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基于组学研究线纹海马生长发育相关基因的调控机制
No full text海马（Genus Hippocampus）是一种珍稀的小型硬骨鱼类，具有特殊的体型特征和繁殖方式，被誉为研究鱼类发育、进化的旗舰物种。近年来，海马的生长发育机制一直被国内外学者视为鱼类研究领域的热点问题。厘清海马生长发育的分子调控机制，有助于更好地剖析海马在海洋环境中的适应机制，为该物种的资源保护与综合利用提供科学理论。
随着高通量测序技术的发展，组学成为研究生物生理代谢及分子调控机制的有力工具。本研究论文以线纹海马（H. erectus）的生长发育机理为切入点，基于转录组、小RNA组及部分全基因组等数据的生物信息学分析，开发海马特异分子标记，研究了不同群体的生长发育状况；并结合小RNA组挖掘生长相关的基因及其调控特征；利用WGCNA分析研究育儿袋生长发育的分子机制。主要研究结果如下：
1、基于不同时期（1-6月龄）线纹海马躯干组织转录组测序与分析，共获得4,115个差异表达的mRNA，其中与脂质代谢和免疫相关的cidec、spink1和crp 基因在五组比较中均存在差异，推测cidec基因表达量的变化与海马食物的组成相关，而肌肉组织中存在spink1和crp基因，可能与海马特殊的免疫反应有关。
2、基于转录组数据开发了46个海马SNP分子标记及53个SSR分子标记。从遗传角度研究了野生群体、养殖群体及杂交群体存在生长差异的原因，发现养殖海马群体的杂合度、等位基因个数和多态信息含量均低于野生群体，近交系数高于野生群体，杂交群体得到部分恢复，推测由于海马特殊的生活史和养殖过程中的人工选择，使得养殖群体产生奠基者效应和近交衰退，引起遗传多样性的降低，造成生长性状的退化。
3、利用不同时期海马躯干组织小RNA组测序，预测1,120个miRNA及其前体。首次发现miR-22a-3p抑制mdfi和igf1r基因转录，调控生肌细胞的增殖和分化；miR-206抑制arntl基因转录，影响肌肉组织的节律。376个差异表达的miRNA，预测了491,878个靶基因，发现6个与海马肌肉组织发育相关的靶基因及调控其转录的miRNA，结果证明海马在1~2月龄肌肉纤维体积增大，肌肉组织的发育较快；3月龄以后发育减慢，运动能力增强。4、依据雄性线纹海马脑、性腺和育儿袋组织转录组数据及其WGCNA分析，发现22,871个基因分为23个基因模块，与雄激素合成相关的基因及性激素核受体属于Blue模块，合成雌激素的关键基因cyp19a1属于Brown模块，雌激素受体gper属于Yellow模块，结果阐明育儿袋的发育和生殖功能受到性激素的调控作用，雄激素通过受体arβ调控育儿袋的发育，雌激素通过受体gper完成妊娠过程。
5、进一步研究发现Magenta模块和Tan模块相关的基因与育儿袋的免疫保护功能相关，其中Toll样受体信号通路、Nod样受体信号通路、溶酶体通路、吞噬泡通路和Jak-Stat信号通路起到主要作用；同步研究发现了10个参与上述通路的hub genes，其余13个hub genes分别与免疫、血液循环系统、细胞外基质等相关。
本文基于海马全基因组，通过转录组和小RNA组高通量测序，挖掘了与海马生长发育相关的基因或通路信息，解析海马生长发育的分子调控机制；其中，基于WGCNA分析获得的与免疫或激素调控相关的基因可为后续海马资源保护与环境适应机制研究提供重要的理论依据
反射/折射地震联合反演在东沙西南海域地壳结构中的应用
No full text南海北部已开展的多条海底地震（OBS）探测均揭示东沙海域附近下地壳存在速度7.0~7.6 km/s的高速层，但其成因存在争议。东沙西南海域长电缆（6 km）多道反射地震剖面MCS-D80的双程旅行时5~10 s段存在丰富的反射同相轴，但由于缺乏可靠速度信息，无法判定其深反射属于正常地壳还是存在高速层的异常地壳。
多道反射地震利用长电缆接收多次覆盖的共反射点记录，可提供精细的地层结构信息，但是深部速度谱能量团分散，难以得到准确的速度。OBS可接收大偏移距折射波走时，可得到可靠速度值，故将二者联合处理，利用反射地震提供深度信息，折射地震提供速度信息，可获得更加完整的地壳结构。
为深入理解MCS-D80显示的深反射的地质意义，我们沿此测线布置OBS（15台）地震测线（OBS-D80），测线长300 km，从水深800 m陆坡延伸至3760 m深海平原。本文利用OBSTOOL软件进行预处理（位置校正和时间校正等）、震相识别。然后使用三种方法进行速度成像：（1）利用FAST tomography软件进行初至折射波层析成像，目的是快速了解地壳基本结构；（2）利用RAYINVR进行射线追踪正演模拟，目的是准确识别震相类型；（3）利用JIVE3D进行反射/折射联合反演获得详细的地壳速度结构信息。
结果表明：新生代沉积层速度1.6~3.5 km/s，厚度约2 km，在洋陆过渡带沉积基底受新生代岩浆活动影响，起伏较大。中生界速度4.0~5.5 km/s，厚度约3 km,主要分布在陆坡区。地壳厚度由陆坡的25~23 km减薄至洋盆的8 km。地壳下部存在7.0~7.6 km/s的高速块体，高速块体分布不均匀。在上陆坡处上地壳存在向上凸起约8 km的高速异常，在多道地震剖面中表现为杂乱反射的背斜构造，上覆晚新生代地层也同步形变，邻近的OBS93、OBS2006-3及其对应的多道剖面均有相同现象，表明东沙盆地在南海停止扩张以后仍有隆起活动的迹象。因上陆坡和洋陆过渡带晚新生代岩浆活动活跃，我们认为下地壳高速块体是由海底扩张停止后岩浆侵入形成，且这期隆起活动与南海北部陆缘下地壳高速块体的形成密切相关。此背斜与高速块体对应，我们推测背斜成因于岩浆侵入作用，不是俯冲挤压作用的结果，俯冲带不在东沙盆地，其具体位置仍需研究
DNA barcoding reflects the diversity and variety of brooding traits of fish species in the family Syngnathidae along China's coast
No full textDNA barcoding offers a rapid and accurate assessment for species labelling and identification. Here, we investigated the performance of DNA barcodes in a sample of Syngnathidae, a unique group of fish with male pregnancy. A total of 1002 DNA barcodes using 649 base-pair fragments of the cytochrome c oxidase subunit I (COI) gene were generated. All species were associated with distinct DNA barcode and could be readily distinguished; seven of the COI barcode clusters represented the first species records submitted to the Barcode of Life Data Systems (BOLD) and GenBank databases. In the Neighbor-joining tree of COI sequences, two major clusters (Gastrophori and Urophori) were displayed, which could also be classified by their brood pouches. However, the tail-brooding Hippichthys cyanospilus and trunk-brooding Syngnathoides biaculeatus were reverse-clustered together with the Gastrophori and the Urophori, respectively. Both seahorse and pipefish sequences showed high frequencies of nucleotide substitutions. The probability of nucleotide substitutions, those in pipefish were higher than that of all seahorses. However, we identified no signal for positive selection based on the COI gene in any of the data sets. Our results supported DNA barcoding as an efficient molecular tool for achieving better monitoring, conservation, and management of fisheries. (C) 2016 Elsevier B.V. All rights reserved
Pyrazolofluostatins A-C, Pyrazole-Fused Benzo[a]fluorenes from South China Sea-Derived Micromonospora rosaria SCSIO N160
No full textPyrazolofluostatins A-C (1-3), three new benzo[a]-fluorenes with an unprecedented carbon skeleton, were obtained from the South China Sea-derived Micromonospora rosaria SCSIO N160. Their structures were elucidated by extensive spectroscopic analyses. The structure of pyrazolofluostatin A (1) was confirmed by X-ray crystallographic analysis. Notably, 1-3 possessed a benzo[cd]indeno[2,1-f]indazol skeleton with a pyrazole-fused 6/5/6/6/5 pentacydic ring system. Pyrazolofluostatin A (I) showed moderate antioxidation activity (EC50 48.6 mu M)
Anti-HSV-1, antioxidant and antifouling phenolic compounds from the deep-sea-derived fungus Aspergillus versicolor SCSIO 41502
No full textChemical investigation of the deep-sea-derived fungus Aspergillus versicolor SCSIO 41502 resulted in the isolation of three new anthraquinones, aspergilols G-I (1-3), one new diphenyl ether, 4-carbglyceryl-3,3'dihydroxy-5,5'-dimethyldiphenyl ether (4), and one new benzaldehyde derivative, 2,4-dihydroxy-6-(4methoxy-2-oxopentyl)-3-methylbenzaldehyde (5), along with 23 known phenolic compounds (6-28). The structures of new compounds were elucidated by extensive spectroscopic analysis. The absolute configuration of 3 was established by CD spectrum and the modified Mosher method. Compounds 2, 3 and 9 had evident antiviral activity towards HSV-1 with EC50 values of 4.68, 6.25, and 3.12 mu M, respectively. Compounds 15, 18, 20 and 22-24 showed more potent antioxidant activity than L-ascorbic acid with IC50 values of 18.92-52.27 mu M towards DPPH radicals. Comparison of the structures and antioxidant activities of 1-28 suggests that the number of phenolic hydroxyl group that can freely rotate can significantly affect the antioxidant activity of phenolic compounds. In addition, 4, 22-24 and 27 had significant antifouling activity against Bugula neritina larval settlement with EC50 values of 1.28, 2.61, 5.48, 1.59, and 3.40 mu g/ml, respectively. (C) 2017 Elsevier Ltd. All rights reserved
Establishment and characterization of a mid-kidney cell line derived from golden pompano Trachinotus ovatus, a new cell model for virus pathogenesis and toxicology studies
No full textGolden pompano Trachinotus ovatus, a popularly cultured and commercially important marine fish worldwide, has been recognized as a promising candidate for mariculture. However, outbreaks of infectious bacterial or viral diseases and environmental deterioration have led to great economic losses in T. ovatus aquaculture recently. In our research, we established a new mid-kidney cell line, designated as TOK, from golden pompano, T. ovatus. The optimized growth temperature and working concentration of fetal bovine serum (FBS) were 28A degrees C and 10-20%, respectively. Foreign genes could express well in TOK cells. The modal number of TOK cells was 54. The TOK cells were susceptive to Singapore grouper iridovirus (SGIV) and red-spotted grouper nervous necrosis virus (RGNNV), and the virus could propagate in cells. Propagation was verified by qRT-PCR, and virions were observed under electron microscopy. Cytotoxicity analysis revealed that TOK cells were sensitive to different concentrations of extracellular products (ECPs) from Vibrio alginolyticus and V. anguillarum. Moreover, heavy metals (Cd, Cu, and Hg) also showed dose-dependent cytotoxicity to the TOK cell line. We established a mid-kidney cell line from T. ovatus which could be applied to cytotoxicity assays of heavy metals. The newly established TOK cell line possesses great application potential in genetic manipulation, virus-host interaction studies, and toxicity assays of bacterial extracellular products and heavy metals
Draft genome of the lined seahorse, Hippocampus erectus
No full textBackground: The lined seahorse, Hippocampus erectus, is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. Findings: A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse (H. comes). Conclusion: We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior
Identification and functional characterization of first alpha-2-macroglobulin in sea cucumbers
No full textThe broad-spectrum protease inhibitor alpha-2-macroglobulin (M-2) is widely found in vertebrates and invertebrates. However, no research regarding M-2 has been described in sea cucumbers to date. In this study, the first sea cucumber M-2 named Stm(2)M was identified from Stichopus monotuberculatus, a tropical species with high edible and economic values in Southern China. The Stm(2)M cDNA is 5276bp in length, containing a 5-untranslated region (UTR) of 279bp, a 3-UTR of 344bp and an open reading frame of 4653bp that encodes a protein of 1550 amino acids. The Stm(2)M possesses all the three characteristics of known M-2 proteins, including the bait region domain, thioester domain and receptor-binding domain. Higher levels of mRNA expression were noticed in intestine, respiratory tree, coelomocytes and tentacle of S.monotuberculatus. Transcriptional expression of Stm(2)M showed the strongest response to lipopolysaccharides (LPS, 8.19-fold up-regulation) after 6h post-challenge in coelomocytes. In addition, the M-2 activity was detected in S.monotuberculatus and protein activity of M-2 increased remarkably at 6h after LPS stimulation. As a whole, this study indicated that Stm(2)M is an important immune-related molecule, and the study on functions of Stm(2)M may provide some new and valuable ideas for preventing and controlling diseases of cultured sea cucumbers
Prey-specific determination of arsenic bioaccumulation and transformation in a marine benthic fish
No full textThe sediments from Chinese coastal waters contain relatively high concentrations of arsenic (As), mainly arsenate As(V), which may be transferred along the marine benthic food chain. The prey-specific determination of As bioaccumulation and transformation in marine benthic fish remains little known. In this study, we focused on a typical marine benthic food chain comprising of sediments, deposit-feeding invertebrates (polychaete Nereis succinea and clam Gafrarium tumidum) and goby fish Mugilogobius chulae. Graded exposed experiments using different As exposure durations and concentrations were conducted to examine their transformation rate and efficiency. Radiotracer techniques were used to determine the rates of As uptake (as arsenate) from seawater, assimilation from two prey and its subsequent efflux in the goby fish. We demonstrated that the two prey (polychates and clams) displayed different As biotransformation in the goby fish. Biotransformation rate was higher in the goby fish fed on the clams than on the polychaetes, and biotransformation efficiency was lower with increasing inorganic As concentration in the prey. The As overall bioaccumulation in the goby fish was very low, mainly because of the low dissolved uptake and dietary assimilation and high efflux. Combining the biotransformation and biokinetics measurements, our findings highlighted that different prey containing different As concentrations and As species resulted in the comparable As bioaccumulation in the goby fish. (C) 2017 Elsevier B.V. All rights reserved
Halogenated organic pollutants in marine biota from the Xuande Atoll, South China Sea: Levels, biomagnification and dietary exposure
No full textSix marine biota species were collected from the Xuande Atoll, South China Sea to investigate the bioaccumulation of dichlorodiphenyltrichloroethane (DDT), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), decabromodiphenyl ethane (DBDPE) and dechlorane plus (DP). Pike conger (Muraenesox talabonoides) had the highest concentrations of halogenated organic pollutants (HOPs) among the six marine biota species. DDTs were the predominant HOPs, followed by PCBs and PBDEs, with minor contributions of DBDPE and DP. Twenty-one percent of samples had ratios of (DDE + DDD)/Sigma DDTs lower than 0.5, implying the presence of fresh DDT inputs in the environment of the Xuande Atoll. The biomagnification factor values for DDTs, PCBs, PBDEs and DP were higher than 1, suggesting biomagnification of these contaminants in the marine food chains. Consumption of seafood from the Xuande Atoll might not subject local residents in the coastal areas of South China to health risks as far as HOPs are concerned. (C) 2017 Elsevier Ltd. All rights reserved