Tumor necrosis factor receptor-associated protein 1 regulates hypoxia-induced apoptosis through a mitochondria-dependent pathway mediated by cytochrome c oxidase subunit Ⅱ

Background:Tumor necrosis factor receptor-associated protein 1(TRAP1)plays a protective effect in hypoxic cardiomyocytes,but the precise mechanisms are not well clarified.The study is aimed to identify the mechanism of TRAP1 on hypoxic damage in cardiomyocytes.Methods:In this study,the effects of TRAP1 and cytochrome c oxidase subunit Ⅱ(COXⅡ)on apoptosis in hypoxia-induced cardiomyocytes were explored using overexpression and knockdown methods separately.Results:Hypoxia induced cardiomyocyte apoptosis,and TRAP1 overexpression notably inhibited apoptosis induced by hypoxia.Conversely,TRAP1 silencing promoted apoptosis in hypoxic cardiomyocytes.Further investigation revealed that the proapoptotic effects caused by the silencing of TRAP1 were prevented by COXⅡ overexpression,whereas COXⅡ knockdown reduced the antiapoptotic function induced by TRAP1 overexpression.Additionally,changes in the release of cytochrome c from mitochondria into the cytosol and the caspase-3 activity in the cytoplasm,as well as reactive oxygen species production,were found to be correlated with the changes in apoptosis.Conclusions:The current study uncovered that TRAP1 regulates hypoxia-induced cardiomyocyte apoptosis through a mitochondria-dependent apoptotic pathway mediated by COXⅡ,in which reactive oxygen species presents as an important component.

Cytochrome c Oxidase Subunit 1-based Human RNA Quantification to Enhance mRNA Profiling in Forensic Biology

RNA analysis offers many potential applications in forensic science,and molecular identification of body fluids by analysis of cell‑specific RNA markers represents a new technique for use in forensic cases.However,due to the nature of forensic materials that often admixed with nonhuman cellular components,human‑specific RNA quantification is required for the forensic RNA assays.Quantification assay for human RNA has been developed in the present study with respect to body fluid samples in forensic biology.The quantitative assay is based on real‑time reverse transcription‑polymerase chain reaction of mitochondrial RNA cytochrome c oxidase subunit I and capable of RNA quantification with high reproducibility and a wide dynamic range.The human RNA quantification improves the quality of mRNA profiling in the identification of body fluids of saliva and semen because the quantification assay can exclude the influence of nonhuman components and reduce the adverse affection from degraded RNA fragments.

Identification of forensically important blow fly species （Diptera： Calliphoridae） in China by mitochondrial cytochrome oxidase I gene differentiation

Unambiguous and rapid sarcosaphagous insect species identification is an essential requirement for forensic investigations. Although some insect species are difficult to classify morphologically, they can be effectively identified using molecular methods based on similarity with abundant authenticated reference DNA sequences in local databases. However, local databases are still relatively incomplete in China because of the large land area with distinct regional conditions. In this study, 75 forensically important blow flies were collected from 23 locations in 16 Chinese provinces, and a 278-bp segment of the cytochrome oxidase subunit I gene of all specimens was successfully sequenced. Phylogenetic analysis of the sequenced segments showed that all Calliphorid specimens were properly assigned into nine species with relatively strong supporting values, thus indicating that the 278-bp cytochrome oxidase subunit one region is suitable for identification of Calliphorid species. The clear difference between intraspecific threshold and interspecific divergence confirmed the potential of this region for Calliphorid species identification, especially for distinguishing between morphologically similar species. Intraspecific geographic variations were observed in Lucilia sericata （Meigen, 1826） and Lucilia caesar （Linnaeus, 1758）.

基于eDNA技术的舟山近海中国团扇鳐定性与定量分析

为探讨环境DNA (environmental DNA, eDNA)技术用于中国团扇鳐监测方面的可行性,同时开展基于eDNA技术的舟山近海中国团扇鳐定性与定量分析。本实验将中国团扇鳐与其同属汤氏团扇鳐COI基因片段序列进行比较分析,使用Primer Express 3.0软件设计中国团扇鳐特异性引物与Taq Man探针。在舟山朱家尖近海设计了A、B、C共3个定置网调查站位,定期收集中国团扇鳐样品。于2017年12月19日、2018年4月13日和2018年7月14日分别采集水样(站位A、B1、B2、C1、C2、D),开展eDNA微滴式数字PCR(droplet digital PCR, ddPCR)检测,并将检测结果与水温和采样点进行差异显著性分析。结果显示,不同站位、不同时间的中国团扇鳐eDNA浓度不同,水样采集点对中国团扇鳐eDNA浓度的影响极显著,不同采样点eDNA在不同季节存在极显著差异。研究表明,eDNA检测技术灵敏度高,水温、底质和水深对中国团扇鳐的分布皆有影响。研究结果为其他海域的中国团扇鳐e DNA追踪监测奠定了基础。

基于In Silicon模拟消化的北极虾DPP-Ⅳ抑制肽活性分析

北极虾具有很高的营养价值,在食品领域已引起越来越多的关注。对北极虾蛋白进行In Silicon模拟消化获得寡肽,通过PeptideRanker活性评分及理化性质分析,从中筛选出具有潜在生物活性的寡肽。使用ToxinPred分析和BIOPEP-UWM生物活性预测,发现部分寡肽具有二肽基肽酶-Ⅳ(dipeptidyl peptidase-Ⅳ,DPP-Ⅳ)抑制活性,最终确定WFP(一种三肽,Trp-Phe-Pro)具有最优的DPP-Ⅳ抑制活性肽。分子对接表明,WFP和DPP-Ⅳ能够形成稳定的复合物,其结合能为-6.93 kcal/mol,进一步研究表明,WFP通过与DPP-Ⅳ S1、S2、S3三个活性口袋中的9个氨基酸残基发生相互作用而抑制其活性。本研究为阐释北极虾营养价值及生物活性肽的开发提供了理论依据。

Benthodytes occidentpalauta sp.nov.,a new species of deep-sea holothuroid(Elasipodida:Psychropotidae)from the west of Kyushu-Palau Ridge in the Western Pacific Ocean

Benthodytes occidentpalauta sp.nov.was collected from the Kyushu-Palau Ridge at a depth of 5481 m in 2021.This new species is characterized by a gelatinous body wall,violet skin,six pairs of dorsal papillae,and a rough mid-ventral surface without tube feet.The dorsal deposits are rod-shaped and tripartite.Two types of papillae deposits as crosses with four arms with central bipartite apophyses.Ventral deposits are rods.Tentacle ossicles are rod-shaped with end protrusions.Gonad deposits are rodshaped,tripartite,and cross-shaped.The phylogenetic analyses based on cytochrome oxidase subunit 1(COI)and 16S individually and a concatenated dataset of COI and 16S genes of this species support that B.occidentpalauta sp.nov.belongs to Benthodytes.

珠江流域常见鱼类及大型底栖动物DNA条形码空缺分析

条形码数据库是开展基于DNA的生物监测关键先决条件。为在珠江流域有效开展基于DNA的生物监测,迫切需要了解物种DNA条形码的覆盖或空缺状况。整理了珠江流域常见鱼类和大型底栖动物的物种清单,从National Center and Biotechnology Information (NCBI)数据库中检索了物种清单的DNA条形码序列,分析了常见鱼类(包括线粒体组和12s rRNA基因)和大型底栖动物(包括线粒体组、COI和18s rRNA基因)的DNA条形码覆盖范围和空缺程度。数据分析表明:(1)珠江流域共记录了常见鱼类221种,隶属于2纲18目51科和137属;常见大型底栖动物105种/属,隶属于6纲14目53科。(2)共检索到常见鱼类线粒体组序列913条和12s rRNA基因序列962条,分别占总物种的81.45%和57.92%;有12.67%的物种没有线粒体组和12s rRNA基因序列,若将条形码阈值设置为至少包含5个参考序列,则空缺度上升至52.94%;(3)共检索到常见大型底栖动物线粒体组65条序列、COI基因26,988条序列和18s rRNA基因175条序列,分别占总种/属数的29.52%、68.57%和37.14%;有25.71%的种/属在线粒体组、COI和18s rRNA基因区域皆无序列收录,若将条形码阈值设置为至少包含5个参考序列,则空缺度上升至41.90%。总之,本研究将为珠江流域开展基于DNA的鱼类和大型底栖动物监测提供基础数据支撑,为完善珠江本土DNA条形码数据库提供参考建议。

Morphological and molecular characterization of the rice root-knot nematode, Meloidogyne graminicola, Golden and Birchfeild, 1965 occurring in Zhejiang, China

The rice root-knot nematode Meloidogyne graminicola is a severe pest of rice. In China, it was first reported from Hainan Province, and later from several other provinces. In the present study, a rice root-knot nematode population found from the rice cultivation areas of Zhejiang Province, China is characterized via molecular analysis using internal transcribed spacer(ITS) and cytochrome c oxidase subunit Ⅱ(coxⅡ)-16 S rRNA genes and scanning electron microscopy(SEM) observations of males and the second-stage juveniles. Morphometric data and molecular sequence comparisons for all M. graminicola populations occurring in China are also provided. The overall morphology of M. graminicola found in Zhejiang match well with the original description, though males have a slightly longer body and stylet, and a shorter tail, while the second-stage juvenile is also slightly longer than in the original description. This is the first report of M. graminicola from Zhejiang. Phylogenetic studies based on coxⅡ suggest that all the Chinese populations belong to Type B. This study expands knowledge of the increasing distribution and phylogenetic relationships of M. graminicola that occur in China.

渤海湾7种虾虎鱼科鱼类COI基因序列特征及分子分类研究

为获得渤海湾天津海域常见虾虎鱼线粒体条形码序列及系统分类信息,采集渤海湾7种虾虎鱼样本,通过形态初步鉴定物种,并提取DNA进行线粒体COI基因部分序列扩增测序,用系统进化分析及分子鉴定软件MEGA对渤海湾常见12种虾虎鱼COI基因部分片断进行序列特征分析及分子分类分析。扩增得到7种虾虎鱼COI基因片断,分析得到其平均GC含量低于AT含量,碱基在密码子位置分布中具有偏向性,且GC含量最高为第2位碱基,与多种鱼类COI基因碱基特点相似。基因密码子碱基变异率为19.4%,转换颠换比为1.3。遗传距离分析及系统进化树分析理清了渤海湾天津海域12种主要虾虎鱼的系统分类及进化关系。遗传距离显示,矛尾刺虾虎鱼(Amblychaeturichthys hexanema)和斑尾复虾虎鱼(Synechogobius ommaturus)为同种鱼。虾虎鱼COI编码基因密码子高变异率可能与其良好的环境适应性有关。

西藏察隅县蜱的分子鉴定

目的 利用分子生物学方法分析西藏察隅县蜱类组成。方法 对察隅3个乡镇10个行政村饲养的家畜和丛林环境中的蜱进行调查采样,提取蜱DNA,对COI基因进行PCR扩增和测序,通过与GenBank数据库在线比对和系统发育进化树构建进行蜱虫种属鉴定。结果 经COI基因序列分析,共鉴定出蜱虫7种,其中牛身上的寄生蜱虫主要为微小扇头蜱,同时也发现了西藏血蜱、长角血蜱、卵形硬蜱,丛林环境中的游离蜱虫有微小扇头蜱、锐跗硬蜱、克拉斯比尔血蜱。结论 西藏察隅县蜱虫分布广泛,本研究可为察隅县蜱虫调查和疾病防控提供重要参考。

DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes

Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish.

Genetic diversity and population structure of the sea star Asterias amurensis in the northern coast of China

The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causing extensive economic and ecological losses to the local aquaculture industry and marine ecosystem.Understanding the genetic diversity and population structure of A.amurensis can provide vital information for resource management.By analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I(COI)gene and ten simple sequence repeat(SSR)microsatellites markers,the genetic diversity and population structure of A.amurensis of four populations along the northern coast of China was uncovered.A total of 36 haplotypes were identified,and a main haplotype was found in four populations.The Qingdao(QD)population displayed the highest genetic diversity among all the populations.The AMOVA and pairwise F_(st)showed that there was small but statistically significant population differentiation among the four populations,especially between QD and Weihai(WH).Moreover,the principal component analysis(PCA)and admixture analysis showed that several individuals in Yantai(YT)and Dalian(DL)had little genetic association with other individuals.Overall,this study provided useful information of the genetic diversity and population structure of A.amurensis and will contribute to the resource management of A.amurensis in China.

基于COI基因的赣北地区小泡巨鼠的鉴定

目的以线粒体细胞色素C氧化酶亚基(COI)基因为目的基因,利用DNA条形码技术对未知鼠样本进行鉴定.方法采用夹夜法对九江市武宁县宋溪镇某村的鼠密度进行调查,经形态学初步鉴定后,以捕获的1只无法明确鉴定的大型鼠样本为对象,提取基因组DNA并采用COI基因通用引物BatL5310和R6036R进行PCR扩增及测序,将测序结果在NCBI网站进行BLAST比对,采用MEGA7软件选择最大似然法构建系统发育树.结果共捕获小型兽类7只,密度为3.38%,经形态学鉴定有褐家鼠2只,黑线姬鼠2只,臭鼩鼱2只,形态学初步鉴定为青毛巨鼠或小泡巨鼠的未知鼠1只,提取的未知鼠样本DNA通过PCR成功扩增出COI基因目的条带,与NCBI基因库中小泡巨鼠(KP995219)序列同源性高达100%,系统发育树显示该鼠样本与小泡巨鼠(KP995219、KP995203)处于同一分支,遗传距离分别为0、0.0016,而青毛巨鼠(NC_036730)单独处于另一分支,遗传距离较远.结论赣北地区首次报道小泡巨鼠,采用COI基因的DNA条形码技术可快速、准确的进行鼠种鉴定,有助于弥补非常见鼠形态学鉴定困难的不足.

生物分类学的新动向——DNA条形编码

过去的一年中 ,DNA条形编码 (DNABarcoding)成为生物分类学中引人注目的新方向。DNA条形编码 ,根据对一个统一的目标基因DNA序列的分析 ,达到物种鉴定的目的 ,它操作的简便性和高效性将以我们无法想象的速度加快物种鉴定和进化历史研究的步伐 ,但国际上对此的争论也不少。本文综述了DNA条形编码的原理、操作过程及最新进展 。

6种帘蛤科贝类及4个地理种群文蛤线粒体COI基因片段序列分析

对文蛤（Meretrix meretrix L.,1758）、青蛤（Cyclina sinensis G.,1791）、硬壳蛤（Mercenaria mercenaria L.,1758）、江户布目蛤（Protothaca jedoensis L.,1874）、薄片镜蛤（Dosinia corrugata R.,1850）和菲律宾蛤仔（Ruditapes philippinarum A.,1850）6种帘蛤科贝类和4个地理种群文蛤（大连、连云港、湛江、防城港）的细胞色素c氧化酶亚基Ⅰ（COⅠ）基因片段的核苷酸序列进行了分析,以探讨这一序列在种质鉴定、种群遗传结构和分子系统发生研究中的应用价值.测序结果表明,所有物种扩增片段长度均为709 bp,序列A＋T含量（62.2%-67.6%）明显高于GC含量.物种间共有变异位点311个,其中简约信息位点202个;文蛤4个地理种群间共有变异位点46个,其中简约信息位点2个.此区段共编码235个氨基酸,种间共有氨基酸变异位点85个;文蛤种群间只有1个氨基酸变异位点.以COⅠ基因片段序列为标记,用大竹蛏（Solen grandis）作外群,构建了帘蛤科贝类的系统发生树,其拓扑结构显示4个地理种群文蛤首先聚为1个单元,然后与青蛤聚在一起,最后所有帘蛤科物种聚为一枝,与外群相区别,其结果与传统形态分类基本一致,说明COⅠ基因适合作为该科贝类种群遗传结构和系统发生研究的分子标记.

中国东南沿海青蟹线粒体COI基因部分序列分析

对我国东南沿海5个地区的72个青蟹个体的线粒体细胞色素氧化酶亚基I（COI）部分序列序列进行了测定和分析。获得的72个细胞色素氧化酶亚基I（COI）序列可分为12个单倍型，与GenBank中已知的Scylla partmmmosain COI序列的相似性达到98％以上，与其它3种青蟹的差异为7．36％～15．54％。这些序列与S．paramamosain的遗传距离仅为0．00783，但是与S．serrata、S．olivacea和S．tranquebarica的遗传距离却分别达到0．11659、0．17812和0．08423。序列特征、遗传距离和系统进化等分析结果都表明本文研究的青蟹为S．paramamosain。结果提示，在进行青蟹属相关研究应当仔细鉴别采集样本的种类。

基于线粒体CO1基因的DNA条形码在石首鱼科(Sciaenidae)鱼类系统分类中的应用

采用CO1基因特异扩增测序及与GenBank已有序列联配分析的方法,进行了石首鱼科19属30种鱼类75个CO1基因片段的序列比较和系统进化研究,结果表明,石首鱼科鱼类该片段的平均GC含量为48.3%,其中第2密码子位点含量最高(51%-58.4%,平均56.6%),第1密码子变化范围最大(27.6%-54.1%,平均44.9%),第3密码子差别较小(41.6%-43.6%,平均42.7%)。依据Kimura-2-parameter模型,30种石首鱼科鱼类种内遗传距离平均值为0.006,种间为0.210,种间遗传距离是种内的35倍;在分子系统树上,28个种(93.3%)可形成单系,18个属(94.7%)可聚为独立的分支;与形态学分类不同的是,由黑鳃梅童鱼(Collichthys lucidus)与棘头梅童鱼(C.niveatus)的遗传距离(0.004)推断二者遗传变异尚未达到种的分化水平,灰鳍彭纳石首鱼(Pennahia anea)与白姑鱼(Argyrosomus argentatus)的形态学特征相似性和条形码序列同源性都提示二者可能为同种异名,而红牙(Otolithes ruber)印度洋和南海两个地理群体间的遗传分化已经达到种的水平。本研究证明线粒体CO1基因可作为DNA条形码对石首鱼科鱼类进行有效的物种鉴定,亦可用于探讨石首鱼科的属、种分类单元系统发育问题。

DNA条形码识别Ⅰ.DNA条形码研究进展及应用前景

DNA条形码(DNA Barcoding)是近年来生物分类学中引人注目的发展热点。本文综述了DNA条形码的发展历史、识别原理以及公共数据库,并讨论了DNA条形码在检疫检验领域的应用前景。DNA条形码与DNA芯片技术的结合,将推动传统物种鉴定方法的更新,可在检疫检验领域中实现非专家检定,这对进出口口岸生物监测具有重要的理论意义和应用价值。

斑腿蝗科Catantopidae七种蝗虫线粒体COⅠ基因的DNA条形码研究

以我国常见的斑腿蝗科Catantopidae7种蝗虫为对象测定了COⅠ基因序列,探讨COⅠ基因作为DNA条形码在识别蝗虫物种方面的可行性。结果表明,斑腿蝗科3属7种的DNA分类和形态学分类基本一致,该基因可以探讨蝗虫属、种分类单元的系统发育问题,为将线粒体基因组的COⅠ基因作为蝗虫DNA条形码进行分类鉴定手段的可行性提供一定的参考。