Differential leaf flooding resilience in Arabidopsis thaliana is controlled by ethylene signaling-activated and age-dependent phosphorylation of ORESARA1.

The phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, ethylene quickly increases to high concentrations owing to its low solubility and diffusion rates in water. Ethylene accumulation in submerged plant tissues makes it a reliable cue for triggering flood acclimation responses, including metabolic adjustments to cope with flood-induced hypoxia. However, persistent ethylene accumulation also accelerates leaf senescence. Stress-induced senescence hampers photosynthetic capacity and stress recovery. In submerged Arabidopsis, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid indiscriminate breakdown of leaves despite high systemic ethylene accumulation. We demonstrate that although submergence triggers leaf-age-independent activation of ethylene signaling via EIN3 in Arabidopsis, senescence is initiated only in old leaves. EIN3 stabilization also leads to overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1) in both old and young leaves during submergence. However, leaf-age-dependent senescence can be explained by ORE1 protein activation via phosphorylation specifically in old leaves, independent of the previously identified age-dependent control of ORE1 via miR164. A systematic analysis of the roles of the major flooding stress cues and signaling pathways shows that only the combination of ethylene and darkness is sufficient to mimic submergence-induced senescence involving ORE1 accumulation and phosphorylation. Hypoxia, most often associated with flooding stress in plants, appears to have no role in these processes. Our results reveal a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses such as flooding. Age-dependent ORE1 activity ensures that older, expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues that are vital to whole-plant survival.

Transmission dynamics of drug-resistant tuberculosis in Ningbo, China: an epidemiological and genomic analysis.

Background: Tuberculosis (TB), particularly drug-resistant TB (DR-TB), remains a significant public health concern in Ningbo, China. Understanding its molecular epidemiology and spatial distribution is paramount for effective control. Methods: From December 24, 2020, to March 12, 2023, we collected clinical Mycobacterium tuberculosis (MTB) strains in Ningbo, with whole-genome sequencing performed on 130 MTB strains. We analyzed DR-related gene mutations, conducted phylogenetic and phylodynamic analyses, identified recent transmission clusters, and assessed spatial distribution. Results: Among 130 DR-TB cases, 41% were MDR-TB, 36% pre-XDR-TB, 19% RR-TB, and 3% HR-TB. The phylogenetic tree showed that 90% of strains were Lineage 2 (Beijing genotype), while remaining 10% were Lineage 4 (Euro-American genotype). The spatial analysis identified hotspots of DR-TB in Ningbo's northern region, particularly in traditional urban centers. 31 (24%) of the DR-TB cases were grouped into 7 recent transmission clusters with a large outbreak cluster containing 15 pre-XDR-TB patients. Epidemiological analyses suggested a higher risk of recent DR-TB transmission among young adult patients who frequently visited Internet cafes, game rooms, and factories. Conclusion: Our study provides comprehensive insights into the epidemiology and genetics of DR-TB in Ningbo. The presence of genomic clusters highlights recent transmission events, indicating the need for targeted interventions. These findings are vital for informing TB control strategies in Ningbo and similar settings.

Cannabidiol protects against acute aortic dissection by inhibiting macrophage infiltration and PMAIP1-induced vascular smooth muscle cell apoptosis.

Acute aortic dissection (AAD) progresses rapidly and is associated with high mortality; therefore, there remains an urgent need for pharmacological agents that can protect against AAD. Herein, we examined the therapeutic effects of cannabidiol (CBD) in AAD by establishing a suitable mouse model. In addition, we performed human AAD single-cell RNA sequencing and mouse AAD bulk RNA sequencing to elucidate the potential underlying mechanism of CBD. Pathological assays and in vitro studies were performed to verify the results of the bioinformatic analysis and explore the pharmacological function of CBD. In a ß-aminopropionitrile (BAPN)-induced AAD mouse model, CBD reduced AAD-associated morbidity and mortality, alleviated abnormal enlargement of the ascending aorta and aortic arch, and suppressed macrophage infiltration and vascular smooth muscle cell (VSMC) apoptosis. Bioinformatic analysis revealed that the pro-apoptotic gene PMAIP1 was highly expressed in human and mouse AAD samples, and CBD could inhibit Pmaip1 expression in AAD mice. Using human aortic VSMCs (HAVSMCs) co-cultured with M1 macrophages, we revealed that CBD alleviated HAVSMCs mitochondrial-dependent apoptosis by suppressing the BAPN-induced overexpression of PMAIP1 in M1 macrophages. PMAIP1 potentially mediates HAVSMCs apoptosis by regulating Bax and Bcl2 expression. Accordingly, CBD reduced AAD-associated morbidity and mortality and mitigated the progression of AAD in a mouse model. The CBD-induced effects were potentially mediated by suppressing macrophage infiltration and PMAIP1 (primarily expressed in macrophages)-induced VSMC apoptosis. Our findings offer novel insights into M1 macrophages and HAVSMCs interaction during AAD progression, highlighting the potential of CBD as a therapeutic candidate for AAD treatment.

H3.3B controls aortic dissection progression by regulating vascular smooth muscle cells phenotypic transition and vascular inflammation.

Aortic dissection is a devastating cardiovascular disease with a high lethality. Histone variants maintain the genomic integrity and play important roles in development and diseases. However, the role of histone variants in aortic dissection has not been well identified. In the present study, H3f3b knockdown reduced the synthetic genes expression of VSMCs, while overexpressing H3f3b exacerbated the cellular immune response of VSMCs induced by inflammatory cytokines. Combined RNA-seq and ChIP-seq analyses revealed that histone variant H3.3B directly bound to the genes related to extracellular matrix, VSMC synthetic phenotype, cytokine responses and TGFß signaling pathway, and regulated their expressions. In addition, VSMC-specific H3f3b knockin aggravated aortic dissection development in mice, while H3f3b knockout significantly reduced the incidence of aortic dissection. In term of mechanisms, H3.3B regulated Spp1 and Ccl2 genes, inducing the apoptosis of VSMCs and recruiting macrophages. This study demonstrated the vital roles of H3.3B in phenotypic transition of VSMCs, loss of media VSMCs, and vascular inflammation in aortic dissection.

CRISPR/Cas12a-Assisted Dual Visualized Detection of SARS-CoV-2 on Frozen Shrimps.

Given the possibility that food contaminated with SARS-CoV-2 might become an infection source, there is an urgent need for us to develop a rapid and accurate nucleic acid detection method for SARS-CoV-2 in food to ensure food safety. Here, we propose a sensitive, specific, and reliable molecular detection method for SARS-CoV-2. It has a mechanism to control amplicon contamination. Swabs from spiked frozen shrimps were used as detection samples, which were processed by heating at 95 °C for 30 s. These preprocessed samples served as the templates for subsequent amplification. A colorimetric LAMP reaction was carried out to amplify both the SARS-CoV-2 target and the MS2 phage simultaneously in one tube. MS2 phage was detected by colorimetric LAMP as the internal control, while SARS-CoV-2 was detected with a CRISPR/Cas12a system. The fluorescence results could be visually detected with an ultraviolet lamp. Meanwhile, uracil was incorporated during the LAMP reaction to provide an amplicon contamination proof mechanism. This test could detect as low as 20 copies of SARS-CoV-2 in one reaction. Additionally, the detection could be finished in 45 min. The test only needs a heating block and an ultraviolet lamp, which shows the potential for field detection.

Integrated slip valve-assisted fluidic chip coupling with CRISPR/Cas12a system for nucleic acid analysis.

Currently, some on-site nucleic acid detection platforms have been developed. However, these platforms still need to be improved in device integration and multiple detection capability. In this work, an integrated dual nucleic acid analysis platform was developed by slip valve-assisted fluidic chip coupled with CRISPR/Cas12a system. All the reagents, including nucleic acid extraction, air-dried loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a detection reagents, were preloaded on the fluidic chip. Liquids transfer and stirring could be controlled by a slip valve and a syringe. By combining duplex LAMP reaction with two CRISPR detection units, CRISPR/Cas12a-based dual nucleic acid analysis was successfully constructed. Benefiting from high-quality nucleic acid extraction on the chip, as low as 30 copies/reaction of Vibrio parahaemolyticus (V. parahaemolyticus) and 20 copies/reaction of Salmonella typhimurium (S. typhimurium) could be simultaneously detected. Detection results could be observed by the naked eye under a portable ultraviolet lamp. The whole detection procedure was finished within 60 min. This method with integrated nucleic acid analysis, dual detection capability and fluorescence visualized results provides a new solution for on-site nucleic acid analysis.

Local light signaling at the leaf tip drives remote differential petiole growth through auxin-gibberellin dynamics.

Although plants are immobile, many of their organs are flexible to move in response to environmental cues. In dense vegetation, plants detect neighbors through far-red light perception with their leaf tip. They respond remotely, with asymmetrical growth between the abaxial and adaxial sides of the leafstalk, the petiole. This results in upward movement that brings the leaf blades into better lit zones of the canopy. The plant hormone auxin is required for this response, but it is not understood how non-differential leaf tip-derived auxin can remotely regulate movement. Here, we show that remote signaling of far-red light promotes auxin accumulation in the abaxial petiole. This local auxin accumulation is facilitated by reinforcing an intrinsic directionality of the auxin transport protein PIN3 on the petiole endodermis, as visualized with a PIN3-GFP line. Using an auxin biosensor, we show that auxin accumulates in all cell layers from endodermis to epidermis in the abaxial petiole, upon far-red light signaling in the remote leaf tip. In the petiole, auxin elicits a response to both auxin itself as well as a second growth promoter; gibberellin. We show that this dual regulation is necessary for hyponastic leaf movement in response to light. Our data indicate that gibberellin is required to permit cell growth, whereas differential auxin accumulation determines which cells can grow. Our results reveal how plants can spatially relay information about neighbor proximity from their sensory leaf tips to the petiole base, thus driving adaptive growth.

The role of IL-35 and IL-37 in breast cancer - potential therapeutic targets for precision medicine.

Breast cancer is still a major concern due to its relatively poor prognosis in women, although there are many approaches being developed for the management of breast cancer. Extensive studies demonstrate that the development of breast cancer is determined by pro versus anti tumorigenesis factors, which are closely related to host immunity. IL-35 and IL-37, anti-inflammatory cytokines, play an important role in the maintenance of immune homeostasis. The current review focuses on the correlation between clinical presentations and the expression of IL-35 and IL-37, as well as the potential underlying mechanism during the development of breast cancer in vitro and in vivo. IL-35 is inversely correlated the differentiation and prognosis in breast cancer patients; whereas IL-37 shows dual roles during the development of breast cancer, and may be breast cancer stage dependent. Such information might be useful for both basic scientists and medical practitioners in the management of breast cancer patients.

Multiple crRNAs-assisted CRISPR/Cas12a assay targeting cytochrome b gene for amplification-free detection of meat adulteration.

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems have been widely applied in nucleic acid analysis for the high specificity. Coupled with pre-amplification steps, the sensitivity of CRISPR-based detection is greatly improved. However, an extra pre-amplification step not only complicates the detection procedures but may also cause aerosol contaminations in the process of transferring amplified solution into CRISPR system. In this study, we demonstrate that combination of multiple crRNAs in CRISPR/Cas12a system can enhance the detection sensitivity. Based on it, we establish a multiple crRNAs enhanced CRISPR (meCRISPR) method and apply it to meat adulteration identification. Take cytochrome b (Cyt b) gene as a target, meCRISPR method can directly detect as low as 1.13 ng/µL extracted pork DNA and 5% (w/w) pork contamination in pork and beef meat mixtures. There is no cross-reaction with extracted chicken, beef, duck and fish DNA. meCRISPR reaction is incubated at an isothermal temperature, and the detection process can be completed in a designed portable apparatus with a heat block, a light emitting diode and filters. For the simplicity, specificity and sufficient sensitivity of meCRISPR method, it will have great prospects in species identification, food adulteration, and genetically modified food detection.

Evaluation of whole-genome sequence to predict drug resistance of nine anti-tuberculosis drugs and characterize resistance genes in clinical rifampicin-resistant Mycobacterium tuberculosis isolates from Ningbo, China.

Setting: Controlling drug-resistant tuberculosis in Ningbo, China. Objective: Whole-genome sequencing (WGS) has not been employed to comprehensively study Mycobacterium tuberculosis isolates, especially rifampicin-resistant tuberculosis, in Ningbo, China. Here, we aim to characterize genes involved in drug resistance in RR-TB and create a prognostic tool for successfully predicting drug resistance in patients with TB. Design: Drug resistance was predicted by WGS in a "TB-Profiler" web service after phenotypic drug susceptibility tests (DSTs) against nine anti-TB drugs among 59 clinical isolates. A comparison of consistency, sensitivity, specificity, and positive and negative predictive values between WGS and DST were carried out for each drug. Results: The sensitivities and specificities for WGS were 95.92 and 90% for isoniazid (INH), 100 and 64.1% for ethambutol (EMB), 97.37 and 100% for streptomycin (SM), 75 and 100% for amikacin (AM), 80 and 96.3%for capreomycin (CAP), 100 and 97.22% for levofloxacin (LFX), 93.33 and 90.91% for prothionamide (PTO), and 70 and 97.96% for para-aminosalicylic acid (PAS). Around 53 (89.83%) and 6 (10.17%) of the isolates belonged to lineage two (East-Asian) and lineage four (Euro-American), respectively. Conclusion: Whole-genome sequencing is a reliable method for predicting resistance to INH, RIF, EMB, SM, AM, CAP, LFX, PTO, and PAS with high consistency, sensitivity, and specificity. There was no transmission that occurred among the patients with RR-TB in Ningbo, China.

The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol.

Strigolactones (SLs) are rhizosphere signalling molecules and phytohormones. The biosynthetic pathway of SLs in tomato has been partially elucidated, but the structural diversity in tomato SLs predicts that additional biosynthetic steps are required. Here, root RNA-seq data and co-expression analysis were used for SL biosynthetic gene discovery. This strategy resulted in a candidate gene list containing several cytochrome P450s. Heterologous expression in Nicotiana benthamiana and yeast showed that one of these, CYP712G1, can catalyse the double oxidation of orobanchol, resulting in the formation of three didehydro-orobanchol (DDH) isomers. Virus-induced gene silencing and heterologous expression in yeast showed that one of these DDH isomers is converted to solanacol, one of the most abundant SLs in tomato root exudate. Protein modelling and substrate docking analysis suggest that hydroxy-orbanchol is the likely intermediate in the conversion from orobanchol to the DDH isomers. Phylogenetic analysis demonstrated the occurrence of CYP712G1 homologues in the Eudicots only, which fits with the reports on DDH isomers in that clade. Protein modelling and orobanchol docking of the putative tobacco CYP712G1 homologue suggest that it can convert orobanchol to similar DDH isomers as tomato.

Modeling and Predicting Pulmonary Tuberculosis Incidence and Its Association with Air Pollution and Meteorological Factors Using an ARIMAX Model: An Ecological Study in Ningbo of China.

The autoregressive integrated moving average with exogenous regressors (ARIMAX) modeling studies of pulmonary tuberculosis (PTB) are still rare. This study aims to explore whether incorporating air pollution and meteorological factors can improve the performance of a time series model in predicting PTB. We collected the monthly incidence of PTB, records of six air pollutants and six meteorological factors in Ningbo of China from January 2015 to December 2019. Then, we constructed the ARIMA, univariate ARIMAX, and multivariate ARIMAX models. The ARIMAX model incorporated ambient factors, while the ARIMA model did not. After prewhitening, the cross-correlation analysis showed that PTB incidence was related to air pollution and meteorological factors with a lag effect. Air pollution and meteorological factors also had a correlation. We found that the multivariate ARIMAX model incorporating both the ozone with 0-month lag and the atmospheric pressure with 11-month lag had the best performance for predicting the incidence of PTB in 2019, with the lowest fitted mean absolute percentage error (MAPE) of 2.9097% and test MAPE of 9.2643%. However, ARIMAX has limited improvement in prediction accuracy compared with the ARIMA model. Our study also suggests the role of protecting the environment and reducing pollutants in controlling PTB and other infectious diseases.

ASPP2 reduction attenuates HBV induced chronic liver damage: A hybrid mouse model study.

BACKGROUND & AIM: P53 Apoptosis Stimulating Protein 2 (ASPP2) is confirmed to participate in cellular activities including apoptosis, proliferation, autophagy, injury and so on. However, the role of ASPP2 in Hepatitis B virus (HBV) infection has not been reported in detail. The study explored the role of ASPP2 in HBV induced chronic liver damage. METHODS: Transcriptome profiling of ASPP2-konckdown mouse liver were analyzed by RNA-sequencing. HBV-ASPP2-knockdown mice was the hybrid offspring of HBV transgenic mice and ASPP2 knockdown mice. Liver tissues were taken for the experiments such as western Blot (WB), PCR, Hematoxylin and Eosin (HE), Immunohistochemistry and high throughput sequencing of transcriptome. RESULTS: Pathological and transcriptomic analysis of liver tissue from ASPP2 knockdown vs con mice showed that after ASPP2 knockdown, the pathological changes in the liver tissue of mice were not significant, but transcriptomics showed obvious changes in immune system process, and response to stimulus, metabolism, Human Diseases and other directions etc. In the HBV-ASPP2-knockdown mice, liver tissue HE staining found less cell swelling and necrosis foci; F4/80 and MPO staining showed less inflammatory cell infiltration; serum ALT and AST decreased than the HBV-ASPP2-con mice. Transcriptome results showed significantly changed in HBV-ASPP2-knockdown mice including immune system process, inflammatory response, and innate immune response etc. Further comparison of the two transcriptomes yielded 9 identical pathways related to inflammatory and cell injury. The PPAR pathway was verified, and found that the increase of PPARγ caused by the reduction of ASPP2 is likely to be the reason for the reduction of HBV-related liver injury. The expression of PPARγ was then analyzed by transcriptome and PCR, it was found that in the absence of HBV, ASPP2 knockdown resulted in a mild decrease in PPARγ, and in the presence of HBV infection, ASPP2 knockdown resulted in a marked increase in PPARγ.In addition, this study found that high expression of ASPP2 had opposite effects on HCC (HBV-none) and HCC (HBV-yes). CONCLUSION: This study demonstrated that reduction of ASPP2 reduces HBV-induced hepatocyte damage during chronic HBV infection. This phenomenon is related to the different regulation of PPARγ by ASPP2 in the presence or absence of HBV stimulation.

Dipstick-based rapid nucleic acids purification and CRISPR/Cas12a-mediated isothermal amplification for visual detection of African swine fever virus.

African swine fever virus (ASFV) can cause highly contagious and fatal disease among domestic pigs, resulting in considerable economic losses for swine breeders. There is a strong demand for accurate, rapid, and simple detection methods especially for on-site application. Nucleic acid testing is the most commonly used method for ASFVdetection. However, traditional nucleic acid purification step is time- and labor-consuming. The nucleic acid purification, amplification and amplicons detection rely on laboratory settings which limits the on-site detection. Here, we proposed a simple and cost-effective detection method that utilized filter paper to purify nucleic acids from swine blood and employed CRISPR/Cas12a-mediated loop-mediated isothermal amplification (LAMP) reaction to detect ASFV. The filter paper which was made into dipsticks could effectively purify nucleic acids from whole blood in 2 min. This simple and low-cost purification method avoided multiple pipetting steps and potential amplification inhibitors (e.g., ethanol) that were generally used in traditional nucleic acids extraction processes. After nucleic acid purification, the lyophilized LAMP reagent dissolved by elution solution was employed to perform isothermal amplification reaction on a portable heating block. The CRISPR/Cas12a system was designed to specifically detect amplicons. Assisted by a portable homemade device, the fluorescent signals produced by positive samples could be observed by the naked eye, while negative samples remained colorless. The whole detection procedure could be finished within 50 min with a detection limit of one copies/µL. This established method provided a novel strategy for rapid visualized detection and showed great potential for on-site application.

Auxin-dependent control of cytoskeleton and cell shape regulates division orientation in the Arabidopsis embryo.

Premitotic control of cell division orientation is critical for plant development, as cell walls prevent extensive cell remodeling or migration. While many divisions are proliferative and add cells to existing tissues, some divisions are formative and generate new tissue layers or growth axes. Such formative divisions are often asymmetric in nature, producing daughters with different fates. We have previously shown that, in the Arabidopsis thaliana embryo, developmental asymmetry is correlated with geometric asymmetry, creating daughter cells of unequal volume. Such divisions are generated by division planes that deviate from a default "minimal surface area" rule. Inhibition of auxin response leads to reversal to this default, yet the mechanisms underlying division plane choice in the embryo have been unclear. Here, we show that auxin-dependent division plane control involves alterations in cell geometry, but not in cell polarity axis or nuclear position. Through transcriptome profiling, we find that auxin regulates genes controlling cell wall and cytoskeleton properties. We confirm the involvement of microtubule (MT)-binding proteins in embryo division control. Organization of both MT and actin cytoskeleton depends on auxin response, and genetically controlled MT or actin depolymerization in embryos leads to disruption of asymmetric divisions, including reversion to the default. Our work shows how auxin-dependent control of MT and actin cytoskeleton properties interacts with cell geometry to generate asymmetric divisions during the earliest steps in plant development.

Impact of Multimorbidity Subgroups on the Health Care Use and Clinical Outcomes of Patients With Tuberculosis: A Population-Based Cohort Analysis.

Background: Multimorbidity is defined as the existence of two or more chronic health conditions in the same individual. While patients with tuberculosis commonly have multiple conditions at diagnosis, such as HIV, diabetes, and depression, to the authors' knowledge, there is limited information on the patterns of multimorbidity, and how the types and combinations of conditions could impact the healthcare utilization, expenditure, and TB outcomes. Methods: An observational cohort study of adult patients diagnosed with tuberculosis was conducted using the Chinese Center for Disease Control and Prevention (CDC)'s National TB Information System (NTBIS) linked to the Ningbo Regional Health Care Database (NRHCD) (2015-2020). Latent class analysis was used to identify comorbidity groups among the subset with ≥2 conditions including TB. Group-level health care use, expenditure, and treatment outcomes were compared with patients without chronic conditions using multivariate regression models. Results: A total of 9,651 patients with TB were identified, of whom approximately 61.4% had no chronic conditions, 17.4% had 1 chronic condition, and 21.3% had ≥2 chronic conditions. Among those with ≥1 chronic condition other than TB, 4 groups emerged: (1) general morbidity (54.4%); (2) cardiovascular morbidity without complications (34.7%); (3) cardiovascular morbidity with complications (5.0%); (4) respiratory morbidity (5.9%). The respiratory morbidity group experienced the highest expenditures, at 16,360 CNY more overall (95% CI, CNY 12,615-21,215) after adjustment compared with TB patients without chronic conditions. The respiratory morbidity and cardiovascular morbidity with complications group also had the lowest odds of favorable TB outcomes [adjusted odds ratio (aOR), 0.68; 95% CI, 0.49-0.93] and (aOR 0.59, 95% CI 0.42-0.83), respectively. The cardiovascular morbidity without complications group had the highest odds of successful TB treatment (aOR, 1.40; 95% CI, 1.15-1.71). Conclusions: Multimorbidity is common among patients with TB. The current study identified four distinct comorbidity subgroups, all of which experienced high, yet differential, rates of health care use. These findings highlight the need for urgent reforms to transform current fragmented TB care delivery and improve access to other specialists and financial assistance.

Exploring new targets for the treatment of hepatitis-B virus and hepatitis-B virus-associated hepatocellular carcinoma: A new perspective in bioinformatics.

BACKGROUND: Hepatitis B Virus (HBV) infection is a global public health problem. After infection, patients experience a natural course from chronic hepatitis to cirrhosis and even Hepatitis B associated Hepatocellular Carcinoma (HBV-HCC). With the multi-omics research, many differentially expressed genes from chronic hepatitis to HCC stages have been discovered. All these provide important clues for new biomarkers and therapeutic targets. The purpose of this study is to explore the differential gene expression of HBV and HBV-related liver cancer, and analyze their enrichments and significance of related pathways. METHODS: In this study, we downloaded four microarray datasets GSE121248, GSE67764, GSE55092, GSE55092 and GSE83148 from the Gene Expression Omnibus (GEO) database. Using these four datasets, patients with chronic hepatitis B (CHB) differentially expressed genes (CHB DEGs) and patients with HBV-related HCC differentially expressed genes (HBV-HCC DEGs) were identified. Then Protein-protein Interaction (PPI) network analysis, Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to excavate the functional interaction of these two groups of DEGs and the common DEGs. Finally, the Kaplan website was used to analyze the role of these genes in HCC prognostic. RESULTS: A total of 241 CHB DEGs, 276 HBV-HCC DEGs, and 4 common DEGs (cytochrome P450 family 26 subfamily A member 1 (CYP26A1), family with sequence similarity 110 member C(FAM110C), SET and MYND domain containing 3(SMYD3) and zymogen granule protein 16(ZG16)) were identified. CYP26A1, FAM110C, SMYD3 and ZG16 exist in 4 models and interact with 33 genes in the PPI network of CHB and HBV-HCC DEGs,. GO function analysis showed that: CYP26A1, FAM110C, SMYD3, ZG16, and the 33 genes in their models mainly affect the regulation of synaptic vesicle transport, tangential migration from the subventricular zone to the olfactory bulb, cellular response to manganese ion, protein localization to mitochondrion, cellular response to dopamine, negative regulation of neuron death in the biological process of CHB. In the biological process of HBV-HCC, they mainly affect tryptophan catabolic process, ethanol oxidation, drug metabolic process, tryptophan catabolic process to kynurenine, xenobiotic metabolic process, retinoic acid metabolic process, steroid metabolic process, retinoid metabolic process, steroid catabolic process, retinal metabolic process, and rogen metabolic process. The analysis of the 4 common DEGs related to the prognosis of liver cancer showed that: CYP26A1, FAM110C, SMYD3 and ZG16 are closely related to the development of liver cancer and patient survival. Besides, further investigation of the research status of the four genes showed that CYP26A1 and SMYD3 could also affect HBV replication and the prognosis of liver cancer. CONCLUSION: CYP26A1, FAM110C, SMYD3 and ZG16 are unique genes to differentiate HBV infection and HBV-related HCC, and expected to be novel targets for HBV-related HCC occurrence and prognostic judgement.

ASPP2 inhibits hepatitis B virus replication by preventing nucleus translocation of HSF1 and attenuating the transactivation of ATG7.

Hepatitis B virus (HBV) is a kind of virus with the capability to induce autophagy, thereby facilitating its replication. Reducing hepatocyte autophagy is proved to be a useful way to inhibit HBV replication. Herein, we reported that p53-binding protein 2 (apoptosis-stimulating protein of p53-2, ASPP2) could attenuate HBV-induced hepatocyte autophagy in a p53-independent manner. Mechanistically, overexpressed ASPP2 binds to HSF1 in cytoplasm of HBV-infected cells, which prevents the translocation of HSF1 to nuclei, thereby inhibiting the transactivation of Atg7. By regulating the transcription of Atg7, ASPP2 reduces hepatocyte autophagy, thereby inhibiting HBV replication. Therefore, ASPP2 is a key regulator of cell autophagy, and overexpression of ASPP2 could be a novel method to inhibit HBV replication in hepatocytes.

Phenotypic and molecular characterization of pyrazinamide resistance among multidrug-resistant Mycobacterium tuberculosis isolates in Ningbo, China.

BACKGROUND: Detection of pyrazinamide (PZA) resistance in Mycobacterium tuberculosis (TB) patients is critical, especially in dealing with multidrug-resistant Mycobacterium tuberculosis (MDR-TB) case. Up to date, PZA drug susceptibility testing (DST) has not been regularly performed in China. The prevalence and molecular characteristics of PZA resistance in M.tuberculosis isolates, especially MDR-TB have not been studied in Ningbo, China. This study aimed to analyze the phenotypic and molecular characterization of PZA resistance among MDR-TB isolates in Ningbo. METHODS: A total of 110 MDR-TB isolates were collected from the TB patients who were recorded at local TB dispensaries in Ningbo. All clinical isolates were examined by drug susceptibility testing and genotyping. DNA sequencing was used to detect mutations in the pncA gene associated with PZA resistance. RESULTS: The prevalence of PZA resistance among MDR-TB strains in Ningbo was 59.1%. With regard to the history and the outcome of treatments among MDR-TB cases, the percentages of re-treated MDR-TB patients in the PZA-resistant group and of successful patients in PZA-susceptible group were significantly higher than the ones in the PZA-susceptible group and in the PZA-resistant group, respectively (P = 0.027, P = 0.020). The results showed that the resistance of streptomycin (67.7% vs 46.7%, P = 0.027), ethambutol (56.9% vs 33.3%, P = 0.015), ofloxacin (43.1% vs 11.1%, P = 0.000), levofloxacin (43.1% vs 11.1%, P = 0.000), pre-XDR (pre-Xtensively Drug Resistance) (38.5% vs 15.6%, P = 0.009), were more frequently adverted among PZA-resistant isolates compared with PZA-susceptible isolates. In addition, 110 MDR-TB was composed of 87 (PZA resistant, 78.5%) Beijing strains and 23 (PZA resistant, 21.5%) non-Beijing strains. Fifty-four out of 65 (83.1%) PZA-resistant MDR strains harbored a mutation located in the pncA gene and the majority (90.7%) were point mutations. Compared with the phenotypic characterization, DNA sequencing of pncA has sensitivity and specificity of 83.1 and 95.6%. CONCLUSION: The mutations within pncA gene was the primary mechanism of PZA resistance among MDR-TB and DNA sequencing of pncA gene could provide a rapid detection evidence in PZA drug resistance of MDR-TB in Ningbo.

Comparative Utility of Genetic Determinants of Drug Resistance and Phenotypic Drug Susceptibility Profiling in Predicting Clinical Outcomes in Patients With Multidrug-Resistant Mycobacterium tuberculosis.

Setting: Programmatic management of drug-resistant tuberculosis in Ningbo, China. Objective: To assess whether data-driven genetic determinants of drug resistance patterns could outperform phenotypic drug susceptibility testing in predicting clinical meaningful outcomes among patients with multidrug-resistant tuberculosis (MDR-TB). Design: We conducted a prospective cohort study of 104 MDR-TB patients. All MDR-TB isolates underwent drug susceptibility testing and genotyping for mutations that could cause drug resistance. Study outcomes were time to sputum smear conversion and probability of treatment success, as well as time to culture conversion within 6 months. Data were analyzed using latent class analysis, Kaplan-Meier curves, and Cox regression models. Results: We report that latent class analysis of data identified two latent classes that predicted sputum smear conversion with P = 0.001 and area under receiver-operating characteristic curve of 0.73. The predicted latent class memberships were associated with superior capability in predicting sputum culture conversion at 6 months and overall treatment success compared to phenotypic drug susceptibility profiling using boosted logistic regression models. Conclusion: These results suggest that genetic determinants of drug resistance in combination with phenotypic drug-resistant tests could serve as useful biomarkers in predicting treatment prognosis in MDR-TB.