Comparative Biochemistry and Physiology Part D: Genomics and Proteomics This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data
Publication date: Available online 26 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Suxu Tan, Wenwen Wang, Tao Zhou, Yujia Yang, Dongya Gao, Rex Dunham, Zhanjiang LiuAbstractPolyadenylation plays important roles in gene expression regulation in eukaryotes, which typically involves cleavage and poly(A) tail addition at the polyadenylation site (PAS) of the pre-mature mRNA. Many eukaryotic genes contain more than one PASs, termed as alternative polyadenylation (APA). As a crucial post-transcriptional regulation, polyadenylation affects various aspects of RNA metabolism su...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 27, 2019 Category: Genetics & Stem Cells Source Type: research

Molecular physiology of copepods - from biomarkers to transcriptomes and back again
Publication date: Available online 19 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Ann M. Tarrant, Birgitte Nilsson, Benni Winding HansenAbstractPlanktonic copepods are a diverse and abundant group of small (~mm sized) aquatic animals that play a critical role in linking the base of the food chain with higher trophic levels. These invertebrates are a primary food source for marine fish larvae. Their ubiquitous presence is thus of vital importance for recruitment of fish stocks and also as promising live feed for finfish production in aquaculture. This paper reviews the...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 21, 2019 Category: Genetics & Stem Cells Source Type: research

Gene expression profiling of ovary identified eggshell proteins regulated by 20-hydroxyecdysone in Bactrocera dorsalis
Publication date: Available online 19 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Dong Wei, Ying-Xin Zhang, Yu-Wei Liu, Wei-Jun Li, Zhi-Xian Chen, Guy Smagghe, Jin-Jun WangAbstractThe oriental fruit fly, Bactrocera dorsalis, is one of the most destructive pests worldwide. The frequent use of chemical insecticides has led B. dorsalis to develop resistance to many insecticides in recent decades. New high-throughput-sequenced transcriptomes, as well as genomes, have revealed a large number of reference genes for functional target identification. Here, we performed digita...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 19, 2019 Category: Genetics & Stem Cells Source Type: research

Genome-wide identification and characterization of glucose transporter (glut) genes in spotted sea bass (Lateolabrax maculatus) and their regulated hepatic expression during short-term starvation
In this study, we identified a total of 21 glut genes in spotted sea bass (Lateolabrax maculatus) through extensive data mining of existing genomic and transcriptomic databases. Glut genes of spotted sea bass were classified into three subfamilies (Class I, Class II and Class III) according to the phylogenetic analysis. Glut genes of spotted sea bass were distributed in 15 out of 24 chromosomes. Deduced gene structure analysis including the secondary structure and the three-dimensional structures, as well as the syntenic analysis further supported their annotations and orthologies. Expression profile in healthy tissues ind...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 19, 2019 Category: Genetics & Stem Cells Source Type: research

Effect of plant-based diets with varying ratios of ω6 to ω3 fatty acids on growth performance, tissue composition, fatty acid biosynthesis and lipid-related gene expression in Atlantic salmon (Salmo salar)
Publication date: Available online 16 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Tomer Katan, Albert Caballero-Solares, Richard G. Taylor, Matthew L. Rise, Christopher C. ParrishAbstractLittle is known about how variation in omega-6 to omega-3 (ω6:ω3) fatty acid (FA) ratios affect lipid metabolism and eicosanoid synthesis in salmon, and the potential underlying molecular mechanisms. The current study examined the impact of five plant-based diets (12-week exposure) with varying ω6:ω3 (0.3–2.7) on the growth, tissue lipid composition (muscle and liver), and hepat...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 16, 2019 Category: Genetics & Stem Cells Source Type: research

Genome-wide characterization and expression of the elongation of very long chain fatty acid (Elovl) genes and fatty acid profiles in the alga (Tetraselmis suecica) fed marine rotifer Brachionus koreanus
Publication date: June 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 30Author(s): Min-Chul Lee, Jun Chul Park, Deok-Seo Yoon, Hyuntae Choi, Hee-Jin Kim, Kyung-Hoon Shin, Atsushi Hagiwara, Jeonghoon Han, Heum Gi Park, Jae-Seong LeeAbstractsTo understand the lipid metabolism in invertebrate species, identification of the fatty acid (FA) synthesis gene families in invertebrate species is important, since some FA are unable to be synthesized in the organisms by themselves. In the study, to identify the elongation of very long chain fatty acid (Elovl) genes in the marine rotifer Bra...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 16, 2019 Category: Genetics & Stem Cells Source Type: research

Divergent proteomics response of Apostichopus japonicus suffering from skin ulceration syndrome and pathogen infection
Publication date: Available online 13 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Zhimeng Lv, Ming Guo, Chenghua Li, Yina Shao, Xuelin Zhao, Weiwei ZhangAbstractSkin ulceration syndrome (SUS) of sea cucumber is a common and serious disease that affects the stable development of Apostichopus japonicus in the culture industry. The part of sea cucumber that suffers from major injury and is directly observed is the body wall, in which protein variations should be the most direct evidence of the disease. To understand the response mechanisms of A. japonicus in SUS progress...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 13, 2019 Category: Genetics & Stem Cells Source Type: research

To what extent may peptide receptor gene diversity/complement contribute to functional flexibility in a simple pattern-generating neural network?
Publication date: Available online 7 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Patsy S. Dickinson, J. Joe Hull, Alexandra Miller, Emily R. Oleisky, Andrew E. ChristieAbstractPeptides are known to contribute to central pattern generator (CPG) flexibility throughout the animal kingdom. However, the role played by receptor diversity/complement in determining this functional flexibility is not clear. The stomatogastric ganglion (STG) of the crab, Cancer borealis, contains CPGs that are models for investigating peptidergic control of rhythmic behavior. Although many Canc...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 7, 2019 Category: Genetics & Stem Cells Source Type: research

Transcriptomic analysis of differentially expressed genes in the oriental armyworm Mythimna separata Walker at different temperatures
Publication date: Available online 5 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Boliao Li, Meimei Li, Junxiang Wu, Xiangli XuAbstractThe oriental armyworm Mythimna separata Walker is a serious migratory and polyphagous pest that damages major crops and some pastures from the family Gramineae. Temperature is a crucial abiotic factor that affects its survival, development and reproduction, but the thermal responses of this moth at the molecular level are largely unknown. In this research, we sequenced the transcriptomes of oriental armyworms that were reared at three t...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 5, 2019 Category: Genetics & Stem Cells Source Type: research

Label-free quantification of protein expression in the rainbow trout (Oncorhynchus mykiss) in response to short-term exposure to heat stress
Publication date: Available online 1 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Yujun Kang, Zhe Liu, Haina Shi, Jianfu Wang, Jinqiang Huang, Yongjuan Li, Jie Li, Yanni WangAbstractRainbow trout (Oncorhynchus mykiss) are a cold-water salmonid species that is highly susceptible to heat stress. Summer temperature stress is a common issue in trout aquaculture. To better understand the molecular mechanisms of the heat-stress response in the trout, we used label-free quantitative proteome techniques to identify differentially expressed proteins in the livers of rainbow tro...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 4, 2019 Category: Genetics & Stem Cells Source Type: research

Genome-wide characterization and expression of the elongation of very long chain fatty acid genes (Elovl) and fatty acid profiles in the alga (Tetraselmis suecica) fed marine rotifer Brachionus koreanus
Publication date: Available online 2 March 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Min-Chul Lee, Jun Chul Park, Deok-Seo Yoon, Hyuntae Choi, Hee-Jin Kim, Kyung-Hoon Shin, Atsushi Hagiwara, Jeonghoon Han, Heum Gi Park, Jae-Seong LeeAbstractsTo understand the lipid metabolism in invertebrate species, identification of the fatty acid (FA) synthesis gene families in invertebrate species is important, since some FA are unable to be synthesized in the organisms by themselves. In the study, to identify the elongation of very long chain fatty acid (Elovl) genes in the marine ro...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 4, 2019 Category: Genetics & Stem Cells Source Type: research

1H NMR metabolomic analysis of skin and blubber of bottlenose dolphins reveals a functional metabolic dichotomy
Publication date: June 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 30Author(s): Misra Biswapriya Biswavas, Ruiz-Hernández Ixchel Mariel, Hernández-Bolio Gloria Ivonne, Hernández-Núñez Emanuel, Díaz-Gamboa Raúl, Colli-Dula Reyna CristinaAbstractThe common bottlenose dolphin (Tursiops truncatus) is a carnivorous cetacean that thrives in marine environments, one of the apex predators of the marine food web. They are found in coastal and estuarine ecosystems, which are known to be sensitive to environmental impacts. Dolphins are considered sentinel organisms for monitoring...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - March 4, 2019 Category: Genetics & Stem Cells Source Type: research

Transcriptome analysis provides insights into the molecular mechanisms responsible for evisceration behavior in the sea cucumber Apostichopus japonicus
In conclusion, through our comparative analysis of A. japonicus in different stages, we identified many candidate evisceration-related genes and signaling pathways that likely are involved in evisceration behavior. These results should help further elucidate the mechanisms underlying evisceration behavior in sea cucumbers.Graphical abstractFigure above is the hierarchical clustering of DEGs in three comparison groups of evisceration behavior (TCQ-vs-TCZ, TCZ-vs-TCH and TCQ-vs-TCH) in A. japonicus. This figure reveals the overall up- and downregulation of differentially expressed genes (DEGs) that involved in the eviscerati...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - February 27, 2019 Category: Genetics & Stem Cells Source Type: research

Identification and expression analysis of candidate chemosensory receptors based on the antennal transcriptome of Lissorhoptrus oryzophilus
Publication date: Available online 27 February 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Xinxin Zhang, Shuang Yang, Juhong Zhang, Xiao Wang, Shang Wang, Mengni Liu, Jinghui XiAbstractThe rice water weevil Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae) is a worldwide agricultural pest that causes serious damage to rice. The olfactory and gustatory behaviors of L. oryzophilus in locating host plants and oviposition sites mostly rely on the detection of chemical stimuli in the environment. To reveal such olfactory and gustatory systems, we performed a systemat...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - February 27, 2019 Category: Genetics & Stem Cells Source Type: research

RNA-seq reveals temporal differences in the transcriptome response to acute heat stress in the Atlantic salmon (Salmo salar)
In this study, we profiled the transcriptome responses of the Atlantic salmon (Salmo salar) to heat stress at 23 °C for 6 or 24 h, compared with that of fish at a normal temperature of 13 °C. The liver was selected as the target tissue for this analysis. A total of 243 and 88 genes were differentially expressed after 6 and 24 h of heat stress, respectively. Of these, only 22 were common to both time points, and most of these common genes were molecular chaperones such as heat shock cognate 71 kDa protein and heat shock protein 90-alpha. Genes such as activating transcription factor 6, calreticulin, protein disu...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - February 25, 2019 Category: Genetics & Stem Cells Source Type: research