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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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https://www.readbyqxmd.com/read/28915415/transcriptomic-analysis-of-the-hepatopancreas-induced-by-eyestalk-ablation-in-shrimp-litopenaeus-vannamei
#1
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
#2
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
#3
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/28822867/de-novo-assembly-and-characterization-of-seabass-lateolabrax-japonicus-transcriptome-and-expression-of-hepatic-genes-following-different-dietary-phosphorus-calcium-levels
#4
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
#5
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
https://www.readbyqxmd.com/read/28822866/profiles-of-soluble-proteins-in-chemosensory-organs-of-three-members-of-the-afro-tropical-anopheles-gambiae-complex
#6
Immacolata Iovinella, Beniamino Caputo, Maria Calzetta, Laurence J Zwiebel, Francesca Romana Dani, Alessandra Della Torre
In female mosquitoes, host-seeking and preference as well as several other important behaviors are largely driven by olfaction. Species of the Afrotropical Anopheles gambiae complex display divergent host-preference that are associated with significant differences in their vectorial capacity for human malaria. Olfactory sensitivity begins with signal transduction and activation of peripheral sensory neurons that populate the antennae, maxillary palps and other appendages. We have used shotgun proteomics to characterize the profile of soluble proteins of antennae and maxillary palps of three different species: An...
August 2, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28806688/concentration-dependent-transcriptome-responses-of-zebrafish-embryos-after-exposure-to-cadmium-cobalt-and-copper
#7
Laura Sonnack, Thorsten Klawonn, Ralf Kriehuber, Henner Hollert, Christoph Schäfers, Martina Fenske
Environmental metals are known to cause harmful effects to fish of which many molecular mechanisms still require elucidation. Particularly concentration dependence of gene expression effects is unclear. Focusing on this matter, zebrafish embryo toxicity tests were used in combination with transcriptomics. Embryos were exposed to three concentrations of copper (CuSO4), cadmium (CdCl2) and cobalt (CoSO4) from just after fertilization until the end of the 48hpf pre- and 96hpf post-hatch stage. The RNA was then analyzed on Agilent's Zebrafish (V3, 4×44K) arrays...
August 2, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28800433/global-gene-expression-analysis-of-the-muscle-tissues-of-medaka-acclimated-to-low-and-high-environmental-temperatures
#8
Daisuke Ikeda, Hiroki Koyama, Nanami Mizusawa, Nobuhiro Kan-No, Engkong Tan, Shuichi Asakawa, Shugo Watabe
Medaka (Oryzias latipes) is a temperate eurythermal fish that is able to survive over a wide range of water temperatures ranging from near zero to over 30°C throughout the year; it maintains its normal physiological and biochemical processes through temperature acclimation. To determine the mechanisms involved in temperature acclimation of fish, the fast skeletal muscle tissues of medaka underwent global gene expression analysis using next-generation sequencing. Ten individuals were placed into two aquariums at 24°C...
August 2, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28822868/preliminary-profiling-of-microrna-in-the-normal-and-regenerating-liver-of-chiloscyllium-plagiosum
#9
Dandan Cheng, Yanna Chen, Conger Lu, Yuezhong Qian, Zhengbing Lv
Liver is a vital organ present in animals for detoxification, protein synthesis, digestion and other functions and its powerful regenerative capacity is well known. C. plagiosum is an abundant fish that is representative of the cartilaginous class in the southeast coastal region of China and its liver accounts for >70% of the fish's visceral weight and contains many bioactive substances. MicroRNAs (microRNAs) play important roles in a wide range of biological processes in eukaryotes, including cell proliferation, differentiation, apoptosis...
July 27, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28756307/identification-and-comparison-of-candidate-odorant-receptor-genes-in-the-olfactory-and-non-olfactory-organs-of-holotrichia-oblita-faldermann-by-transcriptome-analysis
#10
Kebin Li, Hongshuang Wei, Changlong Shu, Shuai Zhang, Yazhong Cao, Chen Luo, Jiao Yin
A sophisticated olfactory system is part of the explanation for the prominence of insects among animals because of the essential roles of the olfactory system in foraging, host seeking, mating, ovipositing and avoiding toxic substances. In this study, we sequenced and analysed the transcriptomes of olfactory tissue (antennae) and non-olfactory tissue (legs) of the scarab beetle, Holotrichia oblita Faldermann, which is a serious underground pest in China. We obtained approximately 80.2 million 150bp reads that were assembled into 61,038 unigenes with an average length of 890bp...
July 24, 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
#11
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...
July 6, 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
#12
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...
June 13, 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
#13
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...
June 2, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28433920/proteomic-analysis-of-sockeye-salmon-serum-as-a-tool-for-biomarker-discovery-and-new-insight-into-the-sublethal-toxicity-of-diluted-bitumen
#14
Sarah L Alderman, Laura A Dindia, Christopher J Kennedy, Anthony P Farrell, Todd E Gillis
Pipelines carrying diluted bitumen (dilbit) from Canada's oil sands traverse North America, including the freshwater habitat of Pacific salmon, posing a risk of environmental release and aquatic exposure. Swimming performance is impacted in juvenile sockeye (Oncorhynchus nerka) exposed to dilbit; therefore biomarkers of dilbit exposure will be valuable for monitoring at-risk salmon stocks. This study characterized changes in the serum proteome of sockeye exposed to a sub-lethal and environmentally relevant concentration of dilbit using isobaric tags for relative and absolute quantitation (iTRAQ), and included a range of experimental conditions to permit identification of biomarkers that are robust across time (1 and 4wk) and exercise level (at rest and following a swim test)...
June 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28433919/identification-of-differentially-expressed-mirnas-through-high-throughput-sequencing-in-the-chicken-lung-in-response-to-mycoplasma-gallisepticum-hs
#15
Yabo Zhao, Yue Hou, Kang Zhang, Bo Yuan, Xiuli Peng
Mycoplasma gallisepticum (MG) infects chickens, causes chronic respiratory diseases (CRD) and severely damages the poultry industry. It has been suggested that micro-ribonucleic acids (miRNAs) are involved in microbial pathogenesis. Here, we identified miRNAs that are associated with MG infection in chicken lungs at 3 and 10days post-infection by deep sequencing. Thirty-six down-regulated and 9 up-regulated miRNAs belonging to 31 miRNA families were detected at 3days post-infection, whereas 50 down-regulated and 18 up-regulated miRNAs belonging to 41 miRNA families were found at 10days post-infection...
June 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28415049/metamorphosis-and-transition-between-developmental-stages-in-european-eel-anguilla-anguilla-l-involve-epigenetic-changes-in-dna-methylation-patterns
#16
Jochen H Trautner, Stefan Reiser, Tina Blancke, Katrin Unger, Klaus Wysujack
The life history of the European eel (Anguilla anguilla, L.) is characterized by a series of metamorphoses and transitions that provoke drastic morphological changes. Most of these changes go along with the catadromous life cycle in eels, involving extensive physiologically adaptations. In this study it was investigated whether these drastic changes have an epigenetic basis by analyzing global methylation patterns in liver, gill and brain tissue from glass eels caught at the British coast as well as yellow and silver eels from River Rhine using methylation-sensitive amplified polymorphisms (MSAP)...
June 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28411580/comparative-analysis-of-the-liver-transcriptome-of-pelteobagrus-vachellii-with-an-alternative-feeding-time
#17
COMPARATIVE STUDY
Chuanjie Qin, Quan Gong, Zhengyong Wen, Yuanchao Zou, Dengyue Yuan, Ting Shao, Huatao Li
Pelteobagrus vachellii, an important freshwater fish in China, shows predominantly nocturnal behavior. To better understand the growth and molecular mechanisms underlying altered feeding times in this species, we studied the growth and liver transcriptome of P. vachellii with shifted feeding times. In this study, a 9-week growth trial was conducted on male P. vachellii (mean weight±S.E.=1.05±0.36g) with commercial feed. Two triplicate groups of fish were fed either at 0800 (day group, control) or at 2000 (night group) with the same amount of feed...
June 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28395238/de-novo-analysis-of-the-oriental-armyworm-mythimna-separata-antennal-transcriptome-and-expression-patterns-of-odorant-binding-proteins
#18
Xiang-Qian Chang, Xiao-Pei Nie, Zan Zhang, Fang-Fang Zeng, Liang Lv, Shu Zhang, Man-Qun Wang
To better understand the olfactory mechanisms in the oriental armyworm Mythimna separate, one of the most serious pests of cereals, an antennal transcriptome was constructed in this study. A total of 130 olfactory related transcripts were identified. These transcripts were predicted to encode 32 odorant-binding proteins (OBPs), 16 chemosensory proteins (CSPs), 71 olfactory receptors (ORs), 8 ionotropic receptors (IRs), 1 gustatory receptor (GR) and 2 sensory neuron membrane proteins (SNMPs). Q-PCR analysis of the temporal expression profiles of seven OBPs in different tissues indicated that, except for MsepOBP19 which was highly expressed in the wings of 0-day-old adult and MsepOBP20 which was low expressed in all tissues, other tested MsepOBPs were significantly more highly expressed in the antenna than in the head (antenna excluded), thorax, abdomen, legs and wings...
June 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28288367/crenomytilus-grayanus-40kda-calponin-like-protein-cdna-cloning-sequence-analysis-tissue-expression-and-post-translational-modifications
#19
Oleg S Matusovsky, Anna V Dobrzhanskaya, Victoria V Pankova, Konstantin V Kiselev, Ulyana V Girich, Nikolay S Shelud'ko
Calponin-like protein (CaP-40), a third major protein after actin and tropomyosin, has recently been identified by us in the Ca(2+)-regulated thin filaments of mussel Crenomytilus grayanus. It contains calponin homology domain, five calponin family repeats and possesses similar biochemical properties as vertebrate smooth muscle calponin. In this paper, we report a full-length cDNA sequence of CaP-40, study its expression pattern on mRNA and protein levels, evaluate CaP-40 post-translational modifications and perform protein-protein interaction analysis...
June 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28288366/oligomeric-protein-complexes-of-apolipoproteins-stabilize-the-internal-fluid-environment-of-organism-in-redfins-of-the-tribolodon-genus-pisces-cypriniformes-cyprinidae
#20
Alla M Andreeva, Marina V Serebryakova, Nina E Lamash
One of the most important functions of plasma proteins in vertebrates is their participation in osmotic homeostasis in the organism. Modern concepts about plasma proteins and their capillary filtration are based on a model of large monomeric proteins that are able to penetrate the interstitial space. At the same time, it was revealed that a considerable amount of oligomeric complexes are present in the low-molecular-weight (LM) protein fraction in the extracellular fluids of fishes. The functions of these complexes are unknown...
June 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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