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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

Christine S Couturier, Jonathan A W Stecyk, Stian Ellefsen, Guro K Sandvik, Sarah L Milton, Howard M Prentice, Göran E Nilsson
We investigated if transcriptional responses are consistent with the arrest of synaptic activity in the anoxic turtle (Trachemys scripta) brain. Thirty-nine genes of key receptors, transporters, enzymes and regulatory proteins of inhibitory and excitatory neurotransmission were partially cloned and their expression in telencephalon of 21 °C- and 5 °C-acclimated normoxic, anoxic (24 h at 21 °C; 1 and 14 days at 5 °C) and reoxygenated (24 h at 21 °C; 13 days at 5 °C) turtles quantified by real-time RT-PCR...
February 13, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Haoliang Chen, Lulu Lin, Farman Ali, Minghui Xie, Guangling Zhang, Weihua Su
Bradysia odoriphaga is a serious pest of the Chinese chive; however, detailed information regarding the developmental stage-specific gene expression patterns of B. odoriphaga is not yet available. In this study, RNA sequencing (RNA-seq) was performed to determine the gene expression patterns of developmental stages including the eggs, second instar larvae, fourth instar larvae, pupae, and adults of B. odoriphaga. Analysis of 15 samples revealed an average of 89.56% of the clean reads could be mapped onto the assembled UniGene database...
February 10, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Yuan-Tao Zhou, Ling Li, Xiao-Rong Zhou, Yao Tan, Bao-Ping Pang
The band-winged grasshopper Oedaleus asiaticus (Orthoptera: Acridoidea) is an important insect pest in north China. Chemosensory membrane proteins are believed to be crucial factors in direct interactions with odorants in the chemosensory process. However, there is much limited information on the chemosensory system in this pest. In this study, a total of 69 candidate chemosensory membrane protein genes, including 60 olfactory receptors (ORs), 6 ionotropic receptors (IRs) and 3 sensory neuron membrane proteins (SNMPs), were identified for the first time from the antennal transcriptomes of O...
February 10, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Biswapriya Biswavas Misra, Ruiz-Hernández Ixchel Mariel, Hernández-Bolio Gloria Ivonne, Hernández-Núñez Emanuel, Díaz-Gamboa Raúl, Colli-Dula Reyna Cristina
The common bottlenose dolphin (Tursiops truncatus) is a carnivorous cetacean thriving in marine environment that is 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 the health of coastal marine ecosystems in their role as predators that can bioaccumulate contaminants. Although recent studies have focused on capturing the circulating metabolomes of these mammals, as well as in the context of pollutants and exposures in the marine environment, the skin and blubber are important surface and protective organs that have not been probed for metabolism...
February 10, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Liam J Hawkins, Minjing Wang, Baowen Zhang, Qi Xiao, Hui Wang, Kenneth B Storey
Vertebrate freeze tolerance requires multiple adaptations underpinned by specialized biochemistry. Freezing of extracellular water leads to intracellular dehydration as pure water is incorporated into growing ice crystals and also results in the cessation of blood supply to tissues, creating an anoxic cellular environment. Hence, the freeze tolerant wood frog, Rana sylvatica, must endure both dehydration and anoxia stresses in addition to freezing. The metabolic responses to freezing, dehydration and anoxia involve both protein/enzyme adaptations and the production of metabolites with metabolic or osmotic functions, particularly glucose and urea...
January 25, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Zengjie Jiang, Xiaoqin Wang, Samuel P S Rastrick, Jinghui Fang, Meirong Du, Yaping Gao, Fengxue Li, Øivind Strand, Jianguang Fang
Rising atmospheric carbon dioxide (CO2 ), primarily from anthropogenic emissions, are resulting in increasing absorption of CO2 by the oceans, leading to a decline in oceanic pH in a process known as ocean acidification (OA). There is a growing body of evidence demonstrating the potential effect of OA on the energetics/physiology and consequently life-history traits of commensally important marine organisms. However, despite this little is known of how fundamental metabolic pathways that underpin changes in organismal physiology are affected by OA...
January 18, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Chunli Xiu, Yong Xiao, Song Zhang, Haibo Bao, Zewen Liu, Yongjun Zhang
In arthropods, the large majority of studies on olfaction have been mainly focused on insects, whereas little on Arachnida, even though olfaction is very important in arachnid behavior. Pardosa pseudoannulata is one of the most common wandering spiders in rice fields, as the important natural enemy against a range of pests. However, little is known about the potential chemosensory proteins involved in olfactory behavior of these spiders. Niemann-Pick proteins type C2 (NPC2) as a new class of binding and transport proteins for semiochemicals in arthropods especially ticks and mites has received more attention in recent years...
January 17, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Hong-Yue Ma, Xiao-Rong Zhou, Yao Tan, Bao-Ping Pang
Galeruca daurica is a new pest causing great losses in the Inner Mongolian grasslands of China. The adults enter obligatory diapause during summer. However, the molecular mechanism of summer diapause remains unknown. We used iTRAQ to conduct proteomic analysis of adult G. daurica at the pre-diapause (PD), diapause (D) and post-diapause (TD) stages during summer diapause. A total of 139 and 118 differentially expressed proteins (DEPs) were detected in D/PD and TD/D comparisons, respectively. Besides a large number of DEPs involved in metabolic process, stress response, cytoskeletal reorganization, and phagosome pathway, many new proteins related to diapause were found in this study, such as encapsulation-relating proteins, odorant binding proteins, chemosensory proteins and ribosomal proteins...
January 15, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Bi-Yue Ding, Li Yang, Yuan-Yuan Peng, Teng-Yu Chang, Chao Ye, Feng Shang, Jinzhi Niu, Jin-Jun Wang
The citrus leaf-mining beetle, Podagricomela weisei Heikertinger, is an important citrus pest that ingests the mesophyll and new shoots. The mechanism underlying the xenobiotic metabolism of P. weisei is not well understood, in part because of a lack of available genomic and transcriptomic data, which has hampered the development of novel pest management approaches [e.g., RNA interference (RNAi)]. In this study, we completed the deep sequencing of the P. weisei transcriptome to identify factors potentially involved in xenobiotic metabolism and the core RNAi machinery...
January 15, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Yang Liu, Jiashou Liu, Shaowen Ye, Dominique P Bureau, Hongbai Liu, Jiasheng Yin, Zhenbo Mou, Hong Lin, Fuhua Hao
High temperature is a powerful stressor for fish living in natural and artificial environments, especially for cold water species. Understanding the impact of thermal stress on physiological processes of fish is crucial for better cultivation and fisheries management. However, the metabolic mechanism of cold water fish to thermal stress is still not completely clear. In this study, a NMR-based metabonomic strategy in combination with high-throughput RNA-Seq was employed to investigate global metabolic changes of plasma and liver in a typical cold water fish species lenok (Brachymystax lenok) subjected to a sub-lethal high temperature...
January 15, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Sinuo Liu, Xiaomei Chen, Shanshan Lian, Xiaoting Dai, Naina Hu, Fengmei Zhang, Lingling Zhang, Zhenmin Bao, Shi Wang
Cellular signaling initiated by various secreted, cysteine-rich Wnt proteins plays essential roles in regulating animal development and cell stemness. By virtue of its functional diversity and importance, the Wnt gene family has received substantial research interests in a variety of animal species, from invertebrates to vertebrates. However, for bivalve molluscs, one of the ancient bilaterian groups with high morphological diversity, systematic identification and analysis of the Wnt gene family remain lacking...
January 15, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Yang Liu, Haishen Wen, Xin Qi, Xiaoyan Zhang, Kaiqiang Zhang, Hongying Fan, Yuan Tian, Yanbo Hu, Yun Li
Na+ /H+ exchangers (NHEs) are one of the major groups of transmembrane proteins that play crucial roles in pH homeostasis, cell volume regulation and Na+ transport in animals. In our study, twelve NHEs were identified from transcriptomic and genomic databases of Lateolabrax maculatus. The evolutionary footprint of each NHE gene was revealed via the analysis of phylogenetic tree, copy numbers, exon-intron structures and motif compositions. NHEs harbored a high proportion of α-helices (54.7% to 67.0%) and a low proportion of β-sheets (1...
January 9, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Aaron M Watson, Fabio Casu, Daniel W Bearden, Justin Yost, Michael R Denson, T Gibson Gaylord, Paul Anderson, Paul A Sandifer, John W Leffler, Frederic T Barrows
A twelve-week feeding trial was conducted to examine potential metabolic and gene expression changes that occur in juvenile red drum, Sciaenops ocellatus, fed diets with increasing soybean meal inclusion. Significant reduction in fish performance characteristics (feed consumption, weight gain, final weight) was observed within the soybean meal based diets as soybean meal level increased (R, linear regression); however, all soybean meal based diets performed statistically equivalent in regards to performance characteristics (weight gain, feed conversion ratio, condition factor, etc...
January 8, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Yaoyao Zhan, Kai Lin, Chen Ge, Jian Che, Yingying Li, Dongyao Cui, Qiantong Pei, Lin Liu, Jian Song, Weijie Zhang, Yaqing Chang
To explore the molecular mechanisms underlying the initial differentiation and formation of papillae in sea cucumbers, the transcriptomes of Apostichopus japonicus pentactulae (without papillae) were compared to those of A. japonicus juveniles (with papillae). From the RNA of the three pentactula libraries and the three juvenile libraries, we obtained 41-46 million raw reads, yielding 39-45 million clean reads. From these, we generated 599,673 transcripts and identified 230,604 unigenes. Across all six transcriptomes, we identified 246,207 single nucleotide polymorphisms (SNPs) and 80,455 single sequence repeats (SSRs)...
December 28, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Zhenzhu Sun, Xiaohong Tan, Minglei Xu, Qingying Liu, Huaqun Ye, Cuiyun Zou, Chaoxia Ye
Cold stress has caused great economic loss in fish culture worldwide. Orange-spotted grouper (Epinephelus coioides) is one of the most serious lost aquatic animals in 2016 cold fronts in South China. However, the molecular mechanism of grouper's cold resistance has remained largely unknown. In the present study, HiSeq™2000 (Illumina) was used to analyze the transcriptomic profiles of the liver from grouper under control temperature (CT, 28 °C) and low temperature (LT, 13 °C). Two normalized liver cDNA libraries of CT and LT groups were created...
December 27, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Li Li, Muyan Chen, Kenneth B Storey
Hypoxia is a severe problem in aquatic environments worldwide and has caused mass mortality of sea cucumbers (& other species) for decades, seriously affecting the sustainable development of aquaculture. Investigations of the metabolic disruptions and biochemical responses associated with acute hypoxia stress in sea cucumbers can provide a theoretical basis and guidance for improving aquaculture. A metabolomics approach to characterize changes in the profiles of endogenous small molecules in response to acute hypoxia can help to identify the main underlying causes of metabolic damage and potentially suggest solutions to alleviate to improve viability...
December 27, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Milena Mechkarska, Jolanta Kolodziejek, Vishal Musale, Laurent Coquet, Jérôme Leprince, Thierry Jouenne, Norbert Nowotny, J Michael Conlon
Peptidomic analysis of norepinephrine-stimulated skin secretions from the Greek stream frog Rana graeca Boulenger, 1891 led to the identification and structural characterization of a range of host-defense peptides. These comprised brevinin-1GRa, brevinin-1GRb and an N-terminally extended form of brevinin-1GRb, ranatuerin-2GR together with its oxidized form and (11-28) fragment, temporin-GRa, temporin-GRb and its non-amidated form, and a melittin-related peptide, MRP-GR and its (1-18) fragment. The most abundant peptide, MRP-GR significantly (P < 0...
December 27, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Sicong Zhou, Yuenan Zhou, Ying Wang, Jiani Chen, Lan Pang, Zhongqiu Pan, Chaoqun Li, Min Shi, Jianhua Huang, Xuexin Chen
The pupal endoparasitoid wasp Trichopria drosophilae (Hymenoptera: Diapriidae) plays an important role in biological control of many frugivorous fruit fly species including Drosophila suzukii, a well-known invasive pest. Here, we report the transcriptomes of T. drosophilae among different developmental stages. A total of 601,148,438 high-quality reads were obtained and de novo assembled into 187,704 unigenes with an average length of 1096 bp. Among them, 21,735 unigenes were annotated into 52 Gene Ontology terms and 36,898 were assigned to 25 Cluster of Orthologous Groups categories, whereas 30,585 unigenes were mapped to 270 Kyoto Encyclopedia of Genes and Genomes different pathways...
December 26, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Ying Zhou, Weiwei Luo, Xiaomu Yu, Qingshan Liu, Jingou Tong
Feed cost is one of the largest variable input costs in aquaculture. In general, dietary energy is directed toward protein deposition and muscle growth. However, most of the dietary energy will be used to support body maintenance if feed conversion efficiency (FCE) is relatively low. Thus, improving feed efficiency will make great contributions to the productivity, profitability, and sustainability of fish farming industry. In the present study, we performed comparative transcriptome analyses of brain and intestine tissues from extreme FCE groups and identified differentially expressed genes (DEGs) and regulatory pathways that may be involved in FCE and related traits in one of the important common carp strains of China, the Yellow River carp (Cyprinus carpio haematopterus)...
December 20, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Yangchun Li, Zhaoping Wang, Zongwu Zhao, Yuting Cui
Low salinity treatment is proven to be the practical polyploidy inducing method for shellfish with advantages of lower cost, higher operability and reliable food security. However, little is known about the possible molecular mechanism of hypotonic induction. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) based proteomic profiling was pursued to investigate the responses of zygotes of the Pacific oyster Crassostrea gigas to low salinity. A total of 2235 proteins were identified and 87 proteins were considered differentially expressed, of which 14 were up-regulated and 69 were down-regulated...
December 11, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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