-1 cells. Our results demonstrate that Ehx plays a crucial role in EHEC O157:H7-induced IL-1β production and its cytotoxicity to THP-1 cells. NLRP3 inflammasome activation is also involved in EHEC O157:H7-stimulated IL-1β release.