Detections of mefA, ermB, and mphA Macrolides Resistant Genes in Bacteria Isolated from Covid-19 Patients from Selected Health Facilities in Ibadan, Nigeria

Background: COVID-19 is a disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Epidemiological data indicated that bacterial complications in COVID-19 would decrease clearance rate of the infecting agent and increase mortality rate. Macrolides such as Azithromycin are usually administered to COVID-19 patients as palliative treatments. Currently, a considerable number of bacterial strains have developed resistance to various antibiotics, especially macrolides. Resistance is reported to be due to possession of mefA, ermB, and mphA genes by Gram positive and Gram negative bacteria. Therefore, this study determined antibiotic resistance patterns and identify mefA, ermB and mphA macrolide-resistant genes in bacterial pathogens isolated from COVID-19 cases in Ibadan, Nigeria. Methods: 400 Nasopharyngeal samples were collected from symptomatic cases before antibiotic medication;structured questionnaires were administered to collect socio-demographic data of participants. Samples were cultured on Blood, Chocolate, MacConkey and Mannitol salt agar at 37°C for 48 hrs. Bacterial identification was performed using VITEK 2.0 ID cards and API 20E for Gram positive and negative bacteria respectively. Antibiotic Susceptibility Testing was performed using Kirby Bauer disc diffusion methods and VITEK 2.0 AST card kits. DNA of multidrug resistant bacterial isolates was extracted;resistant genes were determined using a polymerase chain reaction with specific primers. Amplified genes were detected using agarose gel electrophoresis. Results: 240 (60%) had bacterial growth and 97 (22.2%) yielded no growth. From the 240 bacterial isolates, 38 (15.83%) were multi-drug resistant including resistance to macrolides (Azithromycin) 20 (52.63%) of which were positive for either mefA or ermB, and none (0.0%) possess mphA gene;14 (36.8%) isolates had mefA gene, 10 (26.3%) isolates carried ermB gene. Conclusion: Multi-drug bacterial resistance including macrolides and quinolones was detected. Only mefA and ermB genes were detected in the bacterial isolates, especially in Gram positive organisms. The detection of mefA and ermB genes in the MDR bacterial isolates raised concern on the use of azithromycin as palliative treatment for COVID-19 symptomatic patients.

基于线粒体COI基因的云南西花蓟马种群遗传多样性研究

【背景和目的】西花蓟马传播的番茄斑萎病毒属病毒可侵染烟草,为揭示云南西花蓟马传播扩散趋势。【方法】以线粒体DNA(mitochondrial DNA,mtDNA)COI基因为分子标记,检测23个不同云南西花蓟马地理种群的遗传多样性、遗传分化、分子变异和种群动态。【结果】基于mtDNA COI基因分析,共检测到10种单倍型,总群体的单倍型多样度(Hd)较高,为0.60700;总群体遗传分化指数(Fst)和基因流(Nm)分别为0.48031和4.46,表明云南西花蓟马各地理种群间基因交流水平较高;单倍型中介网络图没有明显分支;种群间分子变异主要来自种群内部;总群体中性检验Taijima’s D达到极显著水平,Fu’s Fs达到显著水平,且错配分布曲线中,除主峰外其余峰不明显,说明云南西花蓟马种群近期或正经历明显的种群扩张。【结论】云南西花蓟马种群遗传多样性丰富,近期种群或正经历明显扩张,应积极监测并采取有效的防控措施,保障农业生产健康发展。

Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis

AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.

Weighted Gene Co-expression Network Analysis of Gene Modules for the Prognosis of Esophageal Cancer

Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.

Genetic Differentiation Analyses Based on mtDNA COⅡ Gene Sequences Among Different Geographic Populations of Aphis glycines(Hemiptera: Aphididae) in Northeast China

Aphis glycines （Hemiptera： Aphididae） is considered as a cosmopolitan pest of cultivated soybean, major difficulties in its control measures may be due to its higher genetic diversity; however, the knowledge about population genetic diversity of this species is limited. This study aimed to represent the genetic differentiation among different geographic populations of soybean aphid in Northeast China. In order to investigate and assess the genetic diversity, genetic differentiation, molecular variance, population structure, ecological importance and evolutionary history of A. glycines, we sequenced a fragment of one protein-coding gene, the cytochrome c oxidase I/of mitochondrial DNA gene. The results showed that four haplotypes were defined among CO 11 gene of 180 sequences of soybean aphid in Northeast China including H1 shared by all the populations. Lower haplotype diversity （Hd=0.3590± 0.0420） and nucleotide diversity （Pi=0.0012±0.0002） were observed and high gene flow was detected in every two populations, while most of the variation （80.81%） arose from variability within A. glycines from individuals. Low genetic differentiation and high gene flow （Nm=2.106） indicated a high migration rate between the populations, which might reveal that gene flow in different geographic populations did not affect by geographical distance. The phylogenetic tree and the haplotype network ofA. glycines were obtained based on sequences of CO Ⅱ gene, there were no significant genealogical branches or clusters recognized in NJ tree, and no clear distribution, delineation of haplotypes were demonstrated in the haplotype network according to geographical location. This study rejected the vicariance hypothesis： geographic isolation could be a barrier and it restricted A. glycines gene flow among 10 populations.

Genetic Differences of Mitten Crabs Based on RFLP Analysis on Mitochondrial Cytochrome Oxidase Subunit I(COI) Gene

The genetic differences of 15 mitten crab populations from 6 river systems in China's Mainland and 1 population from Russia were studied based on RFLP analysis of mitochondrial cytochrome oxidase subunit I （CO I）. The results showed that Tas I-RFLP pattern could be used as a genetic marker to distinguish Eriocheir hepuensis from Eriocheir sinensis, Eriocheirjaponica and Eriocheir leptognathus; genetic distances among 13 populations of Eriocheir sinensis range from 0 to 0.015, indicating that they were different geographic strains; the subspecies status of Eriocheir sinensis and Eriocheir hepuensis （population from Nanliujiang） were considered owning to their genetic distances of 0.02-0.044, indicating that genetic divergence between them was low; Eriocheir leptognathus （population from Nanpaihe, Tianjin） was the most distant taxon with genetic distances value of 0.147-0.195, which could be defined as genetic distances between species in genus Eriocheir.

Measles Virus(Nepal Strain)Hemagglutinin Gene: Cloning,Complete Nucleotide Sequence Analysis and Expression in COS Cells

Hemagglutinin gene of Measles virus(Nepal strain) was amplified by RT PCR technique, cloned and sequenced by the dideoxy mediated chain termination method. The comparison to the standard strain(Edmonston strain) showed many important mutations. The homology of these two strains was 98.17%. Then H gene was cloned into expression vector pCD SRα296 and introduced into COS 7 cells by electroporation method. The expression and function of cloned H gene was checked by hemadsorption assays.

CO-TRANSFECTION OF RAT BONE MARROW MESENCHYMAL STEM CELLS WITH HUMAN BMP2 AND VEGF165 GENES

Objective To explore the feasibility and efficacy of lentivirus-mediated co-transfection of rat bone marrow mesenchymal stem cells (MSCs) with human vascular endothelial growth factor 165 (hVEGF165) gene and human bone morphogenetic protein 2 (hBMP2) gene. Methods The hVEGF165 and hBMP2 cDNAs were obtained from human osteosarcoma cell line MG63 and cloned into lentiviral expression vectors designed to co-express the copepod green fluorescent protein (copGFP). The expression lentivector and packaging Plasmid Mix were co-transferred to 293TN cells, which produced the lentivirus carrying hVEGF165 (Lv-VEGF) or hBMP2 (Lv-BMP), respectively. MSCs of Wistar rats were co-transfected with Lv-BMP and Lv-VEGF (BMP+VEGF group), or each alone (BMP group and VEGF group), or with no virus (Control group). The mRNA and protein expressions of hVEGF165 and hBMP2 genes in each group were detected by real-time PCR and enzyme linked immunosorbent assay (ELISA). Results Lentiviral expression vectors carrying hVEGF165 or hBMP2 were correctly constructed and confirmed by restriction endonucleses analysis and DNA sequencing analysis. A transfer efficiency up to 90% was archieved in all the transfected groups detected by the fraction of fluorescent cells using fluorescent microscopy. From the results generated by real-time PCR and ELISA, VEGF165 and BMP2 genes were co-expressed in BMP+VEGF group. No significant difference of BMP2 expression was detected between BMP+VEGF and BMP groups (P>0.05). Similarly, there was no significant difference of VEGF165 expression between BMP+VEGF and VEGF groups (P>0.05). Conclusion VEGF165 and BMP2 genes were successfully co-expressed in MSCs by lentivirus-mediated co-transfection, which provided a further foundation for the combined gene therapy of bone regeneration.

大灰象甲非典型气味受体基因SvelOrco的克隆及组织表达谱分析

旨在克隆大灰象甲Sympiezomias velatus的Orco基因,明确其分子特征及其组织表达谱。通过分析成虫触角转录组数据并利用RT-PCR克隆出大灰象甲Orco基因,对大灰象甲Orco蛋白进行结构分析和系统发育分析,并采用qPCR测定Orco基因在大灰象甲成虫不同组织中的表达量。克隆获得大灰象甲Orco基因并命名为SvelOrco(GenBank登录号:OM417062),其开放阅读框长1 449 bp,编码482个氨基酸。预测SvelOrco蛋白的分子质量为53.49 ku,等电点为5.66,主要由α-螺旋和无规则卷曲组成,有7个跨膜结构域。系统发育分析表明大灰象甲与云杉八齿小蠹Ips typographus亲缘关系最近。qPCR结果显示:SvelOrco主要在大灰象甲成虫触角上表达,雄虫触角表达量最高,是雌虫触角表达量的1.22倍,SvelOrco在翅部也有少量表达,在头、胸、腹和足的表达量极低。

WGCNA联合LASSO-COX方法筛选甲状腺癌预后关键基因及其临床价值分析

目的筛选甲状腺癌(thyroid cancer,THCA)的关键预后基因并构建预后预测模型。方法从癌症基因组图谱(The Cancer GenomeAtlas,TCGA)数据库中获取THCA和正常样本的基因表达谱,采用Limma算法筛选THCA组织与正常组织间差异表达基因(differentially expressed genes,DEGs),再进行权重基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)和套索联合COX回归分析(least absolute shrinkage and selection operator regression COX analysis,LASSO-COX)获得与其预后相关基因,然后根据关键基因构建预后预测模型,基于风险评分进行生存分析和受试者工作特征(receiver operating characteristic,ROC)曲线分析,最后基于基因表达谱和风险评分进行基因集富集分析(gene set enrichment analysis,GSEA)以评估相关途径和分子机制。结果本研究筛选出5个THCA预后关键基因,即LINC02550、STEAP2、ATP2C2、PLEKHG4B和SALL4。通过这5个基因构建的预后评估模型表明,风险评分越高,预后越差。ROC曲线分析结果表明该模型对患者生存率具有优良的预测性能,结合THCA患者的主要临床特性建立的列线图具有良好的预测性能。GSEA分析发现mTOR信号通路、Hedgehog信号通路、细胞自噬调节、转化生长因子-β信号通路富集在高风险评分组。结论基于筛选出的5个关键基因构建的预后预测模型有助于预测THCA患者的预后,这5个基因是潜在的靶向治疗基因。

Prognostic value of sorting nexin 10 weak expression in stomach adenocarcinoma revealed by weighted gene coexpression network analysis

AIM To detect significant clusters of co-expressed genes associated with tumorigenesis that might help to predict stomach adenocarcinoma(SA) prognosis.METHODS The Cancer Genome Atlas database was used to obtain RNA sequences as well as complete clinical data of SA and adjacent normal tissues from patients. Weighted gene co-expression network analysis(WGCNA) was used to investigate the meaningful module along with hub genes. Expression of hub genes was analyzed in 362 paraffin-embedded SA biopsy tissues by immunohistochemical staining. Patients were classified into two groups(according to expression of hub genes): Weak expression and over-expression groups. Correlation of biomarkers with clinicopathological factors indicated patient survival.RESULTS Whole genome expression level screening identified 6,231 differentially expressed genes. Twenty-four coexpressed gene modules were identified using WGCNA. Pearson's correlation analysis showed that the tan module was the most relevant to tumor stage(r = 0.24, P = 7 × 10-6). In addition, we detected sorting nexin(SNX)10 as the hub gene of the tan module. SNX10 expression was linked to T category(P = 0.042, χ~2 = 8.708), N category(P = 0.000, χ~2 = 18.778), TNM stage(P = 0.001, χ~2 = 16.744) as well as tumor differentiation(P = 0.000, χ~2 = 251.930). Patients with high SNX10 expression tended to have longer diseasefree survival(DFS; 44.97 mo vs 33.85 mo, P = 0.000) as well as overall survival(OS; 49.95 vs 40.84 mo, P = 0.000) in univariate analysis. Multivariate analysis showed that dismal prognosis could be precisely predicted clinicopathologically using SNX10 [DFS: P = 0.014, hazard ratio(HR) = 0.698, 95% confidence interval(CI): 0.524-0.930, OS: P = 0.017, HR = 0.704, 95%CI: 0.528-0.940].CONCLUSION This study provides a new technique for screening prognostic biomarkers of SA. Weak expression of SNX10 is linked to poor prognosis, and is a suitable prognostic biomarker of SA.

酒精性肝炎自噬关键基因的筛选及生物信息学分析

目的筛选酒精性肝炎(AH)的自噬关键基因,探讨AH潜在的生物标志物和治疗靶点。方法采用基因表达综合数据库(GEO)中的2个AH基因芯片和从MSigDB、GeneCards数据库中获得的自噬相关数据集,通过加权基因共表达网络分析(WGCNA)获取关键基因。对筛选的关键基因进行基因本体(GO)、京都基因和基因组百科全书(KEGG)功能富集分析,蛋白质相互作用(PPI)分析,免疫浸润分析,构建信使RNA(mRNA)-微小RNA(miRNA)网络,进行酒精性肝病不同分期的自噬相关关键基因的表达差异分析,并进一步通过实时荧光定量逆转录聚合酶链反应(RT-qPCR)在AH患者和小鼠肝脏组织中验证。结果本研究筛选得到了11个与AH自噬相关的基因(EEF1A2、CFTR、SOX4、TREM2、CTHRC1、HSPB8、TUBB3、PRKAA2、RNASE1、MTCL1、HGF),均为上调基因。在AH患者和小鼠肝脏组织中,SOX4、TREM2、HSPB8、PRKAA2在AH组中的相对表达量均高于对照组。结论SOX4、TREM2、HSPB8、PRKAA2可能是AH潜在的生物标志物和治疗靶点。

PLAGL1 Is Identified as a Potential Diagnostic Marker for Co-Occurrence with Osteoporosis and Multiple Myeloma

Background: Osteoporosis (OP) is a common clinical manifestation of multiple myeloma (MM). The aim of this study was to investigate the possible molecular pathways and shared genes in the co-occurrence of OP and MM. Methods: The Gene Expression Omnibus database was used to retrieve gene expression information. Use WGCNA and differential analysis to screen out Hub genes. The GENEMANIA was used to build protein-protein interaction (PPI) networks. Enrichment analyses were performed to explore the functions. Validation datasets were selected to verify the diagnostic marker reliability of PLAGL1. The immune microenvironment of diseases was analyzed by immune infiltration analyses. Results: We confirmed a hub gene called PLAGL1, which is significantly under-expressed in both OP and MM. We found hub genes were associated with glucose and energy metabolism. Subsequently, the reliability of PLAGL1 for diagnosing OP and MM was verified using ROC curves, with all areas under the curve > 0.75. Moreover, PLAGL1 regulates t lymphocytes and may participate in the occurrence of OP in MM through immune pathways. Conclusions: PLAGL1 is a hub gene for the co-occurrence of OP and MM. It can regulate T-lymphocyte involvement in disease development. PLAGL1 may be a novel diagnostic marker for the co-occurrence of OP and MM.

The Influence of Co-Suppressing Tomato 1-Aminocyclopropane-1-Carboxylic Acid OxidaseⅠon the Expression of Fruit Ripening-Related and Pathogenesis-Related Protein Genes

The purpose of this study is to explore the influence of co-suppressing tomato ACC oxidase Ⅰ on the expression of fruit ripening-related and pathogenesis-related protein genes, and on the biosynthesis of endogenous ethylene and storage ability of fruits. Specific fragments of several fruit ripening-related and pathogenesis-related protein genes from tomato （Lycopersicon esculentum） were cloned, such as the l-aminocyclopropane-1-carboxylic acid oxidase 1 gene （LeAC01）, 1- aminocyclopropane-l-carboxylic acid oxidase 3 gene （LeAC03）, EIN3-binding F-box 1 gene （LeEBF1）, pathogenesis-related protein 1 gene （LePR1）, pathogenesis-related protein 5 gene （LePR5）, and pathogenesis-related protein osmotin precursor gene （LeNP24） by PCR or RT-PCR. Then these specific DNA fragments were used as probes to hybridize with the total RNAs extracted from the wild type tomato Ailsa Craig （AC＋＋） and the LeAC01 co-suppression tomatoes （V1187 and T4B）, respectively. At the same time, ethylene production measurement and storage experiment of tomato fruits were carded out. The hybridization results indicated that the expression of fruit ripening-related genes such as LeACO3 and LeEBF1, and pathogenesis-related protein genes such as LePR1, LePR5, and LeNP24, were reduced sharply, and the ethylene production in the fruits, wounded leaves decreased and the storage time of ripening fruits was prolonged, when the expression of LeACO1 gene in the transgenic tomato was suppressed. In the co-suppression tomatoes, the expression of fruit ripening-related and pathogenesis-related protein genes were restrained at different degrees, the biosynthesis of endogenous ethylene decreased and the storage ability of tomato fruits increased.

MicroPath-A pathway-based pipeline for the comparison of multiple gene expression profiles to identify common biological signatures

High throughput gene expression analysis is swiftly becoming the focal point for deciphering molecular mechanisms underlying various dif-ferent biological questions. Testament to this is the fact that vast volumes of expression profiles are being generated rapidly by scientists worldwide and subsequently stored in publicly available data repositories such as ArrayEx-press and the Gene Expression Omnibus (GEO). Such wealth of biological data has motivated biologists to compare expression profiles gen-erated from biologically-related microarray ex-periments in order to unravel biological mecha-nisms underlying various states of diseases. However, without the availability of appropriate software and tools, they are compelled to use manual or labour-intensive methods of com-parisons. A scrutiny of current literature makes it apparent that there is a soaring need for such bioinformatics tools that cater for the multiple analyses of expression profiles. In order to contribute towards this need, we have developed an efficient software pipeline for the analysis of multiple gene expression data-sets, called Micropath, which implements three principal functions;1) it searches for common genes amongst n number of datasets using a number crunching method of comparison as well as applying the principle of permutations and combinations in the form of a search strat-egy, 2) it extracts gene expression patterns both graphically and statistically, and 3) it streams co-expressed genes to all molecular pathways belonging to KEGG in a live fashion. We sub-jected MicroPath to several expression datasets generated from our tolerance-related in-house microarray experiments as well as published data and identified a set of 31 candidate genes that were found to be co-expressed across all interesting datasets. Pathway analysis revealed their putative roles in regulating immune toler-ance. MicroPath is freely available to download from: www.1066technologies.co.uk/micropath.

Transplantation of Nogo-66 receptor gene-silenced cells in a poly(D,L-lactic-co-glycolic acid) scaffold for the treatment of spinal cord injury

Inhibition of neurite growth, which is in large part mediated by the Nogo-66 receptor, affects neural regeneration following bone marrow mesenchymal stem cell transplantation. The tissue engineering scaffold poly（D,L-lactide-co-glycolic acid） has good histocompatibility and can promote the growth of regenerating nerve fibers. The present study used small interfering RNA to silence Nogo-66 receptor gene expression in bone marrow mesenchymal stem cells and Schwann cells, which were subsequently transplanted with poly（D,L-lactide-co-glycolic acid） into the spinal cord lesion regions in rats. Simultaneously, rats treated with scaffold only were taken as the control group. Hematoxylin-eosin staining and immunohistochemistry revealed that at 4 weeks after transplantation, rats had good motor function of the hind limb after treatment with Nogo-66 receptor gene-silenced ceils prus the poly（O,L-lactide-co-glycolic acid） scaffold compared with rats treated with scaffold only, and the number of bone marrow mesenchymal stem cells and neuron-like cells was also increased. At 8 weeks after transplantation, horseradish peroxidase tracing and transmission electron microscopy showed a large number of unmyelinated and myelinated nerve fibers, as well as intact regenerating axonal myelin sheath following spinal cord hemisection injury. These experimental findings indicate that transplantation of Nogo-66 receptor gene-silenced bone marrow mesenchymal stem cells and Schwann cells plus a poly（D,L-lactide-co-glycolic acid） scaffold can significantly enhance axonal regeneration of spinal cord neurons and improve motor function of the extremities in rats following spinal cord injury.

基于数据库挖掘、网络药理学和试验验证探究葡萄籽多酚缓解溃疡性结肠炎的作用机制

本试验旨在探究葡萄籽多酚缓解葡聚糖硫酸钠诱导的溃疡性结肠炎的机制。试验选用GEO数据库中的两个数据集,使用sva包对其进行整合后,通过加权基因共表达网络的方法鉴定与溃疡性结肠炎相关的基因模块,并利用基因本体论数据库和京都基因与基因组百科全书数据库对基因功能进行注释;使用液相色谱-质谱联用技术检测葡萄籽多酚主要成分,选取含量前10的成分,利用TCMSP、DrugBank、SwissTargetPrediction等数据库和靶点预测工具获取其作用的靶点,并与先前鉴定的溃疡性结肠炎相关模块的基因取交集,使用蛋白质-蛋白质相互作用网络分析,得到葡萄籽多酚缓解溃疡性结肠炎的关键靶点;使用分子对接验证葡萄籽多酚主要成分与关键靶点的连接活性;利用Raw264.7细胞系,通过荧光定量PCR鉴定葡萄籽多酚对关键靶点基因的影响。结果表明,有3个基因模块与溃疡性结肠炎表型高度相关,且模块内的基因主要与炎症反应、细胞周期和代谢、细胞的趋化等功能相关;葡萄籽多酚的主要成分分别为儿茶素、表儿茶素、原花青素B2、刺柄芒花素等,这些成分作用的靶点基因与溃疡性结肠炎相关模块的基因有15个相同,而在这15个基因中,前列腺素内过氧化物合酶2、基质金属酶9、白介素-6、肿瘤坏死因子-α因为在网络中有最高的连接度而被认为是关键靶点;葡萄籽多酚含量最高的10个成分与这4个靶点均具有良好的连接活性,荧光定量PCR也证明了葡萄籽多酚能影响这4个靶点基因的表达。综上,葡萄籽多酚最有可能通过影响前列腺素内过氧化物合酶成2、基质金属酶9、白介素-6和肿瘤坏死因子-α来缓解溃疡性结肠炎。

地下水系统中的抗生素对反硝化的影响研究进展

微生物反硝化过程是地下水中硝酸盐最重要的脱氮形式。再生水利用和养殖业引起的抗生素污染常与硝酸盐共存。因此,需深入研究抗生素及其存在形式对地下水中硝酸盐反硝化过程及抗生素抗性基因(ARGs)产生、富集和传播的影响,以综合解析地下水硝酸盐浓度升高的原因。近年来的研究识别了地下水系统中抗生素的解离/络合形态、吸附形式(层间吸附/表面吸附)、水解与微生物降解产物等存在形式,并从反硝化微生物群落、功能酶的种类与活性、功能基因丰度以及ARGs产生与传播途径阐释了抗生素对反硝化过程的抑制机制。主要结论为:(1)地下水系统中,抗生素以多种形式存在,而不同形式的抗生素对微生物的毒性有显著差异;(2)在每升纳克至微克水平的抗生素存在下,地下水反硝化过程受到抑制,抗生素改变了微生物群落结构,抑制了功能酶活性,增加了ARGs的丰度,在这些作用的协同影响下,硝酸盐降解动力学由零级向一级转变;(3)在抗生素抑制反硝化过程中,还增加了温室气体N2O的释放量,抗生素影响了功能基因nosZ表达,N2O浓度与nosZ丰度呈负指数关系。在综述相关文献的基础上,对未来研究提出了展望:(1)定量识别典型抗生素进入地下水系统后的存在形式;(2)厘清不同存在形式的抗生素对反硝化微生物群落、功能酶种类与活性、功能基因丰度和多样性的影响;(3)探索反硝化功能基因在抗生素不同存在形式和不同输入方式下的变化过程,并建立ARGs产生、富集与传播模式;(4)结合野外观测和室内实验从分子生物学、环境化学和水文地质学多尺度研究复合污染下地下水系统的反硝化过程,可为日益复杂的地下水污染防治和饮用水安全保障提供理论依据。

与苹果Co基因紧密连锁的RAPD标记的筛选及其SCAR标记转换(英文)

以短枝富士 (SpurFuji)×舞姿 (Telamon)的 10 5株F1群体为试材 ,利用RAPD技术 ,结合集群分类分析法(BSA)进行了苹果柱型基因 (Co)分子标记的研究。通过对 30 0条随机引物的筛选 ,获得一个与Co基因紧密连锁的RAPD标记S114 2 682 ,连锁距离为 2 .86cM。对该标记片段进行序列测定 ,然后根据序列特点设计了 4条特异引物(其中正向引物与反向引物各两条 )。PCR结果显示 ,这 4条引物的 4种组合都可以扩增出柱型性状的特征带。选其中之一进行群体上的分析 ,结果表明该SCAR标记特征带与柱型性状的共分离行为与原RAPD标记表现一致。可见 ,此组合的引物可以作为该SCAR标记的特异引物。通过对S114 2 682 标记片段序列分析发现 ,在 +45～ +2 5 1区域含有一个可编码 6 8个氨基酸残基的ORF。

雀形目15种鸟类CoⅠ与Cyt b基因序列的比较

对雀形目Passeriformes6科15种鸟类线粒体DNA的Cyt b基因全序列(1143bp)和CoⅠ基因部分序列(1176bp)进行了比较,结果显示Cyt b和CoⅠ基因序列的变异位点分别为454个和366个,简约信息位点为337个和303个,而且CoⅠ基因比Cytb基因略微保守,进化速率也较低。采用邻接法、最大简约法、最大似然法和贝叶斯法分别构建了CoⅠ和Cyt b基因两组数据集的分子系统发生树及其合一树,并对建树结果进行了比较分析。基于以上两点,本文认为CoⅠ基因比Cyt b基因更适合于确定雀形目科级阶元之间的系统发生关系,而且它也能够作为雀形目物种鉴定的分子标记,但在物种鉴定方面不如Cyt b基因稳定和准确。