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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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https://www.readbyqxmd.com/read/29738886/comparison-of-proteomic-profiles-in-the-ovary-of-sterlet-sturgeon-acipenser-ruthenus-during-vitellogenic-stages
#1
Mohammad Youneszadeh-Fashalami, Amir Parviz Salati, Saeed Keyvanshokooh
One of the challenges of sturgeon aquaculture is that sturgeon takes an extended amount of time to reach sexual maturity. The pattern of the protein expression in relation to the late maturity of sturgeon can help to better understand changes in sexual maturity. 17β-estradiol (E2), testosterone (T) and vitellogenin (Vtg) levels were examined at all stages of sexual maturation in Sterlet sturgeon (Acipenser ruthenus). Two-dimensional gel electrophoresis and mass spectrometry analysis were used to show the pattern of the ovarian proteins...
May 2, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29733998/genome-wide-identification-of-chitinase-and-chitin-deacetylase-gene-families-in-the-oriental-fruit-fly-bactrocera-dorsalis-hendel
#2
Shi-Huo Liu, Hong-Fei Li, Yang Yang, Rui-Lin Yang, Wen-Jia Yang, Hong-Bo Jiang, Wei Dou, Guy Smagghe, Jin-Jun Wang
Chitinases (Chts) and chitin deacetylases (CDAs) are important enzymes required for chitin metabolism in insects. In this study, 12 Cht-related genes (including seven Cht genes and five imaginal disc growth factor genes) and 6 CDA genes (encoding seven proteins) were identified in Bactrocera dorsalis using genome-wide searching and transcript profiling. Based on the conserved sequences and phylogenetic relationships, 12 Cht-related proteins were clustered into eight groups (group I-V and VII-IX). Further domain architecture analysis showed that all contained at least one chitinase catalytic domain, however, only four (BdCht5, BdCht7, BdCht8 and BdCht10) possessed chitin-binding domains...
May 1, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29738887/transcriptome-analysis-reveals-enrichment-of-genes-associated-with-auditory-system-in-swimbladder-of-channel-catfish
#3
Yujia Yang, Xiaozhu Wang, Yang Liu, Qiang Fu, Changxu Tian, Chenglong Wu, Huitong Shi, Zihao Yuan, Suxu Tan, Shikai Liu, Dongya Gao, Rex Dunham, Zhanjiang Liu
In aquatic organisms, hearing is an important sense for acoustic communications and detection of sound-emitting predators and prey. Channel catfish is a dominant aquaculture species in the United States. As channel catfish can hear sounds of relatively high frequency, it serves as a good model for study auditory mechanisms. In catfishes, Weberian ossicles connect the swimbladder to the inner ear to transfer the forced vibrations and improve hearing ability. In this study, we examined the transcriptional profiles of channel catfish swimbladder and other four tissues (gill, liver, skin, and intestine)...
April 30, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29727827/analysis-of-the-grapevine-moth-lobesia-botrana-antennal-transcriptome-and-expression-of-odorant-binding-and-chemosensory-proteins
#4
Valentina Rojas, Héctor Jiménez, Rubén Palma-Millanao, Angélica González-González, Juan Machuca, Ricardo Godoy, Ricardo Ceballos, Ana Mutis, Herbert Venthur
The grapevine moth, Lobesia botrana, is considered a harmful pest for vineyards in Chile as well as in North America and Europe. Currently, monitoring and control methods of L. botrana are based on its main sex pheromone component, being effective for low population densities. In order to improve control methods, antennal olfactory proteins in moths, such as odorant-binding proteins (OBPs) and odorant receptors (ORs) have been studied as promising targets for the discovery of new potent semiochemicals, which have not been reported for L...
April 30, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29772405/a-transcriptomic-comparison-of-theca-and-granulosa-cells-in-chicken-and-cattle-follicles-reveals-esr2-as-a-potential-regulator-of-cyp19a1-expression-in-the-theca-cells-of-chicken-follicles
#5
Ruoxi Jing, Lantao Gu, Jinqiu Li, Yanzhang Gong
Previous studies have shown that theca and granulosa cell layers in follicles do not play the same roles in mammals and birds, especially regarding the synthesis of estrogen. The functions of these two cell types have been well characterized in cattle, but they remain unclear in chickens. To clarify this issue, a comparison of small yellow follicles (SYFs) in chickens and cattle at different follicular development stages was done by weighted gene co-expression network analysis (WGCNA). The modules obtained from WGCNA were used for further identification of the key genes associated with CYP19A1 expression...
April 28, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29702368/de-novo-transcriptome-analysis-and-differentially-expressed-genes-in-the-ovary-and-testis-of-the-japanese-mantis-shrimp-oratosquilla-oratoria-by-rna-seq
#6
Hongwei Yan, Xin Cui, Xufang Shen, Lianshun Wang, Linan Jiang, Haiying Liu, Ying Liu, Qi Liu, Chen Jiang
The mantis shrimp Oratosquilla oratoria is a widely distributed, commercially important crustacean species. Although its conservation and the development of successful artificial breeding technologies have recently received considerable attention, there are currently no available data regarding the molecular mechanisms in controlling reproduction. In this study, we performed transcriptome sequencing of the testis, ovary, female and male eyestalks and the androgenic gland of O. oratoria, and compared the expression pattern of transcripts from the testis and ovary libraries to identify genes involved in gonadal development...
April 14, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29605489/baseline-levels-of-metabolites-in-different-tissues-of-mussel-mytilus-galloprovincialis-bivalvia-mytilidae
#7
Tiziana Cappello, Alessia Giannetto, Vincenzo Parrino, Maria Maisano, Sabrina Oliva, Giuseppe De Marco, Giulia Guerriero, Angela Mauceri, Salvatore Fasulo
The Mediterranean mussel Mytilus galloprovincialis (Lamarck 1819) is a popular shellfish commonly included in human diet and is routinely used as bioindicator in environmental monitoring programmes worldwide. Recently, metabolomics has emerged as a powerful tool both in food research and ecotoxicology for monitoring mussels' freshness and assessing the effects of environmental changes. However, there is still a paucity of data on complete metabolic baseline of mussel tissues. To mitigate this knowledge gap, similarities and differences in metabolite profile of digestive gland (DG), gills (G), and posterior adductor muscle (PAM) of aquaculture-farmed M...
March 27, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29605490/transcriptome-wide-analysis-of-differential-gene-expression-in-response-to-light-dark-cycles-in-a-model-cnidarian
#8
W B Leach, J Macrander, R Peres, A M Reitzel
Animals respond to diurnal shifts in their environment with a combination of behavioral, physiological, and molecular changes to synchronize with regularly-timed external cues. Reproduction, movement, and metabolism in cnidarians have all been shown to be regulated by diurnal lighting, but the molecular mechanisms that may be responsible for these phenotypes remain largely unknown. The starlet sea anemone, Nematostella vectensis, has oscillating patterns of locomotion and respiration, as well as the molecular components of a putative circadian clock that may provide a mechanism for these light-induced responses...
March 22, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29626726/identification-and-evolution-of-olfactory-genes-in-the-small-poplar-longhorn-beetle-saperda-populnea
#9
Yinliang Wang, Jian Zhang, Qi Chen, Hanbo Zhao, Jiatong Wang, Ming Wen, Jinghui Xi, Bingzhong Ren
Saperda populnea is a serious pest of poplar and willow trees in the Palaearctic region, causing extensive damage to forests and the lumber industry. Until recently, there is no safe and effective chemical method to control this pest due to the lack of sufficient knowledge on the molecular basis of its olfactory genes, moreover, the evolutionary history of the olfactory gene family in subfamily Lamiinae is still fully unknown. Our RNA sequencing of the antennae of S. populnea identified 43 odorant binding proteins (OBPs), 15 chemosensory proteins (CSPs), 56 odorant receptors (ORs) and 24 inotropic receptors (IRs) in S...
March 21, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29626725/itraq-based-quantitative-proteomic-analysis-of-the-androgenic-glands-of-the-oriental-river-prawn-macrobrachium-nipponense-during-nonreproductive-and-reproductive-seasons
#10
Shubo Jin, Hongtuo Fu, Shengming Sun, Sufei Jiang, Yiwei Xiong, Yongsheng Gong, Hui Qiao, Wenyi Zhang, Yan Wu
The androgenic gland produces hormones that play crucial roles in driving male sexual development. In this study, we investigated the regulatory proteins and pathways affecting male sexual development of M. nipponense, by analyzing the proteomes of their androgenic glands during their reproductive and nonreproductive seasons using isobaric tags for relative and absolute quantitation (iTRAQ). A total of 13 sex-related protein homologs out of 999 total proteins were identified in the proteome of M. nipponense based on comparisons with the published literature...
March 21, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29482114/proteomic-analysis-reveals-the-distinct-energy-and-protein-metabolism-characteristics-involved-in-myofiber-type-conversion-and-resistance-of-atrophy-in-the-extensor-digitorum-longus-muscle-of-hibernating-daurian-ground-squirrels
#11
Hui Chang, Shanfeng Jiang, Xiufeng Ma, Xin Peng, Jie Zhang, Zhe Wang, Shenhui Xu, Huiping Wang, Yunfang Gao
Previous hibernation studies demonstrated that such a natural model of skeletal muscle disuse causes limited muscle atrophy and a significant fast-to-slow fiber type shift. However, the underlying mechanism as defined in a large-scale analysis remains unclarified. Isobaric tags for relative and absolute quantification (iTRAQ) based quantitative analysis were used to examine proteomic changes in the fast extensor digitorum longus muscles (EDL) of Daurian ground squirrels (Spermophilus dauricus). Although the wet weights and fiber cross-sectional area of the EDL muscle showed no significant decrease, the percentage of slow type fiber was 61% greater (P < 0...
June 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29482113/itraq-based-proteomic-analysis-identifies-proteins-involved-in-limb-regeneration-of-swimming-crab-portunus-trituberculatus
#12
Yuanyuan Fu, Fang Zhu, Lei Liu, Shaokun Lu, Zhiming Ren, Changkao Mu, Ronghua Li, Weiwei Song, Ce Shi, Yangfang Ye, Chunlin Wang
The swimming crab (Portunus trituberculatus) has a striking capacity for limb regeneration, which has drawn the interest of many researchers. In this study, isobaric tag for relative and absolute quantitation (iTRAQ) approach was utilised to investigate protein abundance changes during limb regeneration in this species. A total of 1830 proteins were identified, of which 181 were significantly differentially expressed, with 94 upregulated and 87 downregulated. Our results highlight the complexity of limb regeneration and its regulation through cooperation of various biological processes including cytoskeletal changes, extracellular matrix (ECM) remodelling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism...
June 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29414190/transcriptomic-analysis-of-changes-in-gene-expression-of-immune-proteins-of-gill-tissue-in-response-to-low-environmental-temperature-in-fathead-minnows-pimephales-promelas
#13
Simon A Wentworth, Katrina Thede, Varsha Aravindabose, Ian Monroe, Andrew W Thompson, Neil Molyneaux, Christopher L Owen, John R Burns, Agustin Gonzalez-Vicente, Jeffrey L Garvin, Randall K Packer
In the face of ongoing climate change, it is imperative to understand better the effects of temperature on immune function in freshwater teleosts. It is unclear whether previously observed changes were caused by temperature per se. We studied changes in the gill transcriptome of fathead minnows (Pimephales promelas) at low temperature to understand better the effects of temperature on immune function. De novo assembly of the transcriptome using Trinity software resulted in 73,378 assembled contigs. Annotation using the Trinotate package yielded 58,952 Blastx hits (accessions)...
March 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29287281/comparative-analysis-of-the-transcriptome-responses-of-zebrafish-embryos-after-exposure-to-low-concentrations-of-cadmium-cobalt-and-copper
#14
Laura Sonnack, Thorsten Klawonn, Ralf Kriehuber, Henner Hollert, Christoph Schäfers, Martina Fenske
Metal toxicity is a global environmental challenge. Fish are particularly prone to metal exposure, which can be lethal or cause sublethal physiological impairments. The objective of this study was to investigate how adverse effects of chronic exposure to non-toxic levels of essential and non-essential metals in early life stage zebrafish may be explained by changes in the transcriptome. We therefore studied the effects of three different metals at low concentrations in zebrafish embryos by transcriptomics analysis...
March 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29223774/physiological-and-proteomic-responses-to-corticosteroid-treatments-in-eurasian-perch-perca-fluviatilis-investigation-of-immune-related-parameters
#15
Sylvain Milla, Sophie Massart, Cédric Mathieu, Neil Wang, Caroline Douny, Jessica Douxfils, Marie-Louise Scippo, Edwin De Pauw, Marc Dieu, Frédéric Silvestre, Patrick Kestemont
The comparative effects of cortisol and 11-deoxycorticosterone (DOC), two major corticosteroids in fish, have yet received little attention in teleosts. We evaluated the proteomic and immune responses of Eurasian perch to chronic corticosteroid treatments. We implanted immature perch with cortisol (80mg/kg) or DOC (4mg/kg) and measured the proportions of blood leucocytes, immune indices in the plasma, spleen and liver (complement and lysozyme activity, total immunoglobulin and immune gene expression in the tissues) and differential proteome expression (corticosteroid versus control) in the liver and the spleen on days 2, 4 and 14 post-treatment...
March 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29175757/identification-and-characterization-of-chemosensory-gene-families-in-the-bark-beetle-tomicus-yunnanensis
#16
Nai-Yong Liu, Zong-Bo Li, Ning Zhao, Qi-Sheng Song, Jia-Ying Zhu, Bin Yang
The bark beetle, Tomicus yunnanensis (Coleoptera: Scolytinae), is a seriously destructive pest of Yunnan pine (Pinus yunnanensis) and is distributed solely in Southwestern China. It has been a challenge to control this pest owing to its resistance to chemical pesticides, which have been used as the main control strategy of this species in recent years. Since this approach will continue until an alternative mitigation strategy is implemented, it is essential to develop novel or improved biocontrol approaches...
March 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29156228/effect-of-abiotic-and-biotic-stress-factors-analysis-using-machine-learning-methods-in-zebrafish
#17
Rajasekar Gutha, Suresh Yarrappagaari, Lavanya Thopireddy, Kesireddy Sathyavelu Reddy, Rajeswara Reddy Saddala
In order to understand the mechanisms underlying stress responses, meta-analysis of transcriptome is made to identify differentially expressed genes (DEGs) and their biological, molecular and cellular mechanisms in response to stressors. The present study is aimed at identifying the effect of abiotic and biotic stress factors, and it is found that several stress responsive genes are common for both abiotic and biotic stress factors in zebrafish. The meta-analysis of micro-array studies revealed that almost 4...
March 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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
#18
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...
March 2018: 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
#19
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...
March 2018: 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
#20
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...
March 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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