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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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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
#1
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)...
April 21, 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
#2
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)...
April 12, 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
#3
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...
April 12, 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
#4
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)...
April 6, 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
#5
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...
April 4, 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
#6
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...
March 20, 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
#7
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...
March 2, 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
#8
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...
March 1, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28288365/dexd-h-box-rna-helicase-genes-are-differentially-expressed-between-males-and-females-during-the-critical-period-of-male-sex-differentiation-in-channel-catfish
#9
Changxu Tian, Suxu Tan, Lisui Bao, Qifan Zeng, Shikai Liu, Yujia Yang, Xiaoxiao Zhong, Zhanjiang Liu
DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and syntenic analyses. All the catfish RNA helicases contained conserved helicase signature motifs, demonstrating that the RNA helicase gene family was highly conserved...
March 1, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#10
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Hong Seog Park, Seung-Hwan Park, Young-Su Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28103531/characterization-of-transcriptome-and-identification-of-biomineralization-genes-in-winged-pearl-oyster-pteria-penguin-mantle-tissue
#11
Haimei Li, Baosuo Liu, Guiju Huang, Sigang Fan, Bo Zhang, Jiaqi Su, Dahui Yu
The winged pearl oyster Pteria penguin is a commercially important marine pearl oyster species, with pearls that are quite different from those of other pearl oysters. Among such species, mantle tissue is the main organ responsible for shell and pearl formation, a biomineralization process that is regulated by a series of genes, most of which remain unknown. In this study, we sequenced and characterized the transcriptome of P. penguin mantle tissue using the HiSeq 2000 sequencing platform. A total of 93,204 unique transcripts were assembled from 51,580,076 quality reads, with a mean length of 608bp, and 40,974 unigenes were annotated...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28076754/transcriptome-analysis-of-the-potential-roles-of-foxl2-in-chicken-pre-hierarchical-and-pre-ovulatory-granulosa-cells
#12
COMPARATIVE STUDY
Jing Wang, Chengcheng Zhao, Jinqiu Li, Yanping Feng, Yanzhang Gong
Forkheadbox L2 (FOXL2) is a transcription factor involved in mammalian ovarian development, especially in granulosa cell differentiation. However, this factor's function in mature chicken ovary is unclear. To explore the function of FOXL2 in chicken granulosa cells, we performed RNA-seq to compare the transcriptomes of pre-hierarchical (phGCs) and pre-ovulatory granulosa cells (poGCs) by FOXL2 overexpression. We observed that focal adhesion might be one of the key pathways activated during the differentiation of granulosa cells, and FOXL2 might be involved in follicle selection by regulating the expression of cytokines and the concentration of cyclic adenosine monophosphate (cAMP)...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28063346/integrating-genomic-resources-of-flatfish-pleuronectiformes-to-boost-aquaculture-production
#13
COMPARATIVE STUDY
Diego Robledo, Miguel Hermida, Juan A Rubiolo, Carlos Fernández, Andrés Blanco, Carmen Bouza, Paulino Martínez
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27852008/selection-for-higher-fertility-reflects-in-the-seminal-fluid-proteome-of-modern-domestic-chicken
#14
Mohammad Atikuzzaman, Libia Sanz, Davinia Pla, Manuel Alvarez-Rodriguez, Marie Rubér, Dominic Wright, Juan J Calvete, Heriberto Rodriguez-Martinez
The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n=4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27835832/genome-wide-identification-of-atp-binding-cassette-abc-transporters-and-conservation-of-their-xenobiotic-transporter-function-in-the-monogonont-rotifer-brachionus-koreanus
#15
Chang-Bum Jeong, Hui-Su Kim, Hye-Min Kang, Young Hwan Lee, Bingsheng Zhou, Joonho Choe, Jae-Seong Lee
The ATP-binding cassette (ABC) transporter family is one of the largest gene family in animals, and members of this family are known to be involved in various biological processes due to their ability to transport a wide range of substrates across membranes using ATP cleavage-derived energy. We identified 61 ABC transporters in the genome of the monogonont rotifer Brachionus koreanus, and classified these into eight distinct subfamilies (A-H) by phylogenetic analysis. ABC transporters in the rotifer B. koreanus are comprised of 11 ABCA genes, 19 ABCB genes, 14 ABCC genes, 3 ABCD genes, 1 ABCE gene, 3 ABCF genes, 8 ABCG genes, and 2 ABCH genes...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27821266/effects-of-elevated-carbon-dioxide-on-contraction-force-and-proteome-composition-of-sea-urchin-tube-feet
#16
Nopparat Nasuchon, Katsuya Hirasaka, Kenichi Yamaguchi, Jiro Okada, Atsushi Ishimatsu
This study examined how contraction force and protein profiles of the tube feet of the sea urchin (Pseudocentrotus depressus) were affected when acclimated to 400 (control), 2000 and 10,000μatm CO2 for 48days. Acclimation to higher CO2 conditions significantly reduced contraction force of the tube feet. Two-dimensional gel electrophoresis showed that eight spots changed in protein volume: six up-regulated and two down-regulated. Using matrix-assisted laser desorption/ionization-quadrupole ion trap-time of flight mass spectrometry, three up-regulated spots (tubulin beta chain, tropomyosin fragment, and actin N-terminal fragment) and two down-regulated spots (actin C-terminal fragment and myosin light chain) were identified...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27806254/taste-receptors-and-gustatory-associated-g-proteins-in-channel-catfish-ictalurus-punctatus
#17
Sen Gao, Shikai Liu, Jun Yao, Tao Zhou, Ning Li, Qi Li, Rex Dunham, Zhanjiang Liu
Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particularly true for channel catfish (Ictalurus punctatus) that live in turbid waters with limited visibility. This biological process is mainly mediated by taste receptors expressed in taste buds that are distributed in several organs and tissues, including the barbels and skin. In the present study, we identified a complete repertoire of taste receptor and gustatory associated G protein genes in the channel catfish genome...
March 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28237864/transcriptome-analysis-and-identification-of-induced-genes-in-the-response-of-harmonia-axyridis-to-cold-hardiness
#18
Bin Tang, Xiao-Jun Liu, Zuo-Kun Shi, Qi-Da Shen, Yan-Xia Xu, Su Wang, Fan Zhang, Shi-Gui Wang
Harmonia axyridis is an important predatory lady beetle that is a natural enemy of agricultural and forestry pests. In this research, the cold hardiness induced genes and their expression changes in H. axyridis were screened and detected by the way of the transcriptome and qualitative real-time PCR under normal and low temperatures, using high-throughput transcriptome and digital gene-expression-tag technologies. We obtained a 10Gb transcriptome and an 8Mb gene expression tag pool using Illumina deep sequencing technology and RNA-Seq analysis (accession number SRX540102)...
February 20, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28214702/triploid-atlantic-salmon-shows-similar-performance-fatty-acid-composition-and-proteome-response-to-diploids-during-early-freshwater-rearing
#19
Waldo G Nuez-Ortín, Chris G Carter, Richard Wilson, Ira R Cooke, Gianluca Amoroso, Jennifer M Cobcroft, Peter D Nichols
There is currently renewed interest in farming triploid Atlantic salmon. Improving farming requires identifying triploid specific phenotypic and physiological traits that are uniquely derived from ploidy per se and developed under optimal growing conditions. This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages [34dph (days post-hatching) alevin, 109dph fry, and 162dph parr] and secondly, whether phenotypic differences at these stages were reflected in protein samples collected from whole fish, white muscle or liver tissue...
February 11, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28189874/comparative-rna-seq-analysis-of-differentially-expressed-genes-in-the-testis-and-ovary-of-takifugu-rubripes
#20
Zhicheng Wang, Xuemei Qiu, Derong Kong, Xiaoxu Zhou, Zhongbao Guo, Changfu Gao, Shuai Ma, Weiwei Hao, Zhiqiang Jiang, Shengcong Liu, Tao Zhang, Xuesong Meng, Xiuli Wang
Takifugu rubripes is a classical model organism for studying the role of gonad organogenesis in such physiological processes as fertilization, sex determination, and sexual development. To explicitly investigate the mechanism associated with gonad organogenesis in T. rubripes, we obtained 44.3 million and 55.2 million raw reads from the testis and ovary, respectively, by RNA-seq and from these, 18,523 genes were identified. A total of 680 differentially expressed genes were obtained from comparison transcriptome analysis between the testis and ovary, and of these, 556 genes were up-regulated in the testis, whereas only 124 genes were upregulated in the ovary...
February 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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