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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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https://www.readbyqxmd.com/read/28288367/crenomytilus-grayanus-40kda-calponin-like-protein-cdna-cloning-sequence-analysis-tissue-expression-and-post-translational-modifications
#1
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
#2
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
#3
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/28237864/transcriptome-analysis-and-identification-of-induced-genes-in-the-response-of-harmonia-axyridis-to-cold-hardiness
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/28189057/itraq-reveals-proteomic-changes-during-intestine-regeneration-in-the-sea-cucumber-apostichopus-japonicus
#7
Lina Sun, Dongxue Xu, Qinzeng Xu, Jingchun Sun, Lili Xing, Libin Zhang, Hongsheng Yang
Sea cucumbers have a striking capacity to regenerate most of their viscera after evisceration, which has drawn the interest of many researchers. In this study, the isobaric tag for relative and absolute quantitation (iTRAQ) was utilized to investigate protein abundance changes during intestine regeneration in sea cucumbers. A total of 4073 proteins were identified, and 2321 proteins exhibited significantly differential expressions, with 1100 upregulated and 1221 downregulated proteins. Our results suggest that intestine regeneration constitutes a complex life activity regulated by the cooperation of various biological processes, including cytoskeletal changes, extracellular matrix (ECM) remodeling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism...
February 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28189056/metabolic-responses-to-intestine-regeneration-in-sea-cucumbers-apostichopus-japonicus
#8
Lina Sun, Jingchun Sun, Qinzeng Xu, Xiaoni Li, Libin Zhang, Hongsheng Yang
Sea cucumbers are excellent models for studying organ regeneration due to their striking capacity to regenerate most of their viscera after evisceration. In this study, we applied NMR-based metabolomics to determine the metabolite changes that occur during the process of intestine regeneration in sea cucumbers. Partial least-squares discriminant analysis showed that there was significant differences in metabolism between regenerative intestines at 3, 7, and 14days post evisceration (dpe) and normal intestines...
February 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28187310/proteomic-analysis-of-liver-tissue-from-rainbow-trout-oncorhynchus-mykiss-under-high-rearing-density-after-administration-of-dietary-vitamin-e-and-selenium-nanoparticles
#9
Mahdi Naderi, Saeed Keyvanshokooh, Amir Parviz Salati, Alireza Ghaedi
The aim of the present study was to investigate the effects of dietary vitamin E (vit E) and selenium nanoparticles (nanoSe) on liver proteome profile of rainbow trout under high density condition. To correlate the proteome modifications with physiological aspects, growth, serum metabolites (cortisol, glucose, lactate, ALT, AST, and ALP), and liver antioxidant-related parameters (SOD, GPx, CAT, and MDA) were also examined. A total of 1275 fish (average weight of 42.6±2.3g) were stocked into 12 tanks at a density of 80kgm(-3)...
February 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28187311/candidate-chemosensory-genes-identified-in-the-endoparasitoid-meteorus-pulchricornis-hymenoptera-braconidae-by-antennal-transcriptome-analysis
#10
Sheng Sheng, Cheng-Wu Liao, Yu Zheng, Yu Zhou, Yan Xu, Wen-Miao Song, Peng He, Jian Zhang, Fu-An Wu
Meteorus pulchricornis is an endoparasitoid wasp which attacks the larvae of various lepidopteran pests. We present the first antennal transcriptome dataset for M. pulchricornis. A total of 48,845,072 clean reads were obtained and 34,967 unigenes were assembled. Of these, 15,458 unigenes showed a significant similarity (E-value <10(-5)) to known proteins in the NCBI non-redundant protein database. Gene ontology (GO) and cluster of orthologous groups (COG) analyses were used to classify the functions of M...
January 31, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28199879/gene-expression-patterns-regulating-embryogenesis-based-on-the-integrated-de-novo-transcriptome-assembly-of-the-japanese-flounder
#11
Yuanshuai Fu, Liang Jia, Zhiyi Shi, Junling Zhang, Wenjuan Li
The Japanese flounder (Paralichthys olivaceus) is one of the most important commercial and biological marine fishes. However, the molecular biology involved during embryogenesis and early development of the Japanese flounder remains largely unknown due to a lack of genomic resources. A comprehensive and integrated transcriptome is necessary to study the molecular mechanisms of early development and to allow for the detailed characterization of gene expression patterns during embryogenesis; this approach is critical to understanding the processes that occur prior to mesectoderm formation during early embryonic development...
January 25, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28160609/understanding-regulation-of-micrornas-on-intestine-regeneration-in-the-sea-cucumber-apostichopus-japonicus-using-high-throughput-sequencing
#12
Lina Sun, Jingchun Sun, Xiaoni Li, Libin Zhang, Hongsheng Yang, Qing Wang
The sea cucumber, as a member of the Echinodermata, has the capacity to restore damaged organs and body parts, which has always been a key scientific issue. MicroRNAs (miRNAs), a class of short noncoding RNAs, play important roles in regulating gene expression. In the present study, we applied high-throughput sequencing to investigate alterations of miRNA expression in regenerative intestine compared to normal intestine. A total of 73 differentially expressed miRNAs were obtained, including 59 up-regulated miRNAs and 14 down-regulated miRNAs...
January 25, 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
#13
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...
January 8, 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
#14
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)...
January 5, 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
#15
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...
December 24, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27623325/characterization-of-cold-associated-micrornas-in-the-freeze-tolerant-gall-fly-eurosta-solidaginis-using-high-throughput-sequencing
#16
Pierre J Lyons, Louise Govaere, Nicolas Crapoulet, Kenneth B Storey, Pier Jr Morin
Significant physiological and biochemical changes are observed in freeze-tolerant insects when confronted with cold temperatures. These insects have adapted to winter by retreating into a hypometabolic state of diapause and implementing cryoprotective mechanisms that allow them to survive whole body freezing. MicroRNAs (miRNAs), a family of short ribonucleic acids, are emerging as likely molecular players underlying the process of cold adaptation. Unfortunately, the data is sparse concerning the signature of miRNAs that are modulated following cold exposure in the freeze-tolerant goldenrod gall fly Eurosta solidaginis...
December 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27540874/the-effect-of-temperature-on-the-respiration-and-metabolism-of-the-african-burrowing-scorpion-opistophthalmus-latimanus
#17
Willie J van Aardt, Jacobus M le Roux, Jeremie Z Lindeque, Shayne Mason, Roan Louw
It is well known that scorpions are highly adapted to thermal temperatures. However, little is known of the metabolic and respiration adaptations caused by temperature fluctuations in these animals. Therefore we used the African burrowing scorpion Opistophthalmus latimanus to measure the effect of temperature on its metabolism and respiration. Radioactive d-glucose was injected into the ventral sinus of the circulatory system and metabolites of d-glucose were determined after six hour incubation at four temperatures (7, 17, 25 and 37°C)...
December 2016: 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
#18
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...
November 3, 2016: 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
#19
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...
October 30, 2016: 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
#20
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...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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