Institutional Repository of South China Sea Institute of Oceanology, CAS
Not a member yet
6199 research outputs found
Sort by
鳎超科 (Soleoidea) 3个科鱼类线粒体序列扩增及特征分析
No full text鳎超科 (Soleoidea) 隶属于鲽形目 (Pleuronectiformes)，含有8个科。关于鳎超科之间的系统关系一直没有得到很好的解决，一些研究发现通过重排信息进行系统发育研究，能够校正传统的和其他分子系统发育结果，有助于提高系统发育结果的可靠性。目前鳎超科中只有舌鳎科、冠鲽科、瓦鲽科3个科的物种中发现了重排，其中也出现了一些独特的现象。由于冠鲽科、瓦鲽科、舌鳎科无线鳎属(Symphurus) 物种的线粒体全基因组序列很少 (共5个)，重排数据不足严重限制了以重排信息为分子标记进行系统发育探索的进程。因此我们选取黑鳃舌鳎 (Cynoglossus roulei)、褐斑三线舌鳎(Cynoglossus trigrammus)、波纹无线鳎 (Symphurus undatus) ；褐斜鲽 (Plagiopsetta glossa) 及瓦鲽科的一个物种 (Poecilopsetta.sp，未定种)，并测定了它们的全序列 (或接近全序列)。
结果显示：褐斜鲽、瓦鲽sp、黑鳃舌鳎、褐斑三线舌鳎、波纹无线鳎线粒体基因组长度分别为18723bp、18484bp (未全，接近全长)、16589bp、16407bp、17442bp (未全，接近全长)。黑鳃舌鳎、褐斑三线舌鳎、波纹无线鳎基因组结构组成都包含有13个蛋白基因、2个rRNA基因和22个tRNA基因及1个控制区；褐斜鲽则含有13个蛋白基因、2个rRNA基因和24个tRNA基因及2个控制区；瓦鲽sp含有13个蛋白基因、2个rRNA和23个tRNA基因及3个控制区。这5个物种的线粒体基因组都发生了重排现象：黑鳃舌鳎、褐斑三线舌鳎都有tRNA-Gln基因的倒置并伴随着tRNA-Ile与tRNA-Gln之间的的滑移，控制区也转座到ND1和tRNA-Ile之间；波纹无线鳎线粒体基因重排方式与东方无线鳎相同，tRNA-Val和tRNA-Met基因移位到了16S rRNA基因末端；褐斜鲽线粒体基因组中不同位置的六个tRNA形成了六连体基因簇“Cys1-Tyr1-Ser1-Lys-Arg-Ser2”，“ND5-ND6-Glu-Cytb-Thr”则位于六连体之后，但这11个基因相对的排序没有发生变化；瓦鲽sp线粒体ND2-Trp-Ala及tRNA-Tyr基因移位到了控制区 (CR2) 与tRNA-Pro2之间。
我们用已有的反向复制删除重复基因模型来解释黑鳃舌鳎、褐斑三线舌鳎线粒体基因的重排现象；用复制?随机丢失模型 (TDRL) 来解释波纹无线鳎线粒体基因的重排现象；用双复制随机丢失模型 (DDRL) 来解释褐斜鲽与瓦鲽sp线粒体基因的重排现象。这些鱼类线粒体基因组中存在的间隔区、基因及控制区的重复、假基因等特征也为相应的模型提供了新的证据支持。
本研究结果不但丰富了鲽形目鱼类mtDNA全序列的数据库，通过研究探讨基因重排方式和重排机制等问题，也可以为揭示整个鳎超科系统关系及线粒体基因组进化提供分子生物学理论基础
粤蓝链霉菌隐蔽生物合成基因簇的激活及其次级代谢产物研究
No full text微生物隐蔽次级代谢产物生物合成基因簇的激活是当前面临的重要挑战。本研究在前人研究的基础上系统地总结和阐述了一种效率有所提高的激活策略——“移树养苗”策略，并将其应用于粤蓝链霉菌隐蔽次级代谢产物的挖掘。该菌是本研究室近年命名的一株链霉菌新种，其主导产物是具有抗菌、抗肿瘤活性的榴菌素。其突变株DMR1的榴菌素关键生物合成基因gra-orf1,2,3被敲除。
通过改变营养条件、添加诱导物和热激等方法对突变株DMR1进行发酵，发现其高氏一号和ISP3培养基发酵粗提物对所有受试的革兰氏阳性普通菌和耐药菌均具有显著抑菌活性；添加3%DMSO诱导后，上述两种培养基的发酵粗提物不仅对以上菌株的抑制活性增强，还具有抑制革兰氏阴性普通菌和耐药菌以及白色念珠菌ATCC 10231的活性。以枯草芽孢杆菌ATCC 6633为指示菌，以高氏一号为培养基，设置3因素3水平正交试验对发酵条件进行优化。结果显示，当DMSO添加量为1%，添加时间为6 h，热激温度30℃时，发酵粗提物抑菌活性最大。以该优化的条件对突变株DMR1进行发酵，并用正相与反相硅胶柱、Sephadex LH20凝胶柱和HPLC等方法从发酵粗提物中分离到12单体，利用NMR和MS等波谱方法鉴定了5个化合物，分别为：榴菌素（1），4,5-Dihydroxyhexanoic acid γ-lactone（2），N-苯乙基乙酰胺（3），N-[2-(4-Hydroxyphenyl)ethyl]acetamide（4），Cyclo-(Pro-Phe)（5）。
对突变株DMR1仍能产生微量榴菌素的现象进行了确证。用稀释涂布法对突变株DMR1进一步分离纯化，纯化后菌株发酵产物中仍能检测到榴菌素的存在；PCR检测和克隆测序都表明突变株DMR1的基因型与预期相符，且未受到野生型的污染，提示所分离鉴定的榴菌素确为突变株DMR1所产生。基于基因组测序分析和相关文献推测，突变株DMR1产生微量榴菌素的原因可能是孢子色素基因簇与榴菌素基因簇之间发生了串扰。
利用核糖体工程获得利福平或链霉素抗性菌株共5株。其中利福平抗性菌株R25-2在高氏一号中的发酵产物产量、丰富度和抗菌活性均高于出发菌株，提示其次级代谢能力从整体上获得提升
The complete mitochondria! genome of Pseudaesopia japonica (Pleuronectiformes: Soleidae)
No full textThe Pseudaesopia japonica belongs to family Soleidae in order Pleuronectiformes. In this study, the complete mitochondrial genome of P. japonica was determined and described. The mitogenome is 16 790 by in length and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs, one control region, and a light strand replication origin. The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 28.5%, 25.7%, 30.3%, and 15.5%, for A, T, C, and G, respectively, with a slight bias on A +T content (54.3%). The maximum likelihood phylogeny tree of 22 flatfishes demonstrated that the species from Zebrias and Aesopia firstly formed a sister group, and then clustered in the same Glade with P. japonicas. This study is expected to contributing to the systematic evolution of P. japonicas and further phylogenetic relationship of Soleidae and Pleuronectiformes
A molluscan extracellular signal-regulated kinase is involved in host response to immune challenges in vivo and in vitro
No full textExtracellular signal -regulated kinases (ERKs) are a group of highly conserved serine/threonine-specific protein kinases that function as important signaling intermediates in mitogen-activated protein kinase (MAPK) pathways, which are involved in a wide variety of cellular activities, including proliferation, inflammation and cytokine production. However, little is known about the roles of this kinase in mollusk immunity. In this study, we identified a molluscan ERK homolog (ChERK) in the Hong Kong oyster (Crassostrea hongkongensis) and investigated its biological functions. The open reading frame (ORF) of ChERK encoded a polypeptide of 365 amino acids, with a predicted molecular weight of 41.96 kDa and pI of 6.43. The predicted ChERK protein contained typical characteristic motifs of the ERK family, including a dual threonine-glutamate-tyrosine (TEY) phosphorylation motif and an ATRW substrate binding site. Phylogenetic analysis revealed that ChERK belonged to the mollusk cluster and shared a close evolutionary relationship with ERIC from Crassostrea gigas. In addition, quantitative real-time PCR analysis revealed that ChERK expression was detected in all of the examined tissues and stages of embryonic development; its transcript level was significantly induced upon challenge with bacterial pathogens (Vibrio alginolyticus and Staphylococcus haemolyticus) in vivo and PAMPs (lipopolysaccharide and peptidoglycan) in vitro. Moreover, ChERK was mainly located in the cytoplasm of HEIC293T cells. Taken together, these findings may provide novel insights into the functions of molluscan ERKs, especially their roles in response to immune challenge in oyster. (C) 2017 Published by Elsevier Ltd
The complete genome sequence of Bacillus velezensis 9912D reveals its biocontrol mechanism as a novel commercial biological fungicide agent
No full textBacillus sp. 9912 mutant, 9912D, was approved as a new biological fungicide agent by the Ministry of Agriculture of the People's Republic of China in 2016 owing to its excellent inhibitory effect on various plant pathogens and being environment-friendly. Here, we present the genome of 9912D with a circular chromosome having 4436 coding DNA sequences (CDSs), and a circular plasmid encoding 59 CDSs. This strain was finally designated as Bacillus velezensis based on phylogenomic analyses. Genome analysis revealed a total of 19 candidate gene clusters involved in secondary metabolite biosynthesis, including potential new type II antibiotics. The absence of fengycin biosynthetic gene cluster is noteworthy. Our data offer insights into the genetic, biological and physiological characteristics of this strain and aid in deeper understanding of its biocontrol mechanism.(C) 2017 Elsevier B.V. All rights reserved
MqsR/MqsA Toxin/Antitoxin System Regulates Persistence and Biofilm Formation in Pseudomonas putida KT2440
No full textBacterial toxin/antitoxin (TA) systems have received increasing attention due to their prevalence, diverse structures, and important physiological functions. In this study, we identified and characterized a type II TA system in a soil bacterium Pseudomonas putida KT2440. This TA system belongs to the MqsR/MqsA family. We found that PP_4205 (MqsR) greatly inhibits cell growth in P. putida KT2440 and Escherichia coli, the antitoxin PP_4204 (MqsA) neutralizes the toxicity of the toxin MqsR, and the two genes encoding them are co-transcribed. MqsR and MqsA interact with each other directly in vivo and MqsA is a negative regulator of the TA operon through binding to the promoter. Consistent with the MqsR/MqsA pair in E. coli, the binding of the toxin MqsR to MqsA inhibits the DNA binding ability of MqsA in P. putida KT2440. Disruption of the mqsA gene which induces mqsR expression increases persister cell formation 53-fold, while overexpressing mqsA which represses mqsR expression reduces persister cell formation 220-fold, suggesting an important role of MqsR in persistence in P. putida KT2440. Furthermore, both MqsR and MqsA promote biofilm formation. As a DNA binding protein, MqsA can also negatively regulate an ECF sigma factor AlgU and a universal stress protein PP_3288. Thus, we revealed an important regulatory role of MqsR/MqsA in persistence and biofilm formation in P. putida KT2440
Screening of Anti-Biofilm Compounds from Marine-Derived Fungi and the Effects of Secalonic Acid D on Staphylococcus aureus Biofilm
No full textBiofilm formation of Staphylococcus aureus is one of its mechanisms of drug resistance. Anti-biofilm screening of 106 compounds from marine-derived fungi displayed that 12 compounds inhibited S. aureus biofilm formation by > 50% at the concentration of 100 mu g/ml, and only secalonic acid D (SAD) and B inhibited by > 90% at 6.25 mu g/ml without inhibiting cell growth after 24-h incubation. Meanwhile, it was found that the double bond between C-1 and C-10 of citrinin derivatives and the C-C connection position of two chromone monomers may be important for their anti-biofilm activities. Moreover, SAD slightly facilitated biofilm eradication and influenced its architecture. Furthermore, SAD slowed the cell growth rate in the preceding 18-h incubation and differentially regulated transcriptional expression of several genes, such as agr, isaA, icaA, and icaD, associated with biofilm formation in planktonic and biofilm cells, which may be the reason for the anti-biofilm activity of SAD. Finally, SAD acted synergistically against S. aureus growth and biofilm formation with other antibiotics. These findings indicated that various natural products from marine-derived fungi, such as SAD, could be used as a potential biofilm inhibitor against S. aureus
Identification and characterization of a biosynthetic gene cluster for tryptophan dimers in deep sea-derived Streptomyces sp SCSIO 03032
No full textTryptophan dimers (TDs) are an important class of natural products with diverse bioactivities and share conserved biosynthetic pathways. We report the identification of a partial gene cluster (spm) responsible for the biosynthesis of a class of unusual TDs with non-planar skeletons including spiroindimicins (SPMs), indimicins (IDMs), and lynamicins (LNMs) from the deep-sea derived Streptomyces sp. SCSIO 03032. Bioinformatics analysis, targeted gene disruptions, and heterologous expression studies confirmed the involvement of the spm gene cluster in the biosynthesis of SPM/IDM/LNMs, and revealed the indispensable roles for the halogenase/reductase pair SpmHF, the amino acid oxidase SpmO, and the chromopyrrolic acid (CPA) synthase SpmD, as well as the positive regulator SpmR and the putative transporter SpmA. However, the spm gene cluster was unable to confer a heterologous host the ability to produce SPM/IDM/LNMs. In addition, the P450 enzyme SpmP and the monooxygenase SpmX2 were found to be non-relevant to the biosynthesis of SPM/IDM/LNMs. Sequence alignment and structure modeling suggested the lack of key conserved amino acid residues in the substrate-binding pocket of SpmP. Furthermore, feeding experiments in the non-producing Delta spmO mutant revealed several biosynthetic precursors en route to SPMs, indicating that key enzymes responsible for the biosynthesis of SPMs should be encoded by genes outside of the identified spm gene cluster. Finally, the biosynthetic pathways of SPM/IDM/LNMs are proposed to lay a basis for further insights into their intriguing biosynthetic machinery
Surface sediment quality relative to port activities: A contaminant-spectrum assessment
No full textPorts are facing increasing environmental concerns with their importance to the global economy. Numerous studies indicated sediment quality deterioration in ports; however, the deterioration is not discriminated for each port activity. This study investigated a spectrum of contaminants ( metals and organic pollutants) in surface sediments at 20 sampling points in Port Ningbo, China, one of the top five world ports by volume. The spectrum of contaminants ( metals and organic pollutants) was quantified following marine sediment quality guidelines of China and USA and surface sediment quality was assessed according to thresholds of the two guidelines. Coupling a categorical matrix of port activities with the matrix of sedimentary contaminants revealed that contaminants were highly associated with the port operations. Ship repair posed a severe chemical risk to sediment. Operations of crude oil and coal loadings were two top activities related to organic pollutants in sediments while port operations of ore and container loadings discharged metals. Among the 20 sampling points, Cu, Zn, Pb, and DDT and its metabolites were the priority contaminants influencing sediment quality. Overall, surface sediments in Port Ningbo had relatively low environmental risks but ship repair is an environmental concern that must be addressed. This study provides a practical approach for port activity-related quality assessment of surface sediments in ports that could be applicable in many world sites. (C) 2017 Elsevier B.V. All rights reserved
Cool water brought by upwelling in the Sanya Bay benefits corals in the background of global warming
No full textIt has been reported that global warming has negative effects on coral ecosystems in the past 50 years and the effects vary in different ocean environment. In order to make clear the coral reef status in the background of global warming along the south coast of Hainan Island of China, satellite and in situ data are used to retrieve the information of the coral reef status and surrounding environmental factors. The results show that cool water induced by upwelling along the south coast of Hainan Island is found in the area every summer month, especially in the relatively strong El Nio years (2002-2003 and 2005). From the NOAA satellite data, degree heating week (DHW) index does not exceed 3 in Sanya Bay even in the relatively strong El Nio years. By comparison of a coral reef growth rate in the Sanya Bay with respect to El Nio events from 1957 to 2000, coral's growth rate is relatively greater during 1972, 1991-1994 and 1998 El Nio event. By analyzing the environmental factors, it is found that the cool water induced by upwelling may be the main reason for protecting corals from global warming effects