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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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https://www.readbyqxmd.com/read/30419482/transcriptional-effects-of-dietary-chlorpyrifos%C3%A2-methyl-exposure-in-atlantic-salmon-salmo-salar-brain-and-liver
#1
P A Olsvik, M H G Berntssen, L Søfteland, M Sanden
Elevated levels of chlorpyrifos‑methyl have been detected in plant-based Atlantic salmon feeds. To evaluate the potential negative effects of long-term and continuous dietary exposure to chlorpyrifos‑methyl in fish, we fed juvenile Atlantic salmon three concentrations (0.1, 1.0 and 8.0 mg/kg) of the pesticide for about two months. Brain and liver tissues were collected after 30 and 67 days of exposure. Homogenized brain tissue was examined for effects on acetylcholinesterase, and brain and liver tissue from fish exposed to 8...
November 6, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30412850/comparative-transcriptional-analysis-and-rna-interference-reveal-immunoregulatory-pathways-involved-in-growth-of-the-oriental-river-prawn-macrobrachium-nipponense
#2
Fajun Li, Shiyong Zhang, Chunpeng Fu, Aili Wang, Dezhen Zhang
A source of premium animal protein, crustaceans are widely distributed and cultivated around the world. Short-term or long-term starvation events occur frequently owing to natural environment changes or manual management strategies in the life cycle of crustaceans. The result induced by starvation is that somatic growth of crustaceans will be retarded, while the immune mechanism is activated in this process. The aim of this study was to investigate whether the immune regulatory pathways are involved in the growth of crustaceans...
October 30, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30408678/coding-non-coding-cross-talk-in-intestinal-epithelium-transcriptome-gives-insights-on-how-fish-respond-to-stocking-density
#3
Ana Teresa Gonçalves, Gustavo Núñez-Acuña, Camille Détrée, Cristian Gallardo-Escárate
Fish respond to increasing stocking density as a stressor, adjusting physiological functions to increase energy supply for coping with deleterious effects and adapting. These responses are complex and systemic, and the molecular mechanisms involved remain undetermined. One of the most sensitive organs to environmental and homeostatic disruptions is the intestine, and since it plays several vital functions, understanding the molecular underpinnings of this organ under deleterious conditions is imperative for health improvement in aquaculture systems...
October 30, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30408677/integration-of-small-rnas-and-mrnas-by-high-throughput-sequencing-reveals-a-complex-regulatory-network-in-chinese-sea-cucumber-russian-sea-cucumber-and-their-hybrids
#4
Zhicheng Wang, Jun Cui, Jian Song, Meng Gou, Haoze Wang, Kailun Gao, Xuemei Qiu, Xiuli Wang, Yaqing Chang
The body wall of the sea cucumber is an important tissue with high nutritional value. In this study, the parents of Apostichopus japonicus were derived from Russia (R) and China (C). We examined the transcriptional profiles in the body wall from F1 hybrids (CR and RC) and purebreds (CC and RR) at 9 months. In total, 34.07 G clean data were obtained from the transcriptome, 100,870 unigenes were identified, and 26,483 unigenes were annotated. Based on edgeR, 1097-4,587differentially expressed genes (DEGs) were identified...
October 21, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30419481/transcriptional-shifts-during-juvenile-coho-salmon-oncorhynchus-kisutch-life-stage-changes-in-freshwater-and-early-marine-environments
#5
Aimee Lee S Houde, Angela D Schulze, Karia H Kaukinen, Jeffrey Strohm, David A Patterson, Terry D Beacham, Anthony P Farrell, Scott G Hinch, Kristina M Miller
There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas...
October 18, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30317123/identification-and-characterization-of-micrornas-involved-in-scale-biomineralization-in-the-naked-carp-gymnocypris-przewalskii
#6
Shiguo Li, Weiwei Chen, Aibin Zhan, Jian Liang
The mineralized scale derived from skin plays a protective role for the fish body and also possesses important application values in the biomaterial field. However, little is known about fish scale biomineralization and related molecular regulatory mechanisms. Here, we used a comparative microRNA sequencing approach to identify and characterize differentially expressed microRNAs (DEMs) involved in scale biomineralization in the naked carp Gymnocypris przewalskii. A total of 18, 43, and 66 DEMs were obtained from skin tissues covered with initial, developing, and mature scales (IS, DS, and MS) compared with scale-uncovered skin...
October 9, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30366214/transcriptome-from-pacific-cod-liver-reveals-types-of-apolipoproteins-and-expression-analysis-of-afp-iv-structural-analogue-with-mammalian-apoa-i
#7
Ming-Guang Mao, Yu Chen, Rui-Ting Liu, Hui-Qian Lü, Jie Gu, Zhi-Qiang Jiang, Jie-Lan Jiang
Apolipoproteins (Apos), transporting the lipids through the lymphatic and circulatory systems, are associated with kinds of diseases. Additionally, type IV antifreeze protein (AFP-IV) was related evolutionarily with apolipoproteins. However, the information of Apos in fish was limited. In this study, ApoA-I, ApoA-I-2, ApoA-IV, Apo E, ApoB-100-like and AFP-IV were sequenced from Pacific cod (Gadus macrocephalus) liver transcriptome using Illumina HiSeq 2000, and their 3-D models were constructed based on the most confidence templates ever reported in mammals...
October 7, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30290366/genome-wide-identification-of-the-entire-90-glutathione-s-transferase-gst-subfamily-genes-in-four-rotifer-brachionus-species-and-transcriptional-modulation-in-response-to-endocrine-disrupting-chemicals
#8
Jun Chul Park, Duck-Hyun Kim, Min-Chul Lee, Jeonghoon Han, Hee-Jin Kim, Atsushi Hagiwara, Un-Ki Hwang, Heum Gi Park, Jae-Seong Lee
Genome-wide identification of glutathione S-transferase (GST), a major phase II detoxification enzyme, was investigated in four different aquatic model rotifer species Brachionus koreanus, B. plicatilis, B. rotundiformis, and B. calyciflorus. GSTs are ubiquitous antioxidant enzymes that play versatile function including cellular detoxification, stress alleviation, and production of the radical conjugates. Among the four rotifers, B. rotundiformis was found with the least number of GST genes (total 19 GST genes), whereas the other three species shared 23 to 24 GST genes...
September 26, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30290365/toxin-diversity-revealed-by-the-venom-gland-transcriptome-of-pardosa-pseudoannulata-a-natural-enemy-of-several-insect-pests
#9
Lixin Huang, Zhaoying Wang, Na Yu, Jingjing Li, Zewen Liu
The pond wolf spider, Pardosa pseudoannulata, is one of the most dominant predators of several agriculture insect pests including mainly the rice planthoppers and leafhoppers in paddy fields in Asia. Venom has been an attractive subject as the powerful weapon of spiders due to the complex components secreted from venom gland. The transcriptome of P. pseudoannulata venom gland was sequenced in order to understand the diversity of venom components at the molecular level and provide a new perspective for insect pest management...
September 22, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30265919/genome-wide-identification-of-hsp70-110-genes-in-sea-cucumber-apostichopus-japonicus-and-comparative-analysis-of-their-involvement-in-aestivation
#10
Lei Gao, Zihao Yuan, Simeng Yu, Yujia Yang, Yunfeng Li, Chongbo He
HSP70/110s are a subgroup of heat shock proteins and play crucial roles in protein homeostasis. HSP70/110s can enhance cell survival in response to a multitude of stressful stimuli, of which the most studied one is heat stress. To perform a systematic study of HSP70/110s in sea cucumber Apostichopus japonicus, 15 HSP70/110 genes, including 13 HSP70s and two HSP110s, were identified and characterized from the transcriptome and genome of sea cucumber. Moderate expansion and conserved structure were found by the phylogenetic and syntenic analysis...
September 15, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30241009/de-novo-assembly-and-comparative-transcriptome-analyses-of-purple-and-green-morphs-of-apostichopus-japonicus-during-body-wall-pigmentation-process
#11
Lili Xing, Lina Sun, Shilin Liu, Xiaoni Li, Libin Zhang, Hongsheng Yang
Pigmentation processes provide a traceable and relevant trait for understanding key issues in evolutionary biology such as adaptation, speciation and the maintenance of balanced polymorphisms. The sea cucumber Apostichopus japonicus, which has nutritive and medical properties, is considered the most valuable commercial species in many parts of Asia. Compared with the green morph, the purple morph is rare and has great appeal to consumers. However, little is currently known about the molecular mechanism of body color formation in A...
September 14, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30196245/rna-seq-based-transcriptome-profiling-and-expression-of-16-cytochrome-p450-genes-in-the-benzo-%C3%AE-pyrene-exposed-estuarine-copepod-eurytemora-affinis
#12
Bo-Young Lee, Min-Chul Lee, Chang-Bum Jeong, Hee-Jin Kim, Atsushi Hagiwara, Sami Souissi, Jeonghoon Han, Jae-Seong Lee
The calanoid copepod Eurytemora affinis is one of the most abundant estuarine species and is considered to be an ideal candidate species for ecotoxicological research. An RNA-Seq-based transcriptome was developed from whole bodies of this species. Among 142,442 contigs of the de novo assembly by Trinity, 48,480 open reading frame (ORF) contigs were found using TransDecoder. A total of 17,762 genes were identified by BLAST analysis, which covers about 75% of the annotated genes in the E. affinis genome. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that most annotated sequences were related to metabolism pathways, including xenobiotic biodegradation...
September 4, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30195212/a-whole-body-transcriptome-analysis-and-expression-profiling-of-odorant-binding-protein-genes-in-oedaleus-infernalis
#13
Yu Zhang, Yao Tan, Xiao-Rong Zhou, Bao-Ping Pang
To investigate the olfactory mechanisms in Oedaleus infernalis, one of important pests of cereals and pasture in the northern China, the whole-body transcriptome was constructed by RNA-Seq in this study. By de novo assembly, a total of 92,476 unigenes were generated in the adult sample, and 32,693 unigenes (35.35%) were successfully annotated by Blastx. Eighteen putative odorant binding proteins (OBPs) were identified, and phylogenetic analysis indicated the closest genetic relationship of eight OBPs in O. infernalis with those in its sibling species, Oedaleus asaiticus, while five OBPs in O...
September 4, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30195211/identification-of-candidate-olfactory-genes-in-cicada-subpsaltria-yangi-by-antennal-transcriptome-analysis
#14
Mengmeng Qi, Songshan Wei, Cong Wei
Olfaction in antennae is essential for regulating insect behaviors such as host preference and oviposition site selection. To better understand the olfactory mechanisms in the cicada Subpsaltria yangi that has a very narrow host range far fewer than diets of most other cicadas, an antennal transcriptome was constructed in this study. We identified 10 unigenes encoding putative odorant-binding proteins (OBPs), 10 chemosensory proteins (CSPs), 8 sensory neuron membrane proteins (SNMPs), 7 gustatory receptors (GRs), 29 odorant receptors (ORs) and 13 ionotropic receptors (IRs)...
September 1, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29986214/gene-flow-prevents-mitonuclear-co-adaptation-a-comparative-portrait-of-sympatric-wild-types-and-cybrids-in-the-fish-chrosomus-eos
#15
Bernard Angers, Vincent Chapdelaine, Léo Deremiens, Roland Vergilino, Christelle Leung, Simon-Luc Doucet, Hélène Glémet, Annie Angers
Allospecific mtDNA can occasionally be beneficial for the fitness of populations. It is, however, difficult to assess the effect of mtDNA in natural conditions due to genetic and/or environmental interactions. In the fish Chrosomus eos, the transfer of C. neogaeus mitochondria occurs in a single generation and results in natural cybrids. For a few lakes in Quebec, C. eos can harbor either a C. eos mtDNA (wild types) or a C. neogaeus mtDNA (cybrids). Moreover, mtDNA of cybrids originated either from Mississippian or Atlantic glacial refuges...
September 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29966935/interrogation-of-the-gulf-toadfish-intestinal-proteome-response-to-hypersalinity-exposure-provides-insights-into-osmoregulatory-mechanisms-and-regulation-of-carbonate-mineral-precipitation
#16
Kevin L Schauer, Aalekhya Reddam, Elvis Genbo Xu, Lisa M Wolfe, Martin Grosell
Marine bony fish live in a hyperosmotic environment and maintain osmotic homeostasis by drinking seawater, and absorbing salt and water across their gastrointestinal tract. Although the ion and water transport mechanisms in the intestine have been the subject of much study, numerous questions remain unanswered. To address some of these questions, a shotgun proteomics methodology employing isobaric tandem mass tags (TMT) was used to interrogate the anterior intestine, posterior intestine, and intestinal fluid proteomes of Gulf toadfish (Opsanus beta) acclimated to normal (35 ppt) or hypersaline (60 ppt) seawater...
September 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29787920/identification-and-characterization-of-chemosensory-genes-in-the-antennal-transcriptome-of-spodoptera-exigua
#17
Li-Xiao Du, Yang Liu, Jin Zhang, Xi-Wu Gao, Bing Wang, Gui-Rong Wang
Chemical senses are crucial for insect behaviors such as host preference, mate choice and oviposition site selection. Various protein families are involved in these processes, including odorant receptors (ORs), ionotropic receptors (IRs), gustatory receptors (GRs), chemosensory proteins (CSPs), odorant binding proteins (OBPs) and sensory neuron membrane proteins (SNMPs). To better understand the olfactory mechanism in Spodoptera exigua, we conducted transcriptome analysis of adult antennae and identified a total of 157 candidate chemosensory genes encoding 51 ORs, 20 IRs, 7 GRs, 32 CSPs, 45 OBPs and 2 SNMPs...
September 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
#18
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...
September 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
#19
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)...
September 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29738886/comparison-of-proteomic-profiles-in-the-ovary-of-sterlet-sturgeon-acipenser-ruthenus-during-vitellogenic-stages
#20
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...
September 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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