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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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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
#1
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
#2
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
#3
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/30149319/the-proteome-map-of-the-escamolera-ant-liometopum-apiculatum-mayr-larvae-reveals-immunogenic-proteins-and-several-hexamerin-proteoforms
#4
José A Huerta-Ocampo, María S García-Muñoz, Aída J Velarde-Salcedo, Eric E Hernández-Domínguez, Jorge L González-Escobar, Alberto Barrera-Pacheco, Alicia Grajales-Lagunes, Ana P Barba de la Rosa
The larvae of escamolera ant (Liometopum apiculatum Mayr) have been considered a delicacy since Pre-Hispanic times. The increased demand for this stew has led to massive collection of ant nests. Yet biological aspects of L. apiculatum larvae remain unknown, and mapping the proteome of this species is important for understanding its biological characteristics. Two-dimensional gel electrophoresis (2-DE) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to characterize the larvae proteome profile...
August 17, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30007273/lateralized-expression-of-left-right-axis-formation-genes-is-shared-by-adult-brains-of-lefty-and-righty-scale-eating-cichlids
#5
Yuichi Takeuchi, Asano Ishikawa, Yoichi Oda, Jun Kitano
Variation in the laterality often exists within species and can be maintained by frequency-dependent selection. Although the molecular developmental mechanisms underlying the left-right axis formation have been investigated, the genomic mechanisms underlying variation in laterality remain largely unknown. The scale-eating cichlid Perissodus microlepis in Lake Tanganyika exhibit lateralized predation; lefty individuals with the mouth opening toward the right preferentially attack on the prey's left trunk, while righty individuals with the opposite opening attacks on the right trunk...
July 7, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30005390/response-of-detoxification-and-immune-genes-and-of-transcriptome-expression-in-mythimna-separata-following-chlorantraniliprole-exposure
#6
Jin-Da Wang, Wei-Zhong Wang, Ya-Ru Wang, San-Ji Gao, Mohammed Elzaki, Ran Wang, Rong Wang, Min Wu
The oriental armyworm Mythimna separata is a serious polyphagous pest in China and there are major efforts to control this pest. In the present study, an RNA-Seq method was used to explore transcriptome data of M. separata and identify the responses of genes to chlorantraniliprole. Sequencing and de novo assembly yielded 134,533 transcripts that were further assembled into 77,628 unigenes with an N50 length of 2165 bp. A total of 76 unigenes encoding insecticide targets were identified. Furthermore, 62 cytochrome P450s, 34 glutathione S-transferase (GSTs)and 64 carboxylesterase (CCEs) were curated to construct phylogenetic trees...
July 7, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/30005389/transcriptional-response-to-low-temperature-in-the-yellow-drum-nibea-albiflora-and-identification-of-genes-related-to-cold-stress
#7
Dongdong Xu, Qiaochu You, Changfeng Chi, Shengyu Luo, Hongbin Song, Bao Lou, Yutaka Takeuchi
The yellow drum (Nibea albiflora) is an economically important maricultured fish in China, but the aquaculture of this species is severely affected by overwinter mortality associated with cold stress. Characterization of the molecular mechanisms underlying the susceptibility of the yellow drum to cold might increase our understanding of how this fish adapts to environmental challenges. Here, the transcriptional response of the yellow drum to cold stress (7.5 °C) was investigated with RNA-Seq analysis. We compared brain and muscle transcriptomes among cold-tolerant (Tol) fish that survived the cold treatment, cold-sensitive (Sen) fish that were killed by the cold treatment, and control (Con) fish that were not subjected to cold...
July 7, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29980138/peptidomic-analysis-of-the-host-defense-peptides-in-skin-secretions-of-the-trinidadian-leaf-frog-phyllomedusa-trinitatis-phyllomedusidae
#8
Milena Mechkarska, Laurent Coquet, Jérôme Leprince, Renoir J Auguste, Thierry Jouenne, Maria Luisa Mangoni, J Michael Conlon
Peptidomic analysis (reversed-phase HPLC combined with MALDI-TOF mass spectrometry and automated Edman degradation) of norepinephrine-stimulated skin secretions from the Trinidadian leaf frog Phyllomedusa trinitatis Mertens 1926 led to the identification and structural characterization of 26 host-defense peptides. On the basis of amino acid sequence similarity, the peptides may be divided into the followings groups: dermaseptins with the conserved N-terminal region GLWSKIK (6 peptides), dermaseptins with the N-terminal region ALWKXXLK (5 peptides), dermaseptins with the conserved N-terminal region GLFKTLIKGAGKMLGHVAK (4 peptides), C-terminally α-amidated and non-amidated forms of the phylloseptins (9 peptides), phyllocaerulein, a peptide (GLVSGLLNSVTGLLGNLAGGGL) with structural similarity to the plasticins, and a putative antioxidant peptide (LTWKIPTRFCGVT)...
June 30, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29980137/identification-of-candidate-chemosensory-receptors-in-the-antennal-transcriptome-of-the-large-black-chafer-holotrichia-parallela-motschulsky-coleoptera-scarabaeidae
#9
Jian-Kun Yi, Shuang Yang, Shang Wang, Jun Wang, Xin-Xin Zhang, Yan Liu, Jing-Hui Xi
Olfaction and gustation play critical roles in the daily activities of insects by mediating important behaviors, such as locating host plants, mates and oviposition sites. These behaviors are mediated by a series of chemosensory receptor proteins, including odorant receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs). Holotrichia parallela is a worldwide pest on many crops and particularly on peanuts in China. In the present study, we produced Illumina-based transcriptomes from male and female antennae and ultimately identified 47 candidate ORs, 15 GRs and 27 IRs...
June 23, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29960135/rna-seq-analysis-of-differentially-expressed-genes-in-the-grand-jackknife-clam-solen-grandis-under-aerial-exposure
#10
Hongtao Nie, Shasha Dong, Dongdong Li, Mengge Zheng, Liwen Jiang, Xiaodong Li, Xiwu Yan
Aerial exposure tolerance has been long considered as an important trait for the life survival under acute environmental stress. In this study, we utilized RNA-seq-based transcriptomic profiling to characterize the molecular responses of grand jackknife clam in response to aerial exposure. This assembly yielded 190,856 unigenes with an average length of 1147 bp, a minimum length of 201 bp, and a maximum length of 51,869 bp, with an N50 length of 1875 bp. After differential expression analysis, a total of 1344 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, immune alteration, and apoptosis...
June 21, 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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
https://www.readbyqxmd.com/read/29733998/genome-wide-identification-of-chitinase-and-chitin-deacetylase-gene-families-in-the-oriental-fruit-fly-bactrocera-dorsalis-hendel
#17
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...
September 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
#18
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...
September 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29940392/comparative-transcriptomics-in-three-passerida-species-provides-insights-into-the-evolution-of-avian-mitochondrial-complex-i
#19
Qingqing Wang, Wenkang Lu, Jianke Yang, Lan Jiang, Qin Zhang, Xianzhao Kan, Xiaojun Yang
Recent studies have shown that mitochondria play a crucial role in cellular energy production through the oxidative phosphorylation (OXPHOS) system. Complex I (NADH:ubiquinone oxidoreductase), the first and largest enzyme complex of the OXPHOS system, includes both nuclear- and mitochondrial-encoded proteins. However, the patterns of natural selection and phylogenetic implications of complex I in birds still remain unclear. In this study, we combined transcriptomic and phylogenetic analyses to comprehensively determine the evolution of avian complex I...
June 18, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29940393/transcriptomic-analysis-of-differentially-expressed-genes-in-the-molting-gland-y-organ-of-the-blackback-land-crab-gecarcinus-lateralis-during-molt-cycle-stage-transitions
#20
Sunetra Das, Lindsay Vraspir, Wen Zhou, David S Durica, Donald L Mykles
A transcriptome of the Gecarcinus lateralis molting gland (Y-organ or YO) contained 48,590 contiguous sequences (contigs) from intermolt (IM), early premolt (EP), mid premolt (MP), late premolt (LP), and postmolt (PM) stages. The YO is kept in the basal state in IM by molt-inhibiting hormone (MIH)/cyclic nucleotide-dependent signaling. YO activation in EP requires down-regulation of MIH signaling and activation of mechanistic target of rapamycin (mTOR)-dependent protein synthesis. Transition of the YO to the committed state in MP requires activin/transforming growth factor-beta (TGFβ) signaling...
June 15, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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