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Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics

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https://www.readbyqxmd.com/read/27852008/selection-for-higher-fertility-reflects-in-the-seminal-fluid-proteome-of-modern-domestic-chicken
#1
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
#2
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/27835832/genome-wide-identification-of-atp-binding-cassette-abc-transporters-and-conservation-of-their-xenobiotic-transporter-function-in-the-monogonont-rotifer-brachionus-koreanus
#3
Chang-Bum Jeong, Hui-Su Kim, Hye-Min Kang, Young Hwan Lee, Bingsheng Zhou, Joonho Choe, Jae-Seong Lee
The ATP-binding cassette (ABC) transporter family is one of the largest gene family in animals, and members of this family are known to be involved in various biological processes due to their ability to transport a wide range of substrates across membranes using ATP cleavage-derived energy. We identified 61 ABC transporters in the genome of the monogonont rotifer Brachionus koreanus, and classified these into eight distinct subfamilies (A-H) by phylogenetic analysis. ABC transporters in the rotifer B. koreanus are comprised of 11 ABCA genes, 19 ABCB genes, 14 ABCC genes, 3 ABCD genes, 1 ABCE gene, 3 ABCF genes, 8 ABCG genes, and 2 ABCH genes...
October 24, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27806254/taste-receptors-and-gustatory-associated-g-proteins-in-channel-catfish-ictalurus-punctatus
#4
Sen Gao, Shikai Liu, Jun Yao, Tao Zhou, Ning Li, Qi Li, Rex Dunham, Zhanjiang Liu
Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particularly true for channel catfish (Ictalurus punctatus) that live in turbid waters with limited visibility. This biological process is mainly mediated by taste receptors expressed in taste buds that are distributed in several organs and tissues, including the barbels and skin. In the present study, we identified a complete repertoire of taste receptor and gustatory associated G protein genes in the channel catfish genome...
October 23, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27788413/rapid-evolution-of-symbiotic-bacteria-populations-in-spirotetramat-resistant-aphis-gossypii-glover-revealed-by-pyrosequencing
#5
Juhong Zhang, Yiou Pan, Chao Zheng, Xiwu Gao, Xiang Wei, Jinghui Xi, Tianfei Peng, Qingli Shang
Aphis gossypii is one of the most economically important insect pests for agriculture worldwide. Aphids have developed symbiotic associations with bacterial species, which has led to morphological and molecular differences, such as body color and insecticide resistance. Adults and 3rd instar nymphs of a laboratory-selected spirotetramat-resistant strain of cotton aphid presented 579-fold and 15-fold higher resistance to spirotetramat, respectively, than a susceptible strain (Pan et al., 2015; Peng et al., 2016)...
October 23, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27689822/transcriptomic-profiles-of-the-upper-olfactory-rosette-in-cultured-and-wild-senegalese-sole-solea-senegalensis-males
#6
E Fatsini, R Bautista, M Manchado, N J Duncan
The aims of this study were the characterization of the upper olfactory epithelium of cultured and wild Senegalese sole mature males at histological and transcriptomic (using RNA-Seq) level. No significant differences in tissue structure, cell types and cellular distribution pattern (olfactory sensory neurons) were identified between cultured and wild specimens. Deep transcriptomic analysis showed 2387 transcripts were differentially expressed between cultured and wild groups. A detailed analysis identified the differentially expressed transcripts included some olfactory receptors (OR, TAAR and V2R-like) and transcripts related with the control of reproduction such as the brain aromatase cytochrome P450 and tachykinin-3...
September 20, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27639030/comparative-transcriptomic-analyses-of-two-bighead-carp-hypophthalmichthys-nobilis-groups-with-different-growth-rates
#7
Beide Fu, Xinhua Wang, Xiu Feng, Xiaomu Yu, Jingou Tong
Growth is one of the most important and desired economic traits for aquaculture species, and identification of loci controlling growth is a difficult task without genomic sequences. In this study, the liver transcriptomes of two groups (F and S) of bighead carp (Hypophthalmichthys nobilis) within a full-sib family with significant differences in growth rate were sequenced. Following de novo assembly of the combined reads from the two groups, a total of 410 differentially expressed genes were identified. Functional annotation and analysis of these genes indicated that some of these were involved in regulation of glucose levels and lipid metabolism, particularly fatty acid oxidation and transport...
September 14, 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
#8
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/27693967/rna-seq-reveals-differential-gene-expression-in-the-brains-of-juvenile-resident-and-migratory-smolt-rainbow-trout-oncorhynchus-mykiss
#9
Matthew C Hale, Garrett J McKinney, Frank P Thrower, Krista M Nichols
Many migratory traits are heritable, but there is a paucity of evidence identifying the molecular mechanisms underlying differentiation in alternative migratory tactics, or in linking variation in gene expression to migratory behaviors. To that end, we examined differential gene expression in the brain transcriptome between young steelhead trout that had undergone the smoltification process, and resident rainbow trout (Oncorhynchus mykiss) from Sashin Creek, Alaska. Samples were sequenced from two time points: immediately before (at 20months of age) and during (2years of age) the presumed peak of smoltification...
September 4, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27664811/de-novo-assembly-and-characterization-of-the-ovarian-transcriptome-reveal-mechanisms-of-the-final-maturation-stage-in-chinese-scallop-chlamys-farreri
#10
Jia-Ying Li, Lu-Qing Pan, Jing-Jing Miao, Rui-Yi Xu, Wu-Jie Xu
The objective of the present study was to characterize the pattern of gene expression at the last stage of ovarian maturation in Chlamys farreri. Dynamic transcriptomic analysis of ovaries was performed at four time points prior to ovulation, using the Illumina HiSeq 2500 platform. A total of 174,928 unigenes were obtained, among which 42,534 were annotated according to bioinformatics databases, such as NT, NR, Swiss-Prot, KOG, GO, and KEGG. Results from the transcriptome analysis revealed a time-dependent pattern of global transcriptional responses...
September 4, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27614546/an-optimised-phylogenetic-method-sheds-more-light-on-the-main-branching-events-of-rhodopsin-like-superfamily
#11
Michel E Mickael, Ashish Rajput, Jannetta Steyn, Lyle Wiemerslage, Thomas Bürglin
The comparative genomics between different rhodopsin-like family groups (α, β, γ and δ) is not well studied. We used a combination of phylogenetic analysis and statistical genomic methods to compare rhodopsin-like family proteins in species likely symbolic of this family's evolutionary progression. For intra-cluster relationships, we applied mathematical optimisation to enhance the tree search produced by the neighbour joining method (NJ) and compared it with maximum likelihood (ML) method. To infer inter-clusters relationships, we used Needleman-Wunsch analysis (NW), HHsearch, ancestral sequence reconstruction and phylogenetic network analysis...
September 3, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27398986/spotlight-on-environmental-omics-and-toxicology-a-long-way-in-a-short-time
#12
EDITORIAL
Christopher J Martyniuk, Denina B Simmons
The applications for high throughput omics technologies in environmental science have increased dramatically in recent years. Transcriptomics, proteomics, and metabolomics have been used to study how chemicals in our environment affect both aquatic and terrestrial organisms, and the characterization of molecular initiating events is a significant goal in toxicology to better predict adverse responses to toxicants. This special journal edition demonstrates the scope of the science that leverages omics-based methods in both laboratory and wild populations within the context of environmental toxicology, ranging from fish to mammals...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27397556/high-contaminant-loads-in-lake-apopka-s-riparian-wetland-disrupt-gene-networks-involved-in-reproduction-and-immune-function-in-largemouth-bass
#13
Christopher J Martyniuk, Nicholas J Doperalski, Melinda S Prucha, Ji-Liang Zhang, Kevin J Kroll, Roxanne Conrow, David S Barber, Nancy D Denslow
Lake Apopka (FL, USA) has elevated levels of some organochlorine pesticides in its sediments and a portion of its watershed has been designated a US Environmental Protection Agency Superfund site. This study assessed reproductive endpoints in Florida largemouth bass (LMB) (Micropterus salmoides floridanus) after placement into experimental ponds adjacent to Lake Apopka. LMB collected from a clean reference site (DeLeon Springs) were stocked at two periods of time into ponds constructed in former farm fields on the north shore of the lake...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27395796/comparative-proteomic-analysis-in-aphis-glycines-mutsumura-under-lambda-cyhalothrin-insecticide-stress
#14
Rui Bi, Yiou Pan, Qingli Shang, Tianfei Peng, Shuang Yang, Shang Wang, Xuecheng Xin, Yan Liu, Jinghui Xi
Lambda-cyhalothrin is now widely used in China to control the soybean aphid Aphis glycines. To dissect the resistance mechanism, a laboratory-selected resistant soybean aphid strain (CRR) was established with a 43.42-fold resistance ratio to λ-cyhalothrin than the susceptible strain (CSS) in adult aphids. In this study, a comparative proteomic analysis between the CRR and CSS strains revealed important differences between the susceptible and resistant strains of soybean aphids for λ-cyhalothrin. Approximately 493 protein spots were detected in two-dimensional polyacrylamide gel electrophoresis (2-DE)...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27376927/understanding-mechanism-of-sea-cucumber-apostichopus-japonicus-aestivation-insights-from-tmt-based-proteomic-study
#15
Muyan Chen, Xingke Li, Aijun Zhu, Kenneth B Storey, Lina Sun, Tianxiang Gao, Tianming Wang
Marine invertebrate aestivation is a unique strategy for summer survival in response to hot marine conditions. The sea cucumber, Apostichopus japonicus, is an excellent model marine invertebrate for studies of environmentally-induced aestivation. In the present study, we used a tandem mass tag (TMT)-coupled LC-MS/MS approach to identify and quantify the global proteome expression profile over the aestivation-arousal cycle of A. japonicus. A total of 3920 proteins were identified from the intestine of sea cucumber...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27373348/toxicogenomic-applications-of-chinese-rare-minnow-gobiocypris-rarus-in-aquatic-toxicology
#16
Xuefang Liang, Jinmiao Zha
Rare minnow (Gobiocypris rarus), a Chinese native species, are an excellent emerging model organism for aquatic toxicity testing and chemical safety assessment. "Big data" omics approaches (i.e., genomics, proteomics, and metabolomics) to inform mechanistic toxicology are now applied to studies in rare minnows to better understand toxicity and molecular pathways perturbed by chemicals. This review highlights recent applications of toxicogenomics to study changes in the gene and protein expression profiles in rare minnows in response to chemicals...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27343457/proteomic-analysis-of-the-skin-from-chinese-fire-bellied-newt-and-comparison-to-chinese-giant-salamander
#17
Jingyan Sun, Xiaofang Geng, Jianlin Guo, Xiayan Zang, Pengfei Li, Deming Li, Cunshuan Xu
Animal skin that directly interfaces with the external environment has developed diverse adaptive functions to a variety of ecological conditions laden with pathogenic infection and physical harm. Amphibians exhibit various adaptations related to their "incomplete" shift from the aquatic to the terrestrial habitat. Therefore, it is very necessary to explore the molecular basis of skin function and adaptation in amphibians. Currently, the studies on the molecular mechanisms of skin functions in anuran amphibians have been reported, but in urodele amphibians are rare...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27341139/thermal-stress-induces-a-distinct-transcriptome-profile-in-the-pacific-oyster-crassostrea-gigas
#18
Hyun-Jeong Lim, Bo-Mi Kim, In Joon Hwang, Jeong-Soo Lee, Ik-Young Choi, Youn-Jung Kim, Jae-Sung Rhee
Oysters are frequently subjected to heat stress during tidal emersion/immersion cycles in their habitats due to attachment on the rocky shore. To understand the effect of temperature elevation on the whole transcriptome over time, the Pacific oyster Crassostrea gigas was exposed to seawater temperature 32°C for 72h from the control 20°C. RNA-seq identified differentially expressed stress responsive transcripts upon thermal stress in the gill tissues of C. gigas. The primary effect of heat stress appears to be significantly induced transcription of molecular chaperones, including members of the heat shock protein (hsp) families, while genes typically associated with protein metabolism, such as those involved in protein degradation (e...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27341138/identification-of-putative-circadian-clock-genes-in-the-american-horseshoe-crab-limulus-polyphemus
#19
Kevin N Chesmore, Winsor H Watson, Christopher C Chabot
While the American horseshoe crab, Limulus polyphemus, has robust circadian and circatidal rhythms, virtually nothing is known about the molecular basis of these rhythms in this species or any other chelicerate. In this study, next generation sequencing was used to assemble transcriptomic reads and then putative homologs of known core and accessory circadian genes were identified in these databases. Homologous transcripts were discovered for one circadian clock input gene, five core genes, 22 accessory genes, and two possible output pathways...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27337176/salinity-induced-changes-in-gene-expression-from-anterior-and-posterior-gills-of-callinectes-sapidus-crustacea-portunidae-with-implications-for-crustacean-ecological-genomics
#20
Justin C Havird, Reed T Mitchell, Raymond P Henry, Scott R Santos
Decapods represent one of the most ecologically diverse taxonomic groups within crustaceans, making them ideal to study physiological processes like osmoregulation. However, prior studies have failed to consider the entire transcriptomic response of the gill - the primary organ responsible for ion transport - to changing salinity. Moreover, the molecular genetic differences between non-osmoregulatory and osmoregulatory gill types, as well as the hormonal basis of osmoregulation, remain underexplored. Here, we identified and characterized differentially expressed genes (DEGs) via RNA-Seq in anterior (non-osmoregulatory) and posterior (osmoregulatory) gills during high to low salinity transfer in the blue crab Callinectes sapidus, a well-studied model for crustacean osmoregulation...
September 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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