紫外辐照恢复早期耐辐射奇球菌的转录组学分析（英文）

目的 耐辐射奇球菌是一种对紫外线、电离、干燥和化学试剂具有较强抗性的极端微生物。然而，该菌在紫外辐照后恢复早期的分子响应还不完全清楚。本文的目的是揭示耐辐射奇球菌在这一阶段的转录组响应。方法 本研究采用RNA-seq技术，测定了正常和紫外辐照培养条件下耐辐射奇球菌的转录组。为确定关键的差异表达基因及其调控关系，进行了功能富集分析。选取部分关键差异表达基因，进行实时定量PCR实验验证。利用以往研究中的转录组数据，寻找紫外辐照、电离辐射和干燥胁迫条件下公共的差异表达基因。构建了蛋白质-蛋白质相互作用网络；对蛋白质互作网络中的枢纽基因和主要模块进行了鉴定；对这些枢纽基因和模块进行了功能富集分析。结果 紫外辐照后的恢复早期，上调基因数量是下调基因数量的2倍以上，且多数与应激反应和DNA修复有关。恢复早期的修复途径主要有单链退火（SSA）途径（涉及基因：ddr A-D）、非同源端连接（NHEJ）途径（涉及基因：lig B、ppr A）和核苷酸切除修复（NER）途径（涉及基因：uvr A-C），前两种途径为同源重组（HR）做准备，而NER途径去除紫外线照射带来的嘧啶二聚体。通过比较紫外辐照、电离辐...     

基于比较转录组学分析NaCl胁迫影响德尔卑沙门氏菌的耐渗机制

【目的】研究高渗胁迫条件下德尔卑沙门氏菌(Salmonella enterica subsp. enterica Derby, S. Derby)的转录组调控机制,分析差异表达基因(differentially expressed genes, DEGs)表达水平,探究在高渗胁迫影响下德尔卑沙门氏菌耐渗反应的相关代谢通路。【方法】通过高渗胁迫诱导德尔卑沙门氏菌的耐渗性,提取菌株的总RNA,去除rRNA,构建cDNA文库。利用转录组测序技术及生物学信息技术分析相关DEGs,并通过实时荧光定量PCR (real-time fluorescence quantitative PCR, qRT-PCR)进行验证。【结果】胁迫组德尔卑沙门氏菌通过转录组测序结果发现有3 950个DEGs,其中具有显著上调的基因21个,显著下调基因38个。涉及到细胞膜蛋白、氨基酸的代谢等相关基因上调,协助德尔卑沙门氏菌在高渗环境中存活。与此同时,胁迫组德尔卑沙门氏菌的糖转运系统(sugar transport system, PTS)、糖酵解过程以及抗氧化性相关基因表达显著下调,这是由于高渗环境菌体需要在体内储存大量糖类等物质,从而降低了糖原的消耗,进而导致细胞外膜的脂多糖合成受到抑制,降低了高渗胁迫下德尔卑沙门氏菌细胞膜表面的O抗原的合成。【结论】高渗环境诱导后显著提高了德尔卑沙门氏菌的耐渗性,其中Na⁺/H⁺逆向转运蛋以及谷氨酸的代谢通路发挥着重要的作用,为进一步了解以及更好地控制其在食品中的污染提供了理论依据。     

应用GSEA和WGCNA方法分析细菌性败血症宿主关键差异基因及意义

【目的】采用生物信息学方法分析公共数据库来源的细菌性败血症患者全血转录组学表达谱,探讨细菌败血症相关的宿主关键差异基因及意义。【方法】基于GEO数据库中GSE80496和GSE72829全血转录组基因数据集,采用GEO2R、基因集富集分析(GSEA)联用加权基因共表达网络分析(WGCNA)筛选细菌性败血症患者相比健康人群显著改变的差异基因,通过R软件对交集基因进行GO功能分析和KEGG富集分析。同时,通过String 11.0和Cytoscape分析枢纽基因,验证枢纽基因在数据集GSE72809(Health组52例,Definedsepsis组52例)全血标本中的表达情况,并探讨婴儿性别、月(胎)龄、出生体重、是否接触抗生素等因素与靶基因表达谱间的关系。【结果】分析GSE80496和GSE72829数据集分别筛选得到932个基因和319个基因,联合WGCNA枢纽模块交集得到与细菌性败血症发病相关的10个枢纽基因(MMP9、ITGAM、CSTD、GAPDH、PGLYRP1、FOLR3、OSCAR、TLR5、IL1RN和TIMP1);GSEA分析获得关键通路(氨基酸糖类-核糖代谢、PPAR信号通路、聚糖生物合成通路、自噬调控通路、补体、凝血因子级联反应、尼古丁和烟酰胺代谢、不饱和脂肪酸生物合成和阿尔兹海默症通路)及生物学过程(类固醇激素分泌、腺苷酸环化酶的激活、细胞外基质降解和金属离子运输)。【结论】本项研究通过GEO2R、GSEA联用WGCNA分析,筛选出与细菌性败血症发病相关的2个枢纽模块、10个枢纽基因以及一些关键信号通路和生物学过程,可为后续深入研究细菌性败血症致病机制奠定理论依据。     

NaCl胁迫下哈茨木霉ACCC32524的转录组和代谢组分析

【目的】通过分析NaCl胁迫下哈茨木霉(Trichoderma harzianum)ACCC32524转录组和代谢组数据,研究差异表达基因及次级代谢产物的变化情况,初步探索响应NaCl胁迫的分子机制。【方法】利用Illumina HiSeq XTen高通量测序平台完成0、0.4、0.6 mol/L NaCl浓度胁迫培养下哈茨木霉ACCC32524的转录组测序,GC-TOF-MS技术完成对0mol/L和0.6mol/LNaCl胁迫培养下的差异次级代谢产物检测,利用相关软件及数据库对差异表达基因(DEGs)和次级代谢产物的注释、筛选和分类,并进行RT-qPCR验证。【结果】本研究分别得到0.4 mol/L和0.6 mol/L NaCl胁迫下417和733条差异表达基因;GO富集分析显示,分别有318和582条差异表达基因注释到生物学过程、分子功能和细胞组分3个一级分类和40个二级分类;COG分类结果表明分别有232和414条转录本为20个类别,涉及差异表达基因最多的分别为氨基酸的转运和代谢、一般功能预测、碳水化合物的转运和代谢;KEGG代谢途径分析结果表明,分别有75和96条基因归到25个代谢通路中(P≤0.05),其中涉及差异基因最多的是氨基酸的生物合成和2-氧代羧酸代谢通路。从转录组数据中共筛选出与渗透调节、离子转运、活性氧清除等22个耐盐相关基因。0 mol/L和0.6 mol/L NaCl胁迫下的代谢组数据中共筛选出101个差异次级代谢产物,包括8种积累量上调和93种下调物质,其中36个得到定性,分属于糖类、有机酸和氨基酸等9个分类中。RT-qPCR验证挑选的差异表达基因的表达量变化,均与RNA-seq分析结果一致。【结论】NaCl胁迫下引起哈茨木霉ACCC32524基因及次级代谢产物发生明显变化,细胞代谢途径发生明显偏移,这些进程共同作用减少NaCl对细胞的毒害作用,为木霉菌的耐盐机理研究提供重要信息。     

乙烯诱导水仙成花相关代谢物和基因的筛选与分析

为了解乙烯诱导水仙(Narcissus tazetta var. chinensis)成花的生理和分子机制,利用代谢组和转录组测序技术,筛选乙烯诱导水仙成花的差异表达代谢物和基因。结果表明,乙烯处理的侧芽检测到12个差异表达代谢物(DEM),包括7个上调,5个下调,其中,(±)7-表茉莉酸、多巴胺、亚精胺可能与乙烯诱导水仙成花正相关,而吲哚及其衍生物呈负相关。转录组共获得1 021个差异表达基因(DEG),包括615个上调,406个下调,在DEG中鉴定筛选了45个与乙烯信号传导和开花相关的差异表达基因。乙烯诱导水仙成花启动可能先激活水仙鳞茎内源植物激素(尤其乙烯)信号通路的变化,与开花促进基因FPF1和MADS15的上调表达密切相关。9个基因的qRT-PCR结果验证了RNA-Seq的正确性。这些差异表达的代谢物和基因在水仙成花启动过程中可能具有重要作用。     

Comprehensive candidate gene study highlights UGT1A and BNC2 as new genes determining continuous skin color variation in Europeans

Natural variation in human skin pigmentation is primarily due to genetic causes rooted in recent evolutionary history. Genetic variants associated with human skin pigmentation confer risk of skin cancer and may provide useful information in forensic investigations. Almost all previous gene-mapping studies of human skin pigmentation were based on categorical skin color information known to oversimplify the continuous nature of human skin coloration. We digitally quantified skin color into hue and saturation dimensions for 5,860 Dutch Europeans based on high-resolution skin photographs. We then tested an extensive list of 14,185 single nucleotide polymorphisms in 281 candidate genes potentially involved in human skin pigmentation for association with quantitative skin color phenotypes. Confirmatory association was revealed for several known skin color genes including HERC2, MC1R, IRF4, TYR, OCA2, and ASIP. We identified two new skin color genes: genetic variants in UGT1A were significantly associated with hue and variants in BNC2 were significantly associated with saturation. Overall, digital quantification of human skin color allowed detecting new skin color genes. The variants identified in this study may also contribute to the risk of skin cancer. Our findings are also important for predicting skin color in forensic investigations.     

基于转录组的冬虫夏草菌微循环产孢研究

为研究冬虫夏草菌（Ophiocordyceps sinensis）微循环产孢过程中的分子机理,采用高通量测序技术,对微循环产孢前后冬虫夏草菌的转录组进行研究。筛选获得差异表达基因6 902个。Gene Ontology（GO）功能聚类分析表明,差异表达基因主要参与分子功能、胞内运输、核糖核蛋白复合体等生物学通路。京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes,KEGG)功能富集分析结果表明,差异表达基因参与了核糖体、嘧啶代谢、蛋白酶体、嘌呤代谢、甘氨酸代谢等过程。Mmc、Mcb、MaH1、MaPP5、MaAGA、Pyk等候选基因不同程度的参与了冬虫夏草菌微循环产孢过程,其中Mcb家族基因可能起到关键作用。通过qRT PCR验证差异表达基因,定量结果与转录组测序结果一致。本研究为进一步揭示冬虫夏草菌微循环产孢分子机制以及关键基因的调控提供了重要信息。     

The evolution of teleost pigmentation and the fish‐specific genome duplication

Teleost fishes have evolved a unique complexity and diversity of pigmentation and colour patterning that is unmatched among vertebrates. Teleost colouration is mediated by five different major types of neural‐crest derived pigment cells, while tetrapods have a smaller repertoire of such chromatophores. The genetic basis of teleost colouration has been mainly uncovered by the cloning of pigmentation genes in mutants of zebrafish Danio rerio and medaka Oryzias latipes. Many of these teleost pigmentation genes were already known as key players in mammalian pigmentation, suggesting partial conservation of the corresponding developmental programme among vertebrates. Strikingly, teleost fishes have additional copies of many pigmentation genes compared with tetrapods, mainly as a result of a whole‐genome duplication that occurred 320–350 million years ago at the base of the teleost lineage, the so‐called fish‐specific genome duplication. Furthermore, teleosts have retained several duplicated pigmentation genes from earlier rounds of genome duplication in the vertebrate lineage, which were lost in other vertebrate groups. It was hypothesized that divergent evolution of such duplicated genes may have played an important role in pigmentation diversity and complexity in teleost fishes, which therefore not only provide important insights into the evolution of the vertebrate pigmentary system but also allow us to study the significance of genome duplications for vertebrate biodiversity.