Expression profiles of penaeidin from Fenneropenaeus chinensis in response to WSSV and vibrio infection by real-time PCR

Penaeidin from Chinese shrimp (Fenneropenaeus chinensis) has proved to be one of the most important antimicrobial peptides in the bodies of animals. The relative quantitative real-time PCR method is developed to study through time, the mRNA expression profile of penaeidin in the muscle and haemocyte tissue of Chinese shrimp infected with vibrio (Vibrio anguillarum) and WSSV (white spot syndrome virus). Research results showed that the same pathogens infection experiments produced similar gene expression profile in different tissues while different expression profiles appeared in the same tissues infected by different exterior pathogens. In vibrio infection experiments, a "U" Re expression profile resulted. Expression levels of penaeidin increased and surpassed the non-stimulated level, indicating that penaeidin from Chinese shrimp has noticeable antimicrobial activities. In WSSV infection experiments, the expression profile appeared as an inverse "U" with the expression of penaeidin gradually decreasing to below baseline level after 24 h. The expression of antimicrobial peptides gene in mRNA level in response to virus infection in shrimp showed that international mechanisms of virus to haemocytes and microbial to haemocytes are completely different. Decline of penaeidins expression levels may be due to haemocytes being destroyed by WSSV or that the virus can inhibit the expression of penaeidins by yet undiscovered modes. The expression profiles of penaeidin in response to exterior pathogen and the difference of expression profiles between vibrio and WSSV infection provided some clues to further understanding the complex innate immune mechanism in shrimp.

Species identification in salted products of red snappers by semi-nested PCR-RFLP based on the mitochondria 12S rRNA gene sequence

A molecular approach was developed to distinguish species of red snappers among commercial salted fish products. The specific fragments of the mitocliondrial 12S rRNA gene, which were about 450 bp, were obtained using the semi-nested polymerase chain reaction (semi-nested PCR). Subsequently, PCR amplicons were sequenced, aiming to select restriction endonucleases that generated species-specific restriction fragment length polymorphism (RFLP) profiles. Discrimination of red snappers Lutjanus sanguineus, L. erythopterus from L. argentintaculatus, L. malabarius and other morphologically similar fishes such as Lethrinus leutjanus and Pinjalo pinjalo was feasible by one restriction digestion reaction with three endonucleases Hae III, Sca I and SnaB I, however, for differentiation of L. sattguineus and L. erythopterus, another restriction digestion reaction with single restriction endonuclease Mae II was needed. The seminested PCR-RFLP was demonstrated to be reliable in species identification of salted fish products in this study. (c) 2005 Published by Elsevier Ltd.

Species identification in salted products of red snappers by semi-nested PCR-RFLP based on the mitochondrial 12S rRNA gene sequence

A molecular approach was developed to distinguish species of red snappers among commercial salted fish products. The specific fragments of the mitochondrial 12S rRNA gene, which were about 450bp, were obtained using the semi-nested polymerase chain reaction (semi-nested PCR). Subsequently, PCR arnplicons were sequenced, aiming to select restriction endonucleases that generated species-specific restriction fragment length polymorphism (RFLP) profiles. Discrimination of red snappers Lutjanus sanguineus, Lutjanus erythopterus from Lutjanus argentimaculatus, Lutjanus malabarius and other morphologically similar fishes such as Lethrinus leutjanus and Pinjalo pinjalo was feasible by one restriction digestion reaction with three endonucleases Hae III, Sca I and SnaB I, however, for discrimination of L. sanguineus and L. erythopterus, another restriction digestion reaction with single restriction endonuclease Mae II was needed. The semi-nested PCR-RFLP was demonstrated to be reliable in species identification of salted fish products in this study. (c) 2005 Elsevier Ltd. All rights reserved.

应用PCR-DGGE技术分析长江口低氧区和黄海冷水团的细菌群落组成

利用PCR-DGGE技术对长江口外低氧区海域和黄海冷水团海域的细菌群落组成进行了分析。 长江口外低氧区海域的细菌群落组成分析结果为：对获得的25条DGGE条带进行了克隆、测序，所得到的序列进行了系统进化分析（细菌16S rRNA基因V3区序列），分别归属于4个细菌类群：变形菌门(Proteobacteria)、拟杆菌门(Bacteroides)、厚壁菌门(Firmicutes)和蓝细菌门(Cyanobacteria)。其中有16条分别与变形细菌亚群的γ和δ-Proteobacteria相似。通过时空分析发现，低氧水体的细菌群落组成与非低氧水体的组成是不同的。低氧水体的优势菌群是拟杆菌门(Bacteroides)中的Flavobacteria。 黄海冷水团海域的细菌群落组成和优势菌群分析结果为：细菌16S rDNA V3区特征片段经DGGE分离、条带切割，共得到24条DGGE条带，克隆、测序后，将所得序列进行系统进化分析，分别归属于2个细菌类群：变形细菌门(Proteobacteria)和拟杆菌门(Bacteroides)。在24条序列中有16条分别与变形细菌亚群的γ和δ-Proteobacteria相似，有5条与拟杆菌门相似。通过时空分析发现，10月份（冷水团存在期），冷水团内部水体的细菌群落组成包括γ-Proteobacteria、δ-Proteobacteria和Bacteroides，而冷水团外部的水体的细菌群落组成包括γ-Proteobacteria和Bacteroides。冷水团内部水层的优势菌群为γ-Proteobacteria。4月份虽然冷水团没有形成，但是所调查的海域海水温度都不高，在7℃－12℃范围内，所以4月份所有站位，不管是底层的还是总的的细菌群落组成都与10月份冷水团内部（海水温度低于10℃）水体的相同，与10月份冷水团外部（海水温度大于19℃）的不同。

应用单细胞PCR方法研究胶州湾一株鳍藻的遗传特征

近年来，分子生物学技术与方法被越来越多地应用于有害赤潮研究。其中，单细胞PCR方法是对难以室内培养的有害赤潮藻种进行遗传特征研究的一项重要技术。本实验尝试建立微藻的单细胞PCR方法，并将其应用于鳍藻研究。 应用室内培养的亚历山大藻，研究了微藻的单细胞PCR方法，并对藻细胞的固定和保存方法进行了比较。结果表明，浮游植物研究中常用的甲醛固定方法只能用于短期保存样品（少于5天），而乙醇固定、鲁格氏液固定、或者在-20℃下冷冻保存的样品，在较长的时间后（60天）仍可以得到比较理想的PCR扩增结果。 应用单细胞PCR方法，对青岛近海采集的鳍藻进行了研究，扩增并测定了包括核糖体大亚基（LSU）rDNA的5’端D1-D2区序列，以及5.8S rDNA和ITS区的部分序列信息。通过分析软件对所得到的鳍藻序列信息与基因库中已知的鳍藻序列信息进行了分析与对比。根据ITS和LSU序列信息构建的系统进化树都显示，本文采集的鳍藻藻种与国外报道的圆形鳍藻聚为一支，初步确定采集的鳍藻应为圆形鳍藻，对该藻种形态学特征的观察也支持这一结果。该藻种部分LSU rDNA序列与欧洲同种鳍藻相似度达到99%,与其它等鳍藻遗传距离在18%-20%之间。测定的ITS区序列与同种圆形鳍藻有62个碱基的差异，与LSU rDNA序列相比，ITS序列变异更大。应用LC-MS方法对该鳍藻的进行了DSP毒素分析，结果未检测到OA或DTX1毒素。 这是我国首次应用单细胞PCR方法对鳍藻开展的研究工作，首次报道了我国鳍藻的核糖体部分序列信息。圆形鳍藻在青岛近海海域是初次报道，显示了单细胞PCR方法在鳍藻研究中的重要意义。

PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp (Marsupenaeus japonicus)

In this study, the intestinal microbiota of kuruma shrimp (Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.

Identification of Crassostrea ariakensis and related oysters by multiplex species-specific PCR

Genetic markers are needed for rapid and reliable identification of oysters. In this study, we developed multiplex genus- and species-specific PCR markers for the identification of oysters from China. We used the mitochondrial cytochrome oxidase I (COI) and nuclear 28S ribosomal RNA genes for marker development. DNA sequences from different species were obtained from GenBank or by direct sequencing. Sequences were aligned, and genus- and species-specific nucleotides were identified. Primers were designed for genus/species-specific amplification to generate fragments of different sizes. A multiplex set of genus- and species-specific primers from the 28S gene was able to separate C. ariakensis and C. hongkongensis from other species and assign oysters to four genera. A set of species-specific COI primers provided positive identification of all five Crassostrea species from China, C. ariakensis, C. hongkongensis, C. angulata, C. gigas, and C. sikamea in a single PCR. The multiplex PCR assays do not require fluorescence-labeling or post-PCR enzyme digestion, providing a simple, fast and reliable method for the identification of oysters from China.

基因芯片PCR温度模糊自整定PID控制算法的研究

在核酸扩增反应仪中,基因芯片核酸扩增反应过程要求实现温度高精度快速跟踪控制,常规温控方案和算法难以实现。将模糊推理系统与常规PID控制方式相结合,采用模糊自整定PID控制算法实现了温度快速跟踪控制。实验结果表明:模糊自整定PID控制算法比常规PID算法具有更强的鲁棒性,能够克服控制对象热惯性参数时变性的影响,降低了输出温度最大超调量,提高了稳态精度。

硫酸盐还原菌类群分离培养和PCR分析鉴定

探讨分离培养和聚合酶链反应（PCR）在硫酸盐还原菌类群分析鉴定中的应用。［方法］采用分离培养和PCR 对贵州阿哈湖沉积物中硫酸盐还原菌类群进行分析，并对分离纯化的一株硫酸盐还原菌进行鉴定。 ［结果］ 贵州阿哈湖沉积物硫酸盐还原菌类群为脱硫肠菌属、脱硫叶菌属和脱硫球菌- 脱硫线菌- 脱硫八叠菌属；纯化菌株经PCR 扩增初步鉴定为脱硫叶菌属,菌株形态与鉴定结果相符。 ［结论］ 采用分离培养结合PCR，可以对硫酸盐还原菌类群进行分析和鉴定。