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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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https://www.readbyqxmd.com/read/29149730/divergence-of-insulin-superfamily-ligands-receptors-and-igf-binding-proteins-in-marine-versus-freshwater-stickleback-evidence-of-selection-in-known-and-novel-genes
#1
Tim Pellissier, Hend Al Nafea, Sara V Good
Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29145028/the-complete-mitochondrial-genome-of-the-alvinocaridid-shrimp-shinkaicaris-leurokolos-decapoda-caridea-insight-into-the-mitochondrial-genetic-basis-of-deep-sea-hydrothermal-vent-adaptation-in-the-shrimp
#2
Shao'e Sun, Ming Hui, Minxiao Wang, Zhongli Sha
Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi & Hashimoto, 2000) was determined through Illumina sequencing...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29145027/differential-gene-expression-in-the-intestine-of-sea-cucumber-apostichopus-japonicus-under-low-and-high-salinity-conditions
#3
Libin Zhang, Qiming Feng, Lina Sun, Kui Ding, Da Huo, Yan Fang, Tao Zhang, Hongsheng Yang
Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥2 and divergence probability ≥0...
November 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29126087/label-free-based-quantitative-proteomic-analysis-identifies-proteins-involved-in-the-testis-maturation-of-bactrocera-dorsalis-hendel
#4
Dong Wei, Meng-Yi Zhang, Pei-Ming Gu, Guy Smagghe, Jin-Jun Wang
Complex structural and biochemical processes take place in insect testis maturation, but the mechanisms by which functional proteins induce and regulate male fertility are unknown. Proteomics has been widely used to identify functional proteins involved in such complex physiological processes. In this study, we performed a label-free based quantitative proteomic analysis of developing testis of Bactrocera dorsalis with the aim of shedding light on spermatogenesis, sperm formation and also tissue development...
October 18, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29126086/genome-wide-identification-of-31-cytochrome-p450-cyp-genes-in-the-freshwater-rotifer-brachionus-calyciflorus-and-analysis-of-their-benzo-%C3%AE-pyrene-induced-expression-patterns
#5
Jeonghoon Han, Duck-Hyun Kim, Hui-Su Kim, Hee-Jin Kim, Steven A J Declerck, Atsushi Hagiwara, Jae-Seong Lee
While marine invertebrate cytochrome P450 (CYP) genes and their roles in detoxification mechanisms have been studied, little information is available regarding freshwater rotifer CYPs and their functions. Here, we used genomic sequences and RNA-seq databases to identify 31 CYP genes in the freshwater rotifer Brachionus calyciflorus. The 31 Bc-CYP genes with a few tandem duplications were clustered into CYP 2, 3, 4, mitochondrial, and 46 clans with two marine rotifers Brachionus plicatilis and Brachionus koreanus...
October 17, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29126085/fatty-acid-binding-protein-genes-of-the-ancient-air-breathing-ray-finned-fish-spotted-gar-lepisosteus-oculatus
#6
Ananda B Venkatachalam, Quenton Fontenot, Allyse Farrara, Jonathan M Wright
With the advent of high-throughput DNA sequencing technology, the genomic sequence of many disparate species has led to the relatively new discipline of genomics, the study of genome structure, function and evolution. Much work has been focused on the role of whole genome duplications (WGD) in the architecture of extant vertebrate genomes, particularly those of teleost fishes which underwent a WGD early in the teleost radiation >230 million years ago (mya). Our past work has focused on the fate of duplicated copies of a multigene family coding for the intracellular lipid-binding protein (iLBP) genes in the teleost fishes...
October 13, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29121518/genome-wide-identification-phylogenetic-analysis-and-expression-profiles-of-atp-binding-cassette-transporter-genes-in-the-oriental-fruit-fly-bactrocera-dorsalis-hendel-diptera-tephritidae
#7
Lin-Fan Xiao, Wei Zhang, Tian-Xing Jing, Meng-Yi Zhang, Ze-Qing Miao, Dan-Dan Wei, Guo-Rui Yuan, Jin-Jun Wang
The ATP-binding cassette (ABC) is the largest transporter gene family and the genes play key roles in xenobiotic resistance, metabolism, and development of all phyla. However, the specific functions of ABC gene families in insects is unclear. We report a genome-wide identification, phylogenetic, and transcriptional analysis of the ABC genes in the oriental fruit fly, Bactrocera dorsalis (Hendel). We identified a total of 47 ABC genes (BdABCs) from the transcriptomic and genomic databases of B. dorsalis and classified these genes into eight subfamilies (A-H), including 7 ABCAs, 7 ABCBs, 9 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 15 ABCGs, and 3 ABCHs...
October 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28982093/nmr-based-untargeted-metabolomic-study-of-hydrogen-peroxide-induced-development-and-diapause-termination-in-brine-shrimp
#8
Ming-Chang Hong, Shangwu Ding, Cheng-Chi Lin, Tah-Wei Chu, Kuo-Hsun Chiu
Artemia diapause has been extensively studied in embryonic biology for a long time. It has been demonstrated that hydrogen peroxide (H2O2) can increase the hatching rate in the development and diapause termination of Artemia cysts. This study used an untargeted (1)H NMR-based metabolomic approach to explore the physiological regulation of H2O2 in initiating the development and terminating the diapause of Artemia cysts. This experiment was divided into two parts. In the first part, we analyzed three groups with or without H2O2 as control-0h, control-5h and H2O2 (180μM)-5h; in the second part, after 7-d incubation, the non-hatching cysts were treated with different H2O2 concentrations as low as 180μM and as high 1800μM...
September 21, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28968511/rna-seq-analysis-of-the-head-kidney-transcriptome-response-to-handling-stress-in-the-red-cusk-eel-genypterus-chilensis
#9
Víctor Aballai, Jorge E Aedo, Jonathan Maldonado, Macarena Bastias-Molina, Herman Silva, Claudio Meneses, Sebastian Boltaña, Ariel Reyes, Alfredo Molina, Juan Antonio Valdés
Stress is a primary contributing factor of fish disease and mortality in aquaculture. We have previously reported that the red cusk-eel (Genypterus chilensis), an important farmed marine fish, demonstrates a handling-stress response that results in increased juvenile mortality, which is mainly associated with skeletal muscle atrophy and liver steatosis. To better understand the systemic effects of stress on red cusk-eel immune-related gene expression, the present study assessed the transcriptomic head-kidney response to handling-stress...
September 20, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28915415/transcriptomic-analysis-of-the-hepatopancreas-induced-by-eyestalk-ablation-in-shrimp-litopenaeus-vannamei
#10
Ji-Hyun Lee, Indyaswan T Suryaningtyas, Tae-Ho Yoon, Jeong Min Shim, Hyun Park, Hyun-Woo Kim
Although eyestalk ablation (ESA) is currently considered the most effective method to facilitate molting and maturation, its physiological responses are still not clearly explained in decapod crustaceans. In this study, we analyzed the hepatopancreatic transcriptomes of Litopenaeus vannamei after ESA using the Illumina Miseq platform. After screening 53,029 contigs with high cutoff values (fold change>|10|; P-value<0.05; RPKM>1), we were able to identify 105 differentially expressed genes (DEGs), of which 100 were up-regulated and five were down-regulated...
September 8, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28888727/genome-wide-characterization-of-toll-like-receptor-gene-family-in-common-carp-cyprinus-carpio-and-their-involvement-in-host-immune-response-to-aeromonas-hydrophila-infection
#11
Yiwen Gong, Shuaisheng Feng, Shangqi Li, Yan Zhang, Zixia Zhao, Mou Hu, Peng Xu, Yanliang Jiang
The Toll-like receptor (TLR) gene family is a class of conserved pattern recognition receptors, which play an essential role in innate immunity providing efficient defense against invading microbial pathogens. Although TLRs have been extensively characterized in both invertebrates and vertebrates, a comprehensive analysis of TLRs in common carp is lacking. In the present study, we have conducted the first genome-wide systematic analysis of common carp (Cyprinus carpio) TLR genes. A set of 27 common carp TLR genes were identified and characterized...
September 1, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28886574/comparative-transcriptome-analysis-of-fast-twitch-muscle-and-slow-twitch-muscle-in-takifugu-rubripes
#12
Kailun Gao, Zhicheng Wang, Xiaoxu Zhou, Haoze Wang, Derong Kong, Chen Jiang, Xiuli Wang, Zhiqiang Jiang, Xuemei Qiu
Fast twitch muscle and slow twitch muscle are two important organs of Takifugu rubripes. Both tissues are of ectodermic origin, and the differences between the two muscle fibers reflect the differences in their myofibril protein composition and molecular structure. In order to identify and characterize the gene expression profile in the two muscle fibers of T. rubripes, we generated 54 million and 44 million clean reads from the fast twitch muscle and slow twitch muscle, respectively, using RNA-Seq and identified a total of 580 fast-muscle-specific genes, 1533 slow-muscle-specific genes and 11,806 genes expressed by both muscles...
August 30, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28709111/genome-wide-identification-of-52-cytochrome-p450-cyp-genes-in-the-copepod-tigriopus-japonicus-and-their-b-%C3%AE-p-induced-expression-patterns
#13
Jeonghoon Han, Duck-Hyun Kim, Hui-Su Kim, David R Nelson, Jae-Seong Lee
Cytochrome P450s (CYPs) are enzymes with a heme-binding domain that are found in all living organisms. CYP enzymes have important roles associated with detoxification of xenobiotics and endogenous compounds (e.g. steroids, fatty acids, and hormones). Although CYP enzymes have been reported in several invertebrates, including insects, little is known about copepod CYPs. Here, we identified the entire repertoire of CYP genes (n=52) from whole genome and transcriptome sequences of the benthic copepod Tigriopus japonicus, including a tandem duplication (CYP3026A3, CYP3026A4, CYP3026A5), and examined patterns of gene expression over various developmental stages and in response to benzo[α]pyrene (B[α]P) exposure...
September 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28666194/dietary-cholesterol-induced-transcriptome-differences-in-the-intestine-hepatopancreas-and-muscle-of-oriental-river-prawn-macrobrachium-nipponense
#14
Xizhang Gu, Hongtuo Fu, Shengming Sun, Hui Qiao, Wenyi Zhang, Sufei Jiang, Yiwei Xiong, Shubo Jin, Yongsheng Gong, Yan Wu
Cholesterol is an important nutrient for crustaceans. In this study, we performed comparative transcriptome analyses to explore the transcriptome differences in the intestine, hepatopancreas, and muscle of Macrobrachium nipponense fed either a low cholesterol (LC) or high cholesterol (HC) diet (2.8 or 17.1g cholesterol per kg diet). High-throughput RNA-Seq was conducted, resulting in 7.65, 5.88, and 7.59G clean bases from the intestine, hepatopancreas, and muscle of the LC group, respectively, and 7.59, 6.73, and 6...
September 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28622611/de-novo-transcriptome-sequencing-and-comparative-analysis-to-discover-genes-involved-in-ovarian-maturity-in-strongylocentrotus-nudus
#15
COMPARATIVE STUDY
Zhiying Jia, Qiai Wang, Kaikai Wu, Zhenlin Wei, Zunchun Zhou, Xiaolin Liu
Strongylocentrotus nudus is an edible sea urchin, mainly harvested in China. Correlation studies indicated that S. nudus with larger diameter have a prolonged marketing time and better palatability owing to their precocious gonads and extended maturation process. However, the molecular mechanism underlying this phenomenon is still unknown. Here, transcriptome sequencing was applied to study the ovaries of adult S. nudus with different shell diameters to explore the possible mechanism. In this study, four independent cDNA libraries were constructed, including two from the big size urchins and two from the small ones using a HiSeq™2500 platform...
September 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28601631/ibt-based-quantitative-proteomics-identifies-potential-regulatory-proteins-involved-in-pigmentation-of-purple-sea-cucumber-apostichopus-japonicus
#16
Lili Xing, Lina Sun, Shilin Liu, Xiaoni Li, Libin Zhang, Hongsheng Yang
Sea cucumbers are an important economic species and exhibit high yield value among aquaculture animals. Purple sea cucumbers are very rare and beautiful and have stable hereditary patterns. In this study, isobaric tags (IBT) were first used to reveal the molecular mechanism of pigmentation in the body wall of the purple sea cucumber. We analyzed the proteomes of purple sea cucumber in early pigmentation stage (Pa), mid pigmentation stage (Pb) and late pigmentation stage (Pc), resulting in the identification of 5580 proteins, including 1099 differentially expressed proteins in Pb: Pa and 339 differentially expressed proteins in Pc: Pb...
September 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28578262/exposure-to-deepwater-horizon-oil-and-corexit-9500-at-low-concentrations-induces-transcriptional-changes-and-alters-immune-transcriptional-pathways-in-sheepshead-minnows
#17
Elizabeth R Jones, Christopher J Martyniuk, Jeffrey M Morris, Michelle O Krasnec, Robert J Griffitt
The 2010 Deepwater Horizon (DWH) oil spill caused the release of 4.9 million barrels of crude oil into the Gulf of Mexico, followed by the application of 2.9 million L of the dispersant, Corexit™ to mitigate the spread of oil. The spill resulted in substantial shoreline oiling, potentially exposing coastal organisms to polyaromatic hydrocarbon (PAH) and dispersant contaminants. To investigate molecular effects in fish following exposure to environmentally relevant concentrations of DWH oil and dispersants, we exposed adult sheepshead minnows (Cyprinodon variegatus) to two concentrations of high-energy water-accommodated fraction (HEWAF), chemically enhanced water-accommodated fraction (CEWAF) or Corexit 9500™ for 7 and 14days...
September 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28477566/identification-of-28-cytochrome-p450-genes-from-the-transcriptome-of-the-marine-rotifer-brachionus-plicatilis-and-analysis-of-their-expression
#18
Hui-Su Kim, Jeonghoon Han, Hee-Jin Kim, Atsushi Hagiwara, Jae-Seong Lee
Whole transcriptomes of the rotifer Brachionus plicatilis were analyzed using an Illumina sequencer. De novo assembly was performed with 49,122,780 raw reads using Trinity software. Among the assembled 42,820 contigs, 27,437 putative open reading frame contigs were identified (average length 1235bp; N50=1707bp). Functional gene annotation with Gene Ontology and InterProScan, in addition to Kyoto Encyclopedia of Genes and Genomes pathway analysis, highlighted the metabolism of xenobiotics by cytochrome P450 (CYP)...
September 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28822867/de-novo-assembly-and-characterization-of-seabass-lateolabrax-japonicus-transcriptome-and-expression-of-hepatic-genes-following-different-dietary-phosphorus-calcium-levels
#19
Kang-Le Lu, Zhong-Li Ji, Samad Rahimnejad, Chun-Xiao Zhang, Ling Wang, Kai Song
Fish farming seriously influences the aquatic environment because most dietary phosphorus (P) is excreted in the effluent. To increase the P utilization in fish, molecular techniques should be explored given the remarkable development of these techniques. Thus, to identify the candidate genes related to P utilization and molecular alterations following administration of a P-deficient diet in seabass Lateolabrax japonicus, we assessed the de novo pituitary, gill, intestine, liver, kidney, scales and vertebra transcriptomes, and we compared the expression of hepatic genes with three diets varying in P and Ca levels: diet I (0...
August 9, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28850878/transcriptome-sequencing-reveals-potential-mechanisms-of-diapause-preparation-in-bivoltine-silkworm-bombyx-mori-lepidoptera-bombycidae
#20
Yan-Rong Chen, Tao Jiang, Juan Zhu, Yu-Chen Xie, Zhi-Cheng Tan, Yan-Hua Chen, Shun-Ming Tang, Bi-Fang Hao, Sheng-Peng Wang, Jin-Shan Huang, Xing-Jia Shen
In the bivoltine strain of the silkworm, Bombyx mori, embryonic diapause is induced transgenerationally as a maternal effect. Progeny diapause ability is determined by the environmental condition such as temperature and lightness that mothers experience during their own embryonic development. Diapause preparation is a crucial phase of this process; diapause-destined individuals undergo a series of preparatory events before the entry into developmental arrest. However, the molecular regulatory mechanisms of diapause preparation have largely remained unknown...
August 2, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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