Subject term: gene expression regulation and bioinformatics / Text availability: Citation in PubAg

1. Microarray data analysis using machine learning methods

Author:: Ressom, Habtom W.; Lakshman, Dilip; Yun, Song Joong; Pramanik, Saroj K.; De los Reyes, Benildo G.
Source:: Biosystems engineering / Ahindra Nag pp. -
Subject:: oligonucleotides; complementary DNA; microarray technology; bioinformatics; computer analysis; gene expression; gene expression regulation; algorithms
Handle:: 10113/34772

2. Plant bZIP Gâbox binding factors.â: Modular structure and activation mechanisms

Author:: Yann SibÃ©ril; Pierre Doireau; Pascal Gantet
Source:: European journal of biochemistry 2001 v.268 no.22 pp. 5655-5666
ISSN:: 0014-2956
Subject:: in vivo studies; transcription factors; animals; bioinformatics; models; signal transduction; yeasts; amino acid sequences; leucine zipper; gene expression regulation; sequence homology; hormones
Abstract:: ... In this review we sumâup the knowledge about bZIP Gâbox binding factors (GBFs), which possess an Nâterminal, prolineârich domain. The GBF has been one of the most extensively studied transcription factor family. Based on protein sequence homology with yeast and animal basic leucineâzipper (bZIP) transcription factors, bioinformatic studies have identified their main structural domains (p ...
DOI:: 10.1046/j.0014-2956.2001.02552.x
: https://doi.org/10.1046/j.0014-2956.2001.02552.x

3. Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data

Author:: Ning Sun; Ligeng Ma; Deyun Pan; Hongyu Zhao; Xing Wang Deng
Source:: Plant molecular biology 2003 v.53 no.4 pp. 467-478
ISSN:: 0167-4412
Subject:: Arabidopsis thaliana; Calvin cycle; enzymes; structural genes; transcription (genetics); gene expression; messenger RNA; microarray technology; gene expression regulation; light; bioinformatics
Abstract:: ... Although large-scale gene expression data have been studied from many perspectives, they have not been systematically integrated to infer the regulatory potentials of individual genes in specific pathways. Here we report the analysis of expression patterns of genes in the Calvin cycle from 95 Arabidopsis microarray experiments, which revealed a consistent gene regulation pattern in most experiment ...
DOI:: 10.1023/B:PLAN.0000019071.12878.9e
PubMed:: 15010613
: https://doi.org/10.1023/B:PLAN.0000019071.12878.9e

4. Inferring cellular networks using probabilistic graphical models

Author:: Friedman, N.
Source:: Science 2004 v.303 no.5659 pp. 799-805
ISSN:: 0036-8075
Subject:: bioinformatics; Bayesian theory; gene expression; gene expression regulation; probabilistic models
Abstract:: ... High-throughput genome-wide molecular assays, which probe cellular networks from different perspectives, have become central to molecular biology. Probabilistic graphical models are useful for extracting meaningful biological insights from the resulting data sets. These models provide a concise representation of complex cellular networks by composing simpler submodels. Procedures based on well-und ...
DOI:: 10.1126/science.1094068
: https://doi.org/10.1126/science.1094068

5. Structure, circadian regulation and bioinformatic analysis of the unique sigma factor gene in Chlamydomonas reinhardtii

Author:: Carter, M.L.; Smith, A.C.; Kobayashi, H.; Purton, S.; Herrin, D.L.
Source:: Photosynthesis research 2004 v.82 no.3 pp. 339-349
ISSN:: 0166-8595
Subject:: Chlamydomonas reinhardtii; circadian rhythm; bioinformatics; sigma factors; complementary DNA; messenger RNA; gene expression regulation

6. Low temperature promotes intron retention in two e-cor genes of durum wheat

Author:: Mastrangelo, A.M.; Belloni, S.; Barilli, S.; Ruperti, B.; Di Fonzo, N.; Stanca, A.M.; Cattivelli, L.
Source:: Planta 2005 v.221 no.5 pp. 705-715
ISSN:: 0032-0935
Subject:: messenger RNA; plant genetics; plant stress; RNA splicing; bioinformatics; durum wheat; cold stress; Triticum turgidum subsp. durum; introns; plant proteins
Abstract:: ... Following the screening of a suppression subtractive library developed from durum wheat plants exposed to low temperature for 6 h, two early cold-regulated (e-cor) genes have been isolated. These genes, coding putatively for a ribokinase (7H8) and a C3H2C3 RING-finger protein (6G2), were characterized by the stress-induced retention of a subset of introns in the mature mRNA. This feature was depen ...
DOI:: 10.1007/s00425-004-1475-3
PubMed:: 15666155
: https://doi.org/10.1007/s00425-004-1475-3

7. Bioinformatic analysis of expressed sequence tags derived from a compatible Alternaria brassicicola-Brassica oleracea interaction

Author:: Cramer, Robert A.; La Rota, C. Mauricio; Cho, Yangrae; Thon, Michael; Craven, Kelly D.; Knudson, Dennis L.; Mitchell, Thomas K.; Lawrence, Christopher B.
Source:: Molecular plant pathology 2006 v.7 no.2 pp. 113-124
ISSN:: 1464-6722
Subject:: DNA libraries; complementary DNA; host-pathogen relationships; bioinformatics; expressed sequence tags; reverse transcriptase polymerase chain reaction; Alternaria brassicicola; plant pathogenic fungi; Brassica oleracea; gene expression regulation
Abstract:: ... Alternaria brassicicola is a necrotrophic fungal pathogen that causes black spot disease on members of the Brassicaceae plant family. In order to identify candidate fungal pathogenicity genes and characterize a compatible host response, a suppression subtractive hybridization (SSH) cDNA library enriched for A. brassicicola and Brassica oleracea genes expressed during the interaction was created, a ...
DOI:: 10.1111/j.1364-3703.2006.00324.x
PubMed:: 20507432
: https://doi.org/10.1111/j.1364-3703.2006.00324.x

8. Characterization of five microRNA families in maize

Author:: Mica, Erica; Gianfranceschi, Luca; Pè, Mario Enrico
Source:: Journal of experimental botany 2006 v.57 no.11 pp. 2601-2612
ISSN:: 0022-0957
Subject:: Zea mays; corn; RNA; gene expression; regulatory sequences; phenotype; plant adaptation; gene expression regulation; bioinformatics; chromosome mapping; phylogeny
Abstract:: ... In recent years, microRNAs (miRNAs) have polarized the interest of the scientific community as a new category of gene expression regulators, present in both plants and animals. Plant miRNAs are involved in processes such as plant development, organ identity, and stress response. Nonetheless, knowledge of their functions is still incomplete, and it is conceivable that further new processes in which ...
DOI:: 10.1093/jxb/erl013
PubMed:: 16820394
: https://doi.org/10.1093/jxb/erl013

9. Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana

Author:: Jae-Heung Ko; Eric P. Beers; Kyung-Hwan Han
Source:: Molecular genetics and genomics 2006 v.276 no.6 pp. 517-531
ISSN:: 1617-4615
Subject:: Arabidopsis thaliana; bioinformatics; cell walls; gene expression regulation; genes; guanosinetriphosphatase; metabolism; phloem; promoter regions; proteins; secondary xylem; signal transduction; transcription (genetics); transcriptomics; wood
Abstract:: ... Our knowledge of the genetic control of wood formation (i.e., secondary growth) is limited. Here, we present a novel approach to unraveling the gene network regulating secondary xylem development in Arabidopsis, which incorporates complementary platforms of comparative-transcriptome analyses such as “digital northern” and “digital in situ” analysis. This approach effectively eliminated any genes t ...
DOI:: 10.1007/s00438-006-0157-1
PubMed:: 16969662
: https://doi.org/10.1007/s00438-006-0157-1

10. Identification and characterization of an Arabidopsis homogentisate phytyltransferase paralog

Author:: Venkatesh, T.V.; Karunanandaa, B.; Free, D.L.; Rottnek, J.M.; Baszis, S.R.; Valentin, H.E.
Source:: Planta 2006 v.223 no.6 pp. 1134-1144
ISSN:: 0032-0935
Subject:: Arabidopsis thaliana; transgenic plants; alkyl (aryl) transferases; plant proteins; transgenes; sequence analysis; genetic transformation; gene overexpression; gene expression regulation; tocopherols; tocotrienols; biosynthesis; bioinformatics; amino acid sequences
DOI:: 10.1007/s00425-005-0180-1
PubMed:: 16408209
: https://doi.org/10.1007/s00425-005-0180-1

11. Putative fasciclin-like arabinogalactan-proteins (FLA) in wheat (Triticum aestivum) and rice (Oryza sativa): identification and bioinformatic analyses

Author:: Faik, Ahmed; Abouzouhair, Jaouad; Sarhan, Fathey
Source:: Molecular genetics and genomics 2006 v.276 no.5 pp. 478-494
ISSN:: 1617-4615
Subject:: rice; Oryza sativa; bioinformatics; wheat; gels; electrostatic interactions; insects; cell adhesion; roots; amino acids; Triticum aestivum; gene expression regulation; databases; plant growth; Arabidopsis; seeds; growth and development; adhesion; cold; proteins; stress response; expressed sequence tags; RNA; protein-protein interactions
Abstract:: ... Putative plant adhesion molecules include arabinogalactan-proteins having fasciclin-like domains. In animal, fasciclin proteins participate in cell adhesion and communication. However, the molecular basis of interactions in plants is still unknown and none of these domains have been characterized in cereals. This work reports the characterization of 34 wheat (Triticum aestivum) and 24 rice (Oryza ...
DOI:: 10.1007/s00438-006-0159-z
PubMed:: 16944204
: https://doi.org/10.1007/s00438-006-0159-z

12. The MYB Transcription Factor Superfamily of Arabidopsis: Expression Analysis and Phylogenetic Comparison with the Rice MYB Family

Author:: Chen, Y.; Yang, X.; He, K.; Liu, M.; Li, J.; Gao, Z.; Lin, Z.; Zhang, Y.; Wang, X.; Qiu, X.
Source:: Plant molecular biology 2006 v.60 no.1 pp. 107-124
ISSN:: 0167-4412
Subject:: Arabidopsis thaliana; transcription factors; rice; messenger RNA; complementary DNA; Oryza sativa; bioinformatics; amino acid sequences; gene expression; nucleotide sequences; multigene family; gene expression regulation
DOI:: 10.1007/s11103-005-2910-y
PubMed:: 16463103
: https://doi.org/10.1007/s11103-005-2910-y

13. Transcription factor families in Arabidopsis: major progress and outstanding issues for future research

Author:: Qu, L.J.; Zhu, Y.X.
Source:: Current opinion in plant biology 2006 v.9 no.5 pp. 544-549
ISSN:: 1369-5266
Subject:: Arabidopsis thaliana; transcription factors; open reading frames; bioinformatics; transcription (genetics); gene expression regulation
DOI:: 10.1016/j.pbi.2006.07.005
PubMed:: 16877030
: https://doi.org/10.1016/j.pbi.2006.07.005

14. Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling

Author:: Mandaokar, Ajin; Thines, Bryan; Shin, Byongchul; Markus Lange, B.; Choi, Goh; Koo, Yeon J.; Yoo, Yung J.; Choi, Yang D.; Choi, Giltsu; Browse, John
Source:: plant journal 2006 v.46 no.6 pp. 984-1008
ISSN:: 0960-7412
Subject:: transcription factors; Arabidopsis; buds; flowering; phenotype; jasmonic acid; bioinformatics; isozymes; mutation; biochemical pathways; gene expression; pollen; transcription (genetics); dehiscence; genes; mutants; transcriptome; gene expression regulation
Abstract:: ... In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically ...
DOI:: 10.1111/j.1365-313X.2006.02756.x
PubMed:: 16805732
: https://doi.org/10.1111/j.1365-313X.2006.02756.x

15. A translocation signal for delivery of oomycete effector proteins into host plant cells

Author:: Whisson, S.C.; Boevink, P.C.; Moleleki, L.; Avrova, A.O.; Morales, J.G.; Gilroy, E.M.; Armstrong, M.R.; Grouffaud, S.; Van West, P.; Chapman, S.
Source:: Nature 2007 v.450 no.7166 pp. 115-118
ISSN:: 0028-0836
Subject:: blight; host-pathogen relationships; fungal diseases of plants; bioinformatics; Solanum tuberosum; Phytophthora infestans; potatoes; protein transport; fungal proteins; signal peptide; genes; gene induction; protein secretion; protein-protein interactions; hypersensitive response
Abstract:: ... Bacterial, oomycete and fungal plant pathogens establish disease by translocation of effector proteins into host cells, where they may directly manipulate host innate immunity. In bacteria, translocation is through the type III secretion system, but analogous processes for effector delivery are uncharacterized in fungi and oomycetes. Here we report functional analyses of two motifs, RXLR and EER, ...
DOI:: 10.1038/nature06203
: https://doi.org/10.1038/nature06203

16. Analysis of expression profile of selected genes expressed during auxin-induced somatic embryogenesis in leaf base system of wheat (Triticum aestivum) and their possible interactions

Author:: Singla, Bhumica; Tyagi, Akhilesh K.; Khurana, Jitendra P.; Khurana, Paramjit
Source:: Plant molecular biology 2007 v.65 no.5 pp. 677-692
ISSN:: 0167-4412
Subject:: 2,4-D; Triticum aestivum; apoptosis; auxins; bioinformatics; cDNA libraries; cell division; clones; complementary DNA; data analysis; gene expression; gene expression regulation; genes; leaves; signal transduction; somatic cells; somatic embryogenesis; totipotency; wheat
Abstract:: ... Somatic embryogenesis is a notable illustration of plant totipotency and involves reprogramming of development in somatic cells toward the embryogenic pathway. Auxins are key components as their exogenous application recuperates the embryogenic potential of the mitotically quiescent somatic cells. In order to unravel the molecular basis of somatic embryogenesis, cDNA library was made from the rege ...
DOI:: 10.1007/s11103-007-9234-z
PubMed:: 17849219
: https://doi.org/10.1007/s11103-007-9234-z

17. Global functional analyses of rice promoters by genomics approaches

Author:: Yu, Su-May; Ko, Swee-Suak; Hong, Chwan-Yang; Sun, Hsou-Jan; Hsing, Yue-Ie; Tong, Chii-Gong; Ho, Tuan-Hua David
Source:: Plant molecular biology 2007 v.65 no.4 pp. 417-425
ISSN:: 0167-4412
Subject:: abscisic acid; bioinformatics; biotechnology; cells; environmental law; flowers; gene expression; gene expression regulation; genes; genomics; hormones; leaves; microarray technology; mutants; peroxidase; rice; tissues; transfer DNA
Abstract:: ... Promoters play key roles in conferring temporal, spatial, chemical, developmental, or environmental regulation of gene expression. Promoters that are subject to specific regulations are useful for manipulating foreign gene expression in plant cells, tissues, or organs with desirable patterns and under controlled conditions, and have been important for both basic research and applications in agricu ...
DOI:: 10.1007/s11103-007-9232-1
PubMed:: 17922261
: https://doi.org/10.1007/s11103-007-9232-1

18. Identification of differentially expressed genes in female Culex pipiens pallens

Author:: Hong-Hong Chen; Ren-Li Zhang; Yi-Jie Geng; Jin-Quan Cheng; Shun-Xiang Zhang; Da-Na Huang; Lei Yu; Shi-Tong Gao; Xing-Quan Zhu
Source:: Parasitology research 2007 v.101 no.3 pp. 511-515
ISSN:: 0932-0113
Subject:: Brugia malayi; bioinformatics; hematophagy; encephalitis; blood; reproduction; Culex pipiens pallens; rapid amplification of cDNA ends; clones; viruses; Wuchereria bancrofti; gene expression regulation; pathogens; complementary DNA; humans; cDNA libraries; suppression subtractive hybridization; Northern blotting; expressed sequence tags; reverse transcriptase polymerase chain reaction
Abstract:: ... Culex pipiens pallens is the mosquito vector of a number of human pathogens such as Wuchereria bancrofti, Brugia malayi, and epidemic encephalitis B virus. Female C. pipiens pallens play an important role in transmitting pathogens by sucking blood, which is essential for reproduction. In the present study, a subtractive cDNA library for female C. pipiens pallens was constructed by the suppression ...
DOI:: 10.1007/s00436-007-0506-y
PubMed:: 17347850
: https://doi.org/10.1007/s00436-007-0506-y

19. Identification of functional candidate genes for drought tolerance in rice

Author:: Fu, Bin-Ying; Xiong, Jian-Hua; Zhu, Ling-Hua; Zhao, Xiu-Qin; Xu, Hua-Xue; Gao, Yong-Ming; Li, Yang-Sheng; Xu, Jian-Long; Li, Zhi-Kang
Source:: Molecular genetics and genomics 2007 v.278 no.6 pp. 599-609
ISSN:: 1617-4615
Subject:: Oryza sativa; biochemical pathways; bioinformatics; complementary DNA; data analysis; drought; drought tolerance; gene expression; gene expression regulation; genes; introgression; nucleotide sequences; quantitative trait loci; reverse transcriptase polymerase chain reaction; rice; suppression subtractive hybridization
Abstract:: ... Drought tolerance (DT) in rice is known to be controlled by many quantitative trait loci (QTLs) and involved differential expression of large numbers of genes, but linking QTLs with their underlying genes remains the most challenging issue in plant molecular biology. To shed some light on this issue, differential gene expression in response to PEG simulated drought in 3 unique genetic materials (a ...
DOI:: 10.1007/s00438-007-0276-3
PubMed:: 17665216
: https://doi.org/10.1007/s00438-007-0276-3

20. Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens

Author:: Andrew C. Cuming; Sung Hyun Cho; Yasuko Kamisugi; Helen Graham; Ralph S. Quatrano
Source:: new phytologist 2007 v.176 no.2 pp. 275-287
ISSN:: 0028-646X
Subject:: bioinformatics; drought tolerance; signal transduction; drought; genes; mosses and liverworts; embryophytes; water stress; gene expression; embryogenesis; gene expression regulation; oligonucleotides; transcription factors; transcriptomics; Arabidopsis; transcription (genetics); salt stress; regulatory sequences; Physcomitrella patens; microarray technology; abscisic acid; stomata; chloroplasts; seed development
Abstract:: ... • Dehydration tolerance was an adaptive trait necessary for the colonization of land by plants, and remains widespread among bryophytes: the nearest extant relatives of the first land plants. A genome‐wide analysis was undertaken of water‐stress responses in the model moss Physcomitrella patens to identify stress‐responsive genes. • An oligonucleotide microarray was used for transcriptomic analysi ...
DOI:: 10.1111/j.1469-8137.2007.02187.x
PubMed:: 17696978
: https://doi.org/10.1111/j.1469-8137.2007.02187.x

21. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses

Author:: Kilian, Joachim; Whitehead, Dion; Horak, Jakub; Wanke, Dierk; Weinl, Stefan; Batistic, Oliver; D'Angelo, Cecilia; Bornberg-Bauer, Erich; Kudla, Jörg; Harter, Klaus
Source:: plant journal 2007 v.50 no.2 pp. 347-363
ISSN:: 0960-7412
Subject:: Arabidopsis thaliana; RNA; bioinformatics; cold; cold stress; data collection; drought; energy balance; gene expression; gene expression regulation; genes; genotype; heat; microarray technology; osmolarity; stress response; tissue transplantation; transcription (genetics); ultraviolet radiation
Abstract:: ... The tolerance responses of plants to many abiotic stresses are conjectured to be controlled by complex gene networks. In the frame of the AtGenExpress project a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray in order to understand these regulatory networks in detail. In contrast to earlier studies, we subjected, side-by-side ...
DOI:: 10.1111/j.1365-313X.2007.03052.x
PubMed:: 17376166
: https://doi.org/10.1111/j.1365-313X.2007.03052.x

22. A Novel Gene Involved in Lesion Formation in Magnaporthe grisea

Author:: Yang, J.; Li, H.; Liu, L.; Su, Y.; Li, J.B.; Chang, Q.; Qu, L.J.; Wang, Y.Y.; Zhu, Y.Y.; Li, C.Y.
Source:: Phytopathologische Zeitschrift 2008 v.156 no.2 pp. 99-103
ISSN:: 0931-1785
Subject:: Magnaporthe grisea; bioinformatics; blast disease; fungi; gene expression; gene expression regulation; genes; leaves; molecular cloning; mycelium; necrosis; protein synthesis; quantitative polymerase chain reaction; rice; rice protein; signal peptide
Abstract:: ... To date, a number of genes that are expressed in the early stages of infection have been reported, while few genes that are expressed during the course of colonization, after the initiation of plant infection, have been studied. Plant inoculations, real-time polymerase chain reaction (PCR), gene cloning, protein expression and bioinformatics analysis were combined to identify a novel gene, MgNIP04 ...
DOI:: 10.1111/j.1439-0434.2007.01334.x
: https://doi.org/10.1111/j.1439-0434.2007.01334.x

23. Characterization of a profilin-like protein from Schistosoma japonicum, a potential new vaccine candidate

Author:: Zhang, Shuang-min; Lv, Zhi-yue; Zhou, He-jun; Zhang, Li-yan; Yang, Lin-lin; Yu, Xinbing; Zheng, Huanqin; Wu, Zhong-dao
Source:: Parasitology research 2008 v.102 no.6 pp. 1367-1374
ISSN:: 0932-0113
Subject:: Escherichia coli; Schistosoma japonicum; Western blotting; bioinformatics; complementary DNA; developmental stages; gene expression regulation; immunohistochemistry; interleukin-12; isoelectric point; mice; molecular weight; open reading frames; parasites
Abstract:: ... The tegumental membrane of platyhelminth parasites is of crucial importance for modulation of the host response and parasite survival. A complementary deoxyribonucleic acid (cDNA) containing an open reading frame of 390 bp, which encodes a profilin-like tegumental protein with a theoretical isoelectric point of 6.02 and a molecular weight of 14.42 kDa, had been identified by bioinformatic analysis ...
DOI:: 10.1007/s00436-008-0919-2
: https://doi.org/10.1007/s00436-008-0919-2

24. Do two mutually exclusive gene modules define the phenotypic diversity of mammalian smooth muscle

Author:: Larsson, Erik; McLean, Sean E.; Mecham, Robert P.; Lindahl, Per; Nelander, Sven
Source:: Molecular genetics and genomics 2008 v.280 no.2 pp. 127-137
ISSN:: 1617-4615
Subject:: asthma; atherosclerosis; bioinformatics; biomarkers; cell cycle; gene expression; gene expression regulation; genes; mammals; myocytes; phenotype; phenotypic variation; pregnancy; smooth muscle; statistical analysis; tissue repair; transcription (genetics); transcriptome
Abstract:: ... Smooth muscle cells (SMCs) are key components of all hollow organs, where they perform contractile, synthetic and other functions. Unlike other muscle cells, SMCs are not terminally differentiated, but exhibit considerable phenotypic variation. Such variation is manifested both across disease states such as asthma and atherosclerosis, and physiological states such as pregnancy and wound healing. W ...
DOI:: 10.1007/s00438-008-0349-y
PubMed:: 18509681
: https://doi.org/10.1007/s00438-008-0349-y

25. Eimeria tenella: Analysis of differentially expressed genes in the monensin- and maduramicin-resistant lines using cDNA array

Author:: Chen, Tong; Zhang, Wei; Wang, Jianmin; Dong, Haitao; Wang, Ming
Source:: Experimental parasitology 2008 v.119 no.2 pp. 264-271
ISSN:: 0014-4894
Subject:: Eimeria tenella; line differences; drug resistance; monensin; maduramicin; resistance mechanisms; cDNA libraries; microarray technology; expressed sequence tags; complementary DNA; sequence analysis; gene expression regulation; bioinformatics
Abstract:: ... Drug resistance in coccidial populations has been a major problem to the prophylactic chemotherapy. Nevertheless, the mechanisms of the resistance are still poorly understood. In this report, cDNA array was designed based on the cDNA library for analysis of gene expression profile of the drug-resistant lines and their sensitive parental lines of Eimeria tenella. Two thousand eight hundred and six ...
DOI:: 10.1016/j.exppara.2008.02.010
PubMed:: 18395203
: https://doi.org/10.1016/j.exppara.2008.02.010

26. Expression profiles of the organic acid metabolism-associated genes during rat liver regeneration

Author:: G. B. Guo; C. S. Xu
Source:: Amino acids 2008 v.34 no.4 pp. 597-604
ISSN:: 0939-4451
Subject:: acetates; anaphase; bioinformatics; biosynthesis; carnitine; cell differentiation; cell proliferation; creatine; gene expression; gene expression regulation; genes; liver; liver regeneration; malates; metaphase; prophase; propionic acid; pyruvic acid; rats; succinic acid
Abstract:: ... In this study, 55 of the organic acid metabolism-involved genes were primarily confirmed to be associated with liver regeneration (LR) by bioinformatics and gene expression profiling analysis. Number of the initially and totally expressed genes occurring in initiation phase of LR, G₀/G₁, cell proliferation, cell differentiation and liver tissue structure-function reconstruction were 21, 5, 33, 1 a ...
DOI:: 10.1007/s00726-007-0013-6
: https://doi.org/10.1007/s00726-007-0013-6

27. Grapevine habituation: Understanding of factors that contribute to neoplastic transformation and somaclonal variation

Author:: V. Repka; I. Baumgartnerová
Source:: Acta agronomica Academiae Scientiarum Hungaricae 2008 v.56 no.4 pp. 399-408
ISSN:: 0238-0161
Subject:: Vitis vinifera; apoptosis; carcinogenesis; cell culture; cell differentiation; gene expression regulation; microarray technology; models; prediction; proteome; somaclonal variation; two-dimensional gel electrophoresis
Abstract:: ... Two-dimensional gel electrophoresis coupled to protein microarray analysis was used to examine for the first time the molecular mechanisms of grapevine habituation (Vitis vinifera L., cv. Limberger) at both the proteome and the interactome level. The examination of 2-D maps derived from control and habituated cell cultures revealed the presence of 55 protein spots displaying a differential ...
DOI:: 10.1556/AAgr.56.2008.4.4
: https://doi.org/10.1556/AAgr.56.2008.4.4

28. A Key Enzyme of the Leloir Pathway Is Involved in Pathogenicity of Leptosphaeria maculans Toward Oilseed Rape

Author:: Remy, E.; Meyer, M.; Blaise, F.; Simon, U.K.; Kuhn, D.; Balesdent, M.H.; Rouxel, T.
Source:: Molecular plant-microbe interactions 2009 v.22 no.6 pp. 725-736
ISSN:: 0894-0282
Subject:: genetic complementation test; insertional mutagenesis; phenotype; Plenodomus lingam; cell walls; bioinformatics; transfer DNA; biochemical pathways; gene expression; pathogenicity; microbial growth; mutants; Brassica napus; gene expression regulation; microbial genetics; rapeseed
Abstract:: ... Agrobacterium tumefaciens-mediated random insertional mutagenesis was used to investigate pathogenicity determinants in Leptosphaeria maculans. One tagged nonpathogenic mutant, termed m186, is analyzed in detail here. Microscopic analyses of infected plant tissues revealed that m186 is specifically blocked at the invasive growth phase after an unaffected initial penetration stage and is unable to ...
DOI:: 10.1094/MPMI-22-6-0725
PubMed:: 19445597
: https://doi.org/10.1094/MPMI-22-6-0725

29. BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis: bioinformatics and gene expression

Author:: Yu, Xiao-Hong; Gou, Jin-Ying; Liu, Chang-Jun
Source:: Plant molecular biology 2009 v.70 no.4 pp. 421-442
ISSN:: 0167-4412
Subject:: Arabidopsis thaliana; Northern blotting; Populus; acyltransferases; bioinformatics; chromosome mapping; conserved sequences; databases; gene expression; gene expression regulation; genes; metabolism; microarray technology; nucleotide sequences; phylogeny; plant development; plant growth; polymerase chain reaction
Abstract:: ... Plant acyl-CoA dependent acyltransferases constitute a large specific protein superfamily, named BAHD. Using the conserved sequence motifs of BAHD members, we searched the genome sequences of Populus and Arabidopsis, and identified, respectively, 94- and 61-putative genes. Subsequently, we analyzed the phylogeny, gene structure, and chromosomal distribution of BAHD members of both species; then, w ...
DOI:: 10.1007/s11103-009-9482-1
PubMed:: 19343509
: https://doi.org/10.1007/s11103-009-9482-1

30. Changes in microRNAs associated with hepatic stellate cell activation status identify signaling pathways

Author:: Guo, Can-Jie; Pan, Qin; Cheng, Tao; Jiang, Bo; Chen, Guang-Yu; Li, Ding-Guo
Source:: FEBS journal 2009 v.276 no.18 pp. 5163-5176
ISSN:: 1742-464X
Subject:: Western blotting; apoptosis; bioinformatics; caspase-9; gene expression regulation; liver; liver cirrhosis; microRNA; microarray technology; reverse transcriptase polymerase chain reaction; signal transduction
Abstract:: ... Activation of hepatic stellate cells (HSCs), which is regulated by multiple signal transduction pathways, is the key event in liver fibrosis. Moreover, members of these pathways are important targets for microRNAs (miRNAs). To better understand the critical pathways of HSC activation, we performed comprehensive comparative bioinformatics analysis of microarrays of quiescent and activated HSCs. Cha ...
DOI:: 10.1111/j.1742-4658.2009.07213.x
PubMed:: 19674103
: https://doi.org/10.1111/j.1742-4658.2009.07213.x

31. Characterization of the Mesorhizobium loti MAFF303099 Type-Three Protein Secretion System

Author:: Sanchez, Cintia; Iannino, Florencia; Deakin, William J.; Ugalde, Rodolfo A.; Lepek, Viviana C.
Source:: Molecular plant-microbe interactions 2009 v.22 no.5 pp. 519-528
ISSN:: 0894-0282
Subject:: nitrogen-fixing bacteria; symbiosis; symbionts; host plants; bioinformatics; transcription (genetics); operon; type III secretion system; bacterial proteins; flavonoids; nodulation; Mesorhizobium loti; gene expression regulation; promoter regions
Abstract:: ... Type III secretion systems (T3SS) have been found in several species of rhizobia. Proteins (termed effectors) secreted by this system are involved in host-range determination and influence nodulation efficiency. Mesorhizobium loti MAFF303099 possesses a functional T3SS in its symbiotic island whose expression is induced by flavonoids. As in other rhizobia, conserved cis-elements (tts box) were fou ...
DOI:: 10.1094/MPMI-22-5-0519
PubMed:: 19348570
: https://doi.org/10.1094/MPMI-22-5-0519

32. Differential expression of ubiquitin-conjugating enzyme E2r in the developing ovary and testis of penaeid shrimp Marsupenaeus japonicus

Author:: Shen, Bingling; Zhang, Ziping; Wang, Yilei; Wang, Guodong; Chen, Yun; Lin, Peng; Wang, Shuhong; Zou, Zhihua
Source:: Molecular biology reports 2009 v.36 no.5 pp. 1149-1157
ISSN:: 0301-4851
Subject:: Marsupenaeus japonicus; amino acids; animal ovaries; animals; bioinformatics; developmental stages; gene expression regulation; genes; molecular weight; oogenesis; polymerase chain reaction; spermatogenesis; testes
Abstract:: ... In order to identify genes involved in oogenesis and spermatogenesis in penaeid shrimp Marsupenaeus japonicus, a modified annealing control primer (ACP) system was adapted to identify genes differentially expressed in ovary and testis at different developmental stages. By using 20 pairs of ACP primers, 8 differentially expressed genes were obtained. One of these genes is ubiquitin-conjugating enzy ...
DOI:: 10.1007/s11033-008-9291-7
PubMed:: 18581257
: https://doi.org/10.1007/s11033-008-9291-7

33. Emerging technologies for amino acid nutrition research in the post-genome era

Author:: Wang, Junjun; Wu, Guoyao; Zhou, Huaijun; Wang, Fenglai
Source:: Amino acids 2009 v.37 no.1 pp. 177-186
ISSN:: 0939-4451
Subject:: DNA; amino acids; biochemical pathways; bioinformatics; dietary recommendations; epigenetics; gene expression regulation; genes; humans; messenger RNA; metabolites; metabolomics; microRNA; nucleotide sequences; nutrients; nutrition research; phenotype; protein synthesis; proteins; proteomics; technology; tissues; transcription (genetics); transcriptomics
Abstract:: ... Amino acids (AA) are not only the building blocks of proteins but are also key regulators of metabolic pathways in cells. However, the mechanisms responsible for the effects of AA are largely unknown. With the completion of human and other mammalian genome projects, revolutionary technologies in life sciences characterized by high throughput, high efficiency, and rapid computation are now availabl ...
DOI:: 10.1007/s00726-008-0193-8
: https://doi.org/10.1007/s00726-008-0193-8

34. Glycoproteomic analysis of WGA-bound glycoprotein biomarkers in sera from patients with lung adenocarcinoma

Author:: Hongsachart, Piyorot; Huang-Liu, Rosa; Sinchaikul, Supachok; Pan, Fu-Ming; Phutrakul, Suree; Chuang, Yu-Min; Yu, Chong-Jen; Chen, Shui-Tein
Source:: Electrophoresis 2009 v.30 no.7 pp. 1206-1220
ISSN:: 0173-0835
Subject:: screening; adiponectin; blood serum; humans; biomarkers; adenocarcinoma; glycosylation; bioinformatics; lectins; lung neoplasms; Western blotting; wheat germ; patients; agglutinins; electrophoresis; gene expression regulation; glycoproteins; prediction
Abstract:: ... Differential protein expression profiles in the serum samples from patients with lung adenocarcinoma may be associated with glycosylation during cancer development. In this study, we used various glycoproteomic approaches to investigate the different glycoproteomic profiles of human normal and lung adenocarcinoma serum samples and to investigate putative altered glycoprotein biomarkers. In our pre ...
DOI:: 10.1002/elps.200800405
: https://doi.org/10.1002/elps.200800405

35. Identification of a novel gene K23 over-expressed in fish cross-subfamily cloned embryos

Author:: Pei, De-Sheng; Sun, Yong-Hua; Zhu, Zuo-Yan
Source:: Molecular biology reports 2009 v.36 no.6 pp. 1375-1380
ISSN:: 0301-4851
Subject:: Danio rerio; amino acids; bioinformatics; fish; gene expression regulation; gene overexpression; genes; open reading frames; ova; phosphorylation; signal peptide
Abstract:: ... A novel gene--K23, differentially expressed in cross-subfamily cloned embryos, was isolated by RACE-PCR technique. It had 2580 base pairs (bp) in length, with a 1,425 bp open reading frame (ORF) encoding a putative protein of 474 amino acids (aa). Bioinformatic analysis indicated that K23 had 22 phosphorylation sites, but it had no signal peptides. Developmental expression analysis in zebrafish sh ...
DOI:: 10.1007/s11033-008-9323-3
PubMed:: 18654838
: https://doi.org/10.1007/s11033-008-9323-3

36. Individuality and epigenetics in obesity

Author:: Campión, J.; Milagro, F.I.; Martínez, J.A.
Source:: Obesity reviews 2009 v.10 no.4 pp. 383-392
ISSN:: 1467-7881
Subject:: DNA; DNA methylation; adipogenesis; bioinformatics; biomarkers; chromatin; diet; environmental factors; epigenetics; gene expression regulation; genes; histones; inflammation; insulin; metabolism; microRNA; obesity; promoter regions; weight gain
Abstract:: ... Excessive weight gain arises from the interactions among environmental factors, genetic predisposition and the individual behavior. However, it is becoming evident that interindividual differences in obesity susceptibility depend also on epigenetic factors. Epigenetics studies the heritable changes in gene expression that do not involve changes to the underlying DNA sequence. These processes inclu ...
DOI:: 10.1111/j.1467-789X.2009.00595.x
PubMed:: 19413700
: https://doi.org/10.1111/j.1467-789X.2009.00595.x

37. Malate dehydrogenase is negatively regulated by miR-1 in Trichomonas vaginalis

Author:: Lin, Wei-Chen; Huang, Kuo-Yang; Chen, Shih-Chieh; Huang, Ting-Yun; Chen, Shu-Jen; Huang, Po-Jung; Tang, Petrus
Source:: Parasitology research 2009 v.105 no.6 pp. 1683-1689
ISSN:: 0932-0113
Subject:: Trichomonas vaginalis; bioinformatics; gene expression regulation; genes; malate dehydrogenase; messenger RNA; microRNA; protein synthesis; proteomics; transfection; translation (genetics)
Abstract:: ... MicroRNAs are highly conserved small noncoding RNAs that can suppress protein translation through complementary binding to target mRNAs. We used a novel approach to identify miRNA targets in the protist Trichomonas vaginalis by comparing the levels of differentially expressed proteins and genes in the trophozoite and amoeboid stages. We observed that the T. vaginalis malate dehydrogenase (Tv_MDH) ...
DOI:: 10.1007/s00436-009-1616-5
PubMed:: 19777264
: https://doi.org/10.1007/s00436-009-1616-5

38. Noninvasive imaging of microRNA124a-mediated repression of the chromosome 14 ORF 24 gene during neurogenesis

Author:: Ko, Hae Young; Lee, Dong Soo; Kim, Soonhag
Source:: FEBS journal 2009 v.276 no.17 pp. 4854-4865
ISSN:: 1742-464X
Subject:: bioinformatics; chromosomes; cytoplasm; databases; gene expression regulation; genes; image analysis; luciferase; messenger RNA; metabolism; mice; microRNA; monitoring; neoplasm cells; neurogenesis; open reading frames; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; translation (genetics)
Abstract:: ... The function of microRNAs (miRNAs) is translational repression or mRNA cleavage of target genes by binding to 3'-UTRs of target mRNA. In this study, we investigated the functions and the target genes of microRNA124a (miR124a), and imaged the miR124a-mediated repression of chromosome 14 open reading frame24 (c14orf24, unknown function) during neurogenesis, using noninvasive luciferase systems. The ...
DOI:: 10.1111/j.1742-4658.2009.07185.x
PubMed:: 19663910
: https://doi.org/10.1111/j.1742-4658.2009.07185.x

39. Serial Expression Analysis of Liver Regeneration-Related Genes in Rat Regenerating Liver

Author:: Wang, Wen-Bo; Fan, Jian-ming; Zhang, Xiao-li; Xu, Jun; Yao, Wu
Source:: Molecular biotechnology 2009 v.43 no.3 pp. 221-231
ISSN:: 1073-6085
Subject:: apoptosis; bioinformatics; gene expression regulation; genes; glycoproteins; inflammation; liver; liver regeneration; physiological response; rats; signal transduction
Abstract:: ... We investigated the gene expression changes in rat hepatic restoration with Rat Genome 230 2.0 chip containing 11,789 known genes and 13,231 unknown genes (taking up 90 percent of rat whole genome) following a 2/3 hepatectomy. The expression profiles and roles of these genes in rat liver regeneration (LR) were assayed using bioinformatics and systems biology method. Among the above genes, 1,004 kn ...
DOI:: 10.1007/s12033-009-9199-z
: https://doi.org/10.1007/s12033-009-9199-z

40. Structural and bioinformatic analysis of the Roman snail Cd-Metallothionein gene uncovers molecular adaptation towards plasticity in coping with multifarious environmental stress

Author:: Egg, Margit; Hockner, Martina; Brandstatter, Anita; Schuler, Dietmar; Dallinger, Reinhard
Source:: Molecular ecology 2009 v.18 no.11 pp. 2426-2443
ISSN:: 0962-1083
Subject:: screening; sequence analysis; epigenetics; transcription factors; stress response; bioinformatics; Helix pomatia; cadmium; snails; environmental factors; binding sites; genes; immunocompetence; gene expression regulation; promoter regions; prediction
Abstract:: ... Metallothioneins (MTs) are a family of multifunctional proteins involved, among others, in stress response. The Cadmium (Cd)-MT gene of the Roman snail (Helix pomatia), for example, encodes for a protein induced upon cadmium exposure. While our previous studies have demonstrated that the expressed Cd-MT isoform of Roman snails assists detoxification of cadmium, the present work focuses on the pote ...
DOI:: 10.1111/j.1365-294X.2009.04191.x
PubMed:: 19457198
: https://doi.org/10.1111/j.1365-294X.2009.04191.x

41. The gene road to royalty - differential expression of hydroxylating genes in the mandibular glands of the honeybee

Author:: Malka, Osnat; Karunker, Iris; Yeheskel, Adva; Morin, Shai; Hefetz, Abraham
Source:: FEBS journal 2009 v.276 no.19 pp. 5481-5490
ISSN:: 1742-464X
Subject:: active sites; bioinformatics; biosynthesis; caste determination; cytochrome P-450; enzymes; gene expression; gene expression regulation; genes; hydroxylation; mandibular glands; models; pheromones; quantitative polymerase chain reaction; queen honey bees; stearic acid
Abstract:: ... The advances in honeybee sociogenomics have paved the way for the study of social communication processes at the gene level, in particular the expression of caste-specific pheromones. The queen honeybee mandibular pheromone provides an excellent model system, in that biosynthesis of the hydroxylating fatty acid caste-specific pheromone appears to be reduced to a single chemical hydroxylation step ...
DOI:: 10.1111/j.1742-4658.2009.07232.x
PubMed:: 19702829
: https://doi.org/10.1111/j.1742-4658.2009.07232.x

42. The ionic effects of NaCl on physiology and gene expression in rice genotypes differing in salt tolerance

Author:: Roshandel, Parto; Flowers, Timothy
Source:: Plant and soil 2009 v.315 no.1-2 pp. 135-147
ISSN:: 0032-079X
Subject:: bioinformatics; biomass; gene expression; gene expression regulation; genes; genotype; heat shock proteins; leaves; mannitol; messenger RNA; osmotic pressure; potassium; rice; root growth; roots; salt stress; salt tolerance; sequence homology; shoots; sodium; sodium chloride
Abstract:: ... The effects of ionic stress on the physiology and gene expression of two rice genotypes (IR4630 and IR15324) that differ in salt tolerance, were investigated by evaluating changes in the biomass, Na⁺ and K⁺ concentrations and applying the cDNA-AFLP technique to highlight changes in gene expression. Over 8 days of salinisation, the effect of NaCl on the reduction of biomass (dry weight) was apparen ...
DOI:: 10.1007/s11104-008-9738-6
: https://doi.org/10.1007/s11104-008-9738-6

43. Transcript Profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR Arrhythmic Triple Mutant Reveals a Role for the Circadian Clock in Cold Stress Response

Author:: Nakamichi, Norihito; Kusano, Miyako; Fukushima, Atsushi; Kita, Masanori; Ito, Shogo; Yamashino, Takafumi; Saito, Kazuki; Sakakibara, Hitoshi; Mizuno, Takeshi
Source:: Plant & cell physiology 2009 v.50 no.3 pp. 447-462
ISSN:: 0032-0781
Subject:: messenger RNA; Arabidopsis; salinity; stress response; bioinformatics; cold stress; gene expression regulation; raffinose; surveys; gene expression; water stress; genes; mutants; circadian rhythm
Abstract:: ... Arabidopsis PSEUDO RESPONSE REGULATOR (PRR) genes are components of the circadian clock mechanism. In order to understand the scope of genome-wide transcriptional regulation by PRR genes, a comparison survey of gene expression in wild-type Arabidopsis and a prr9-11 prr7-10 prr5-10 triple mutant (d975) using mRNA collected during late daytime was conducted using an Affymetrix ATH-1 GeneChip®. The e ...
DOI:: 10.1093/pcp/pcp004
PubMed:: 19131357
: https://doi.org/10.1093/pcp/pcp004

44. cis-Regulatory elements in plant cell signaling

Author:: Priest, Henry D; Filichkin, Sergei A; Mockler, Todd C
Source:: Current opinion in plant biology 2009 v.12 no.5 pp. 643-649
ISSN:: 1369-5266
Subject:: transcription factors; plant growth; plant stress; plant development; regulatory sequences; plant hormones; experimental design; genome; bioinformatics; signal transduction; biochemical pathways; transcription (genetics); plant adaptation; genomics; circadian rhythm; gene expression regulation
Abstract:: ... Plant cell signaling pathways are in part dependent on transcriptional regulatory networks comprising circuits of transcription factors (TFs) and regulatory DNA elements that control the expression of target genes. Here, we describe experimental and bioinformatic approaches for identifying potential cis-regulatory elements. We also discuss recent integrative genomics studies aimed at elucidating t ...
DOI:: 10.1016/j.pbi.2009.07.016
PubMed:: 19717332
: https://doi.org/10.1016/j.pbi.2009.07.016

45. A multidimensional electrophoretic system of separation for the analysis of gene expression (MESSAGE)

Author:: Lindemann, Elena; Rohde, Bettina; Rupp, Steffen; Regenbogen, Johannes; Sohn, Kai
Source:: Electrophoresis 2010 v.31 no.8 pp. 1330-1343
ISSN:: 0173-0835
Subject:: DNA microarrays; RNA; algorithms; bioinformatics; complementary DNA; denaturing gradient gel electrophoresis; gene expression; gene expression regulation; infrastructure; instrumentation; laboratory equipment; nucleotide sequences; reverse transcriptase polymerase chain reaction; sequence analysis; transcription (genetics)
Abstract:: ... Differential gene expression profiling has become of central importance for the analysis of cellular systems at the transcriptional level. By now, many platform technologies including DNA-microarrays, serial analysis of gene expression or RNA-seq have been established in order to facilitate transcriptional profiling. However, these technologies are all subjected to specific limitations, as they re ...
DOI:: 10.1002/elps.200900624
: https://doi.org/10.1002/elps.200900624

46. Alpha-1 antitrypsin variants in plasma from HIV-infected patients revealed by proteomic and glycoproteomic analysis

Author:: Zhang, Lijun; Jia, Xiaofang; Zhang, Xiaojun; Cao, Jing; Yang, Pengyuan; Qiu, Chao; Shen, Yinzhong; Ma, Fang; Liu, Li; Sun, Jianjun; Shen, Fang; Yin, Lin; Liu, Liwen; Yao, Yamin; Lu, Hongzhou
Source:: Electrophoresis 2010 v.31 no.20 pp. 3437-3445
ISSN:: 0173-0835
Subject:: HIV infections; Human immunodeficiency virus; Western blotting; antiretroviral agents; bioinformatics; biomarkers; electrophoresis; gels; gene expression regulation; molecular weight; patients; proteins; proteome; proteomics; sequence analysis
Abstract:: ... Novel tools are necessary to explore proteins related to human immunodeficiency virus (HIV) infection. In this work, proteomic and glycoproteomic technology were employed to examine plasma samples from HIV-positive patients. Through comparative proteome analysis of normal and HIV-positive plasma samples, 19 differentially expressed protein spots related to 12 non-redundant proteins were identified ...
DOI:: 10.1002/elps.201000153
: https://doi.org/10.1002/elps.201000153

47. Cloning and Characterization of Functional Trehalose-6-Phosphate Synthase Gene in Maize

Author:: Wei Jiang; Feng-Ling Fu; Su-Zhi Zhang; Ling Wu; Wan-Chen Li
Source:: Journal of plant biology = 2010 v.53 no.2 pp. 134-141
ISSN:: 1226-9239
Subject:: Arabidopsis; alpha,alpha-trehalose-phosphate synthase (UDP-forming); amino acids; bacteria; bioinformatics; cold stress; corn; gene expression regulation; gene overexpression; genes; glucose; heat; mutants; open reading frames; phylogeny; potatoes; prediction; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; rice; solutes; stress tolerance; tobacco; tomatoes; trehalose; trehalose-phosphatase; yeasts
Abstract:: ... Trehalose is a non-reducing disaccharide of glucose that functions as a compatible solute in the stabilization of biological structures under heat and desiccation stress in bacteria, fungi, and some “resurrection plants”. In the plant kingdom, trehalose is biosynthesized by trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). Over-expression of exogenous and endogenous ...
DOI:: 10.1007/s12374-010-9098-7
: https://doi.org/10.1007/s12374-010-9098-7

48. Cloning and Characterization of a Maize cDNA Encoding Glutamate Decarboxylase

Author:: Zhuang, Yunlong; Ren, Guijie; He, Chunmei; Li, Xinye; Meng, Qingmei; Zhu, Chuanfu; Wang, Rongchun; Zhang, Juren
Source:: Plant molecular biology reporter 2010 v.28 no.4 pp. 620-626
ISSN:: 0735-9640
Subject:: bioinformatics; genes; glutamate decarboxylase; Southern blotting; open reading frames; enzyme substrates; gene expression regulation; sequence analysis; Zea mays; complementary DNA; corn; amino acid sequences; abiotic stress; calmodulin; plant tissues; plant stress; pyridoxal phosphate; plant growth substances; reverse transcriptase polymerase chain reaction; binding sites
Abstract:: ... A putative glutamate decarboxylase (GAD) gene, designated ZmGAD1, was cloned from Zea mays with a combination of reverse-transcriptase polymerase chain reaction (RT-PCR) and bioinformatic approaches. The ZmGAD1 cDNA sequence contained a complete open reading frame encoding a putative protein of 496 amino acids, which contained a pyridoxal-5′-phosphate binding domain and a calmodulin (CaM)-binding ...
DOI:: 10.1007/s11105-010-0191-3
: https://doi.org/10.1007/s11105-010-0191-3

49. Cloning and analysis of fetal ovary microRNAs in cattle

Author:: Tripurani, Swamy K.; Xiao, Caide; Salem, Mohamed; Yao, Jianbo
Source:: Animal reproduction science 2010 v.120 no.1-4 pp. 16-22
ISSN:: 0378-4320
Subject:: ovarian follicles; genome; bioinformatics; embryo (animal); cows; cell differentiation; cell cleavage; interspecific variation; oogenesis; gene banks; gene expression regulation; sequence analysis; fetus; molecular cloning; oocytes; follicular development; nucleotide sequences; genomics; genetic variation; RNA
Abstract:: ... Ovarian folliculogenesis and early embryogenesis are complex processes, which require tightly regulated expression and interaction of a multitude of genes. Small endogenous RNA molecules, termed microRNAs (miRNAs), are involved in the regulation of gene expression during folliculogenesis and early embryonic development. To identify miRNAs in bovine oocytes/ovaries, a bovine fetal ovary miRNA libra ...
DOI:: 10.1016/j.anireprosci.2010.03.001
PubMed:: 20347535
: https://doi.org/10.1016/j.anireprosci.2010.03.001

50. Cloning and characterization of HbJAZ1 from the laticifer cells in rubber tree (Hevea brasiliensis Muell. Arg.)

Author:: Tian, W.-W.; Huang, W.-F.; Zhao, Y.
Source:: Trees 2010 v.24 no.4 pp. 771-779
ISSN:: 0931-1890
Subject:: Arabidopsis thaliana; Hevea brasiliensis; TATA box; amino acids; bioinformatics; biosynthesis; complementary DNA; ethephon; gene expression regulation; genes; genome walking; jasmonic acid; open reading frames; proteins; rubber; trees
Abstract:: ... Although jasmonate (JA) signaling has recently been well elucidated in Arabidopsis thaliana, the JASMONATE ZIM domain proteins (JAZs) are suggested to have an important role in regulating specific JA responses in plants, not much is known about how the specific JA responses are regulated in plants. Laticifer is the sole site of natural rubber biosynthesis in rubber tree. Here, the full-length cDNA ...
DOI:: 10.1007/s00468-010-0447-4
: https://doi.org/10.1007/s00468-010-0447-4

51. Design and Performance of a Turbot (Scophthalmus maximus) Oligo-microarray Based on ESTs from Immune Tissues

Author:: Millán, Adrián; Gómez-Tato, Antonio; Fernández, Carlos; Pardo, Belén G.; Álvarez-Dios, José A.; Calaza, Manuel; Bouza, Carmen; Vázquez, María; Cabaleiro, Santiago; Martínez, Paulino
Source:: Marine biotechnology 2010 v.12 no.4 pp. 452-465
ISSN:: 1436-2228
Subject:: nucleic acid hybridization; oligonucleotides; RNA; microarray technology; bioinformatics; variance; expressed sequence tags; turbot; pathogens; gene expression; Scophthalmus maximus; spleen; tissues; Aeromonas; gene expression regulation; databases; fluorescent dyes
Abstract:: ... An expressed sequence tag database from immune tissues was used to design the first high-density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. An Agilent custom oligo-microarray 8 × 15 k (five replicates/gen ...
DOI:: 10.1007/s10126-009-9231-0
PubMed:: 19844759
: https://doi.org/10.1007/s10126-009-9231-0

52. Differentially expressed genes associated with Staphylococcus aureus mastitis in dairy goats

Author:: Pisoni, G.; Moroni, P.; Genini, S.; Stella, A.; Boettcher, P.J.; Cremonesi, P.; Scaccabarozzi, L.; Giuffra, E.; Castiglioni, B.
Source:: Veterinary immunology and immunopathology 2010 v.135 no.3-4 pp. 208-217
ISSN:: 0165-2427
Subject:: Staphylococcus aureus; goats; bioinformatics; milk; genes; dairy animals; mammary glands; temporal variation; messenger RNA; somatic cells; transcription (genetics); immunologic factors; immune response; immune system; in vitro studies; mastitis; transcriptional activation; biosynthesis; immunogenetics; microarray technology; goat diseases
Abstract:: ... To study gene expression within the mammary glands of dairy goats with mastitis, mRNA was collected from milk somatic cells (MSCs) of left udder halves challenged with Staphylococcus aureus and right udder halves infused with PBS, as control, at different time points (0, 12, 24 and 48h post-infection). Transcriptional profiles were investigated using bovine cDNA microarrays; of the total 288 diffe ...
DOI:: 10.1016/j.vetimm.2009.11.016
PubMed:: 20060596
: https://doi.org/10.1016/j.vetimm.2009.11.016

53. Disrupting the Amblyomma americanum (L.) CD147 receptor homolog prevents ticks from feeding to repletion and blocks spontaneous detachment of ticks from their host

Author:: Mulenga, Albert; Khumthong, Rabuesak
Source:: Insect biochemistry and molecular biology 2010 v.40 no.7 pp. 524-532
ISSN:: 0965-1748
Subject:: ticks; immunoglobulin G; protein structure; RNA interference; glycoproteins; physiological regulation; genome; bioinformatics; hematophagy; tick control; gene expression; cell membranes; molecular cloning; receptors; Amblyomma americanum
Abstract:: ... The CD147 receptor is a cell-surface glycoprotein in the IgG family that plays pivotal roles in intercellular interactions involved with numerous physiological and pathological processes such as extracellular matrix remodeling. We previously found an Amblyomma americanum (Aam) tick CD147 receptor homolog among genes that were up regulated in response to tick feeding stimuli. This study characteriz ...
DOI:: 10.1016/j.ibmb.2010.04.012
PubMed:: 20451606
: https://doi.org/10.1016/j.ibmb.2010.04.012

54. GIGANTEA is a component of a regulatory pathway determining wall ingrowth deposition in phloem parenchyma transfer cells of Arabidopsis thaliana

Author:: Edwards, Joshua; Martin, Antony P.; Andriunas, Felicity; Offler, Christina E.; Patrick, John W.; McCurdy, David W.
Source:: Plant journal 2010 v.63 no.4 pp. 651-661
ISSN:: 0960-7412
Subject:: Arabidopsis thaliana; bioinformatics; cold; cold treatment; data collection; gene expression regulation; genes; leaves; microarray technology; mutants; nutrient transport; parenchyma (plant tissue); plasma membrane; proteins; surface area
Abstract:: ... Transfer cells are specialised transport cells containing invaginated wall ingrowths that generate an amplified plasma membrane surface area with high densities of transporter proteins. They trans-differentiate from differentiated cells at sites at which enhanced rates of nutrient transport occur across apo/symplasmic boundaries. Despite their physiological importance, little is known of the molec ...
DOI:: 10.1111/j.1365-313X.2010.04269.x
PubMed:: 20545890
: https://doi.org/10.1111/j.1365-313X.2010.04269.x

55. Gene Expression Atlas at the European Bioinformatics Institute

Author:: Kapushesky, Misha; Emam, Ibrahim; Holloway, Ele; Kurnosov, Pavel; Zorin, Andrey; Malone, James; Rustici, Gabriella; Williams, Eleanor; Parkinson, Helen; Brazma, Alvis
Source:: Nucleic acids research 2010 v.38 no.suppl_1 pp. D690
ISSN:: 0305-1048
Subject:: bioinformatics; developmental stages; gene expression; gene expression regulation; gene ontology; genes; genomics; nucleic acids; statistical analysis
Abstract:: ... The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Arc ...

56. Genomics of metabolic adaptations in the peripartal cow

Author:: Loor, J.J.
Source:: Animal 2010 v.4 no.7 pp. 1110-1139
ISSN:: 1751-7311
Subject:: dairy cows; transcriptomics; metabolism; messenger RNA; liver; physiological regulation; genome; adipose tissue; bioinformatics; pregnancy; genomics; transcriptome; mammary glands; biochemical mechanisms; gene expression regulation; perinatal period
Abstract:: ... The peripartal period is characterized by dramatic alterations in metabolism and function of key tissues such as liver, adipose and mammary. Metabolic regulation relies partly on transcriptional control of gene networks, a collection of DNA segments, which interact with a transcription factor or nuclear receptor, as a mechanism controlling the concentration of key enzymes in cells. These ‘global’ ...
DOI:: 10.1017/S1751731110000960
PubMed:: 22444613
: https://doi.org/10.1017/S1751731110000960

57. Histamine signalling in Schistosoma mansoni: Immunolocalisation and characterisation of a new histamine-responsive receptor (SmGPR-2)

Author:: El-Shehabi, Fouad; Ribeiro, Paula
Source:: International journal for parasitology 2010 v.40 no.12 pp. 1395-1406
ISSN:: 0020-7519
Subject:: G-protein coupled receptors; RNA; Saccharomyces cerevisiae; Schistosoma mansoni; adults; antagonists; bioinformatics; cercariae; complementary DNA; gene expression regulation; genome; histamine; mammals; metabolism; peripheral nervous system; quantitative polymerase chain reaction; reproduction; schistosomula
Abstract:: ... In parasitic platyhelminthes, including Schistosoma mansoni, biogenic amines play several important roles in the control of motility, metabolism and reproduction. A bioinformatics analysis of the S. mansoni genome identified approximately 16 full-length G protein-coupled receptors (GPCRs) that share significant homology with aminergic receptors from other species. Six of these sequences are struct ...
DOI:: 10.1016/j.ijpara.2010.04.006
: https://doi.org/10.1016/j.ijpara.2010.04.006

58. Methodological framework for functional characterization of plant microRNAs

Author:: Chen, Ming; Meng, Yijun; Mao, Chuanzao; Chen, Dijun; Wu, Ping
Source:: Journal of experimental botany 2010 v.61 no.9 pp. 2271-2280
ISSN:: 0022-0957
Subject:: animals; bioinformatics; clones; complementary DNA; gene expression regulation; microRNA; rapid amplification of cDNA ends; research methods
Abstract:: ... Since the beginning of this century, microRNAs (miRNAs), which are tiny RNA molecules, have become one of the major research topics on gene expression regulation in both animals and plants. The major task of miRNA study is to elucidate how the miRNAs are expressed in vivo, how they exert regulatory effects on their targets, and how they can be qualitatively or quantitatively cloned. For these purp ...
DOI:: 10.1093/jxb/erq087
PubMed:: 20388745
: https://doi.org/10.1093/jxb/erq087

59. Proteome changes of lungs artificially infected with H-PRRSV and N-PRRSV by two-dimensional fluorescence difference gel electrophoresis

Author:: Shuqi Xiao; Qiwei Wang; Jianyu Jia; Peiqing Cong; Delin Mo; Xiangchun Yu; Limei Qin; Anning Li; Yuna Niu; Kongju Zhu; Xiaoying Wang; Xiaohong Liu; Yaosheng Chen
Source:: Virology journal 2010 v.7 no.1 pp. 107
ISSN:: 1743-422X
Subject:: Betaarterivirus suid 1; bioinformatics; cytoskeleton; fluorescence; gel electrophoresis; gene expression regulation; mass spectrometry; oxidation; pathogenesis; porcine reproductive and respiratory syndrome; pork industry; protein content; protein synthesis; proteome; stress response; swine; virology; virulence; China; Vietnam
Abstract:: ... BACKGROUND: Porcine reproductive and respiratory syndrome with PRRS virus (PRRSV) infection, which causes significant economic losses annually, is one of the most economically important diseases affecting swine industry worldwide. In 2006 and 2007, a large-scale outbreak of highly pathogenic porcine reproductive and respiratory syndrome (PRRS) happened in China and Vietnam. However little data is ...
DOI:: 10.1186/1743-422X-7-107
: https://doi.org/10.1186/1743-422X-7-107

60. Seasonal effect on sperm messenger RNA profile of domestic swine (Sus Scrofa)

Author:: Yang, C.C.; Lin, Y.S.; Hsu, C.C.; Tsai, M.H.; Wu, S.C.; Cheng, W.T.K.
Source:: Animal reproduction science 2010 v.119 no.1-2 pp. 76-84
ISSN:: 0378-4320
Subject:: reproductive disorders; oligonucleotides; messenger RNA; boars; winter; spermatogenesis; microarray technology; thermoregulation; bioinformatics; heat stress; transcription (genetics); seasonal variation; male fertility; physiological response; summer; spermatozoa; gene expression regulation
Abstract:: ... Seasonal infertility is a well-known problem in the modern swine (Sus scrofa) industry. The molecular mechanisms responsible for thermal effects on spermatogenesis are, however, just beginning to be elucidated. The existence of specific messenger RNA (mRNA) remnants contained within freshly ejaculated sperm has been identified in several species. Investigators have obtained differential RNA profil ...
DOI:: 10.1016/j.anireprosci.2009.12.002
PubMed:: 20056359
: https://doi.org/10.1016/j.anireprosci.2009.12.002

61. Systems genetics, bioinformatics and eQTL mapping

Author:: Li, Hong; Deng, Hongwen
Source:: Genetica 2010 v.138 no.9-10 pp. 915-924
ISSN:: 0016-6707
Subject:: Internet; bioinformatics; biologists; chromosome mapping; computers; databases; gene expression; gene expression regulation; genetic markers; genetic variation; genome-wide association study; genomics; microarray technology; quantitative trait loci; sequence analysis; statistical analysis; transcription (genetics); transcriptome
Abstract:: ... Jansen and Nap (Trends Genet 17(7):388-391, 2001) and Jansen (Nat Rev Genet 4:145-151, 2003) first proposed the concept of genetical genomics, or genome-wide genetic analysis of gene expression data, which is also called transcriptome mapping. In this approach, microarrays are used for measuring gene expression levels across genetic mapping populations. These gene expression patterns have been use ...
DOI:: 10.1007/s10709-010-9480-x
: https://doi.org/10.1007/s10709-010-9480-x

62. The tyrosyl-DNA phosphodiesterase gene family in Medicago truncatula Gaertn.: bioinformatic investigation and expression profiles in response to copper- and PEG-mediated stress

Author:: Macovei, Anca; Balestrazzi, Alma; Confalonieri, Massimo; Carbonera, Daniela
Source:: Planta 2010 v.232 no.2 pp. 393-407
ISSN:: 0032-0935
Subject:: DNA damage; DNA repair; DNA topoisomerase; Medicago truncatula; bioinformatics; copper; crops; gene expression regulation; genes; physiology; plantlets; polyethylene glycol; quantitative polymerase chain reaction; reactive oxygen species; rehydration; stress tolerance
Abstract:: ... The Tdp1 gene encoding tyrosyl-DNA phosphodiesterase has been extensively investigated in animal cells, due to the role of this enzyme in the repair of topoisomerase I-DNA covalent lesions. In contrast, information in this regard is totally missing in plants. We report for the first time in plants on the Tdp1 gene family from barrel medic (Medicago truncatula Gaertn.), composed of two members, her ...
DOI:: 10.1007/s00425-010-1179-9
PubMed:: 20458495
: https://doi.org/10.1007/s00425-010-1179-9

63. Toxicogenomics using yeast DNA microarrays

Author:: Yasokawa, Daisuke; Iwahashi, Hitoshi
Source:: Journal of bioscience and bioengineering 2010 v.110 no.5 pp. 511-522
ISSN:: 1389-1723
Subject:: DNA microarrays; Saccharomyces cerevisiae; alcohols; aldehydes; bakers yeast; bioinformatics; eukaryotic cells; gene expression; gene expression regulation; genes; metal ions; toxic substances; toxicity; toxicogenomics
Abstract:: ... Development of genomics and bioinformatics enable us to analyze the global gene expression profiles of cells by DNA microarray. Changes in gene expression patterns indicate changes in its physiological conditions. Following the exposure of an organism or cell to toxic chemicals or other environmental stresses, the global genetic responses can be expeditiously and easily analyzed. Baker's yeast, Sa ...
DOI:: 10.1016/j.jbiosc.2010.06.003
: https://doi.org/10.1016/j.jbiosc.2010.06.003

64. Transcription of LINE‐derived sequences in exercise‐induced stress in horses

Author:: Capomaccio, S.; Verini‐Supplizi, A.; Galla, G.; Vitulo, N.; Barcaccia, G.; Felicetti, M.; Silvestrelli, M.; Cappelli, K.
Source:: Animal genetics 2010 v.41Suppls2 pp. 23-27
ISSN:: 0268-9146
Subject:: transposons; horses; bioinformatics; data collection; expressed sequence tags; gene expression; transcriptome; mononuclear leukocytes; gene expression regulation; databases
Abstract:: ... A large proportion of mammalian genomes is represented by transposable elements (TE), most of them being long interspersed nuclear elements 1 (LINE‐1 or L1). An increased expression of LINE‐1 elements may play an important role in cellular stress-related conditions exerting drastic effects on the mammalian transcriptome. To understand the impact of TE on the known horse transcriptome, we masked th ...
DOI:: 10.1111/j.1365-2052.2010.02094.x
PubMed:: 21070272
: https://doi.org/10.1111/j.1365-2052.2010.02094.x

65. 454 Genome Sequencing of Pseudoperonospora cubensis Reveals Effector Proteins with a QXLR Translocation Motif

Author:: Tian, Miaoying; Win, Joe; Savory, Elizabeth; Burkhardt, Alyssa; Held, Michael; Brandizzi, Federica; Day, Brad
Source:: Molecular plant-microbe interactions 2011 v.24 no.5 pp. 543-553
ISSN:: 0894-0282
Subject:: Cucurbitaceae; DNA; Pseudoperonospora cubensis; bioinformatics; downy mildew; gene expression regulation; genome; nucleotide sequences; pathogenicity; pathogens; peptides; proteins; sequence analysis; signal peptide
Abstract:: ... Pseudoperonospora cubensis is a biotrophic oomycete pathogen that causes downy mildew of cucurbits, a devastating foliar disease threatening cucurbit production worldwide. We sequenced P. cubensis genomic DNA using 454 pyrosequencing and obtained random genomic sequences covering approximately 14% of the genome, thus providing the first set of useful genomic sequence information for P. cubensis. U ...
DOI:: 10.1094/MPMI-08-10-0185
PubMed:: 21261462
: https://doi.org/10.1094/MPMI-08-10-0185

66. A cross-species compendium of proteins/gene products related to cold stress identified by bioinformatic approaches

Author:: Martin A. Carrasco; John C. Tan; John G. Duman
Source:: Journal of insect physiology 2011 v.57 no.8 pp. 1127-1135
ISSN:: 0022-1910
Subject:: Collembola; reptiles; amphibians; bioinformatics; genes; fish; mammals; mosses and liverworts; insects; bacteria; ribosomal proteins; Nematoda; Angiospermae; gene expression regulation; databases; transcriptomics; yeasts; temperature; proteomics; cold; cold stress; Gymnospermae; researchers
Abstract:: ... The purpose of this investigation was to construct a compendium of low temperature responsive proteins/gene products across species as identified by bioinformatics based approaches, thus allowing low temperature researchers a searchable database. Another purpose was to identify specific low temperature responsive proteins/gene products across at least two different species. We generated a database ...
DOI:: 10.1016/j.jinsphys.2011.04.021
PubMed:: 21565197
: https://doi.org/10.1016/j.jinsphys.2011.04.021

67. A novel gene with a vWD domain and three Kazal-type domains: Molecular cloning and expression in the ovary of the oriental river prawn, Macrobrachium nipponense

Author:: F. Zhang; L. Chen; J. Qin; W. Zhao; P. Wu
Source:: Russian journal of genetics 2011 v.47 no.9 pp. 1052-1057
ISSN:: 1022-7954
Subject:: messenger RNA; Macrobrachium; bioinformatics; polymerase chain reaction; gene expression; egg yolk; amino acids; blood coagulation factors; genes; molecular cloning; shrimp; molecular weight; gene expression regulation
Abstract:: ... A novel gene encoding a von Willebrand factor D (vWD) domain and three Kazal-type domains was firstly indentified from the ovary of the oriental river prawn Macrobrachium nipponense and this gene was named as MnvWD-Kazal. Bioinformatics analyses showed that this gene encodes a protein of 857 amino acids with a predicted molecular mass of 92.7 kDa. Real-time quantitative PCR (RT-QPCR) analyses reve ...
DOI:: 10.1134/S1022795411090183
: https://doi.org/10.1134/S1022795411090183

68. Application of Proteomic and Bioinformatic Techniques for Studying the Hepatoprotective Effect of Dioscin against CCl4-induced Liver Damage in Mice

Author:: Lu, Binan; Yin, Lianhong; Xu, Lina; Peng, Jinyong
Source:: Planta medica 2011 v.77 no.5 pp. 407-415
ISSN:: 0032-0943
Subject:: Western blotting; alanine transaminase; alkaline phosphatase; aspartate transaminase; bioinformatics; biomarkers; blood serum; gel electrophoresis; gene expression regulation; genes; heat shock proteins; hepatoprotective effect; histopathology; in vitro digestion; lactate dehydrogenase; liver; liver diseases; mice; nucleoside-diphosphate kinase; proteomics; silymarin; therapeutics
Abstract:: ... In this study, the significant hepatoprotective effect of dioscin against CCl4-induced acute liver damage in mice was first discovered, and the effect produced by dioscin at the dose of 100 mg/kg was equal to the action produced by silymarin at the dose of 200 mg/kg. Then, 1-dimension gel electrophoresis was used to separate the liver proteins, and five differentially expressed bands were selected ...
DOI:: 10.1055/s-0030-1250461
: https://doi.org/10.1055/s-0030-1250461

69. Application of digital gene expression tag profiling on differential gene expression of two developmental stages in bulbs of Lycoris sprengeri

Author:: Le Chang; Yi-ping Xia; Jing-jue Chen; Yu-mian Xiao
Source:: Indian journal of horticulture 2011 v.68 no.4 pp. 522-528
ISSN:: 0974-0112
Subject:: Lycoris; bioinformatics; bulbs; catalytic activity; data quality; gene expression; gene expression regulation; gene ontology; genes; horticulture; juveniles
Abstract:: ... Gene expression-profiling data are necessary to understand more clearly the differential gene expression that occurs in biological developmental process. This study is aimed to compare the differential gene expression between bulb and bulblet of Lycoris sprengeri, as to reveal the biological and molecular mechanisms in bulb development. Method: Two Digital Gene Expression tag profiling (DGE) libra ...

70. Bioinformatic characterization and gene expression pattern of apoptosis inhibitor from Macrobrachium rosenbergii challenged with infectious hypodermal and hematopoietic necrosis virus

Author:: Jesu Arockiaraj; Puganeshwaran Vanaraja; Sarasvathi Easwvaran; Arun Singh; Rofina Yasmin Othman; Subha Bhassu
Source:: Fish & shellfish immunology 2011 v.31 no.6 pp. 1259-1267
ISSN:: 1050-4648
Subject:: Aedes aegypti; Camponotus floridanus; Infectious hematopoietic necrosis virus; Ixodes scapularis; Macrobrachium rosenbergii; Pan troglodytes; Pediculus humanus; amino acid sequences; apoptosis; arthropods; bioinformatics; embryogenesis; fish; gene expression; gene expression regulation; genes; hepatopancreas; homeostasis; immune response; insects; messenger RNA; metamorphosis; molecular weight; nucleotides; phylogeny; polypeptides; quantitative polymerase chain reaction; sequence homology
Abstract:: ... Apoptosis is genetically programmed cellular killing processes that execute unnecessary or infected cells. It plays an important role in embryogenesis, homeostasis, insect metamorphosis and immunity. Apoptosis inhibitor (MrIAP) was sequenced from the freshwater giant prawn Macrobrachium rosenbergii using Illumina Solexa Genome Analyzer Technique. MrIAP consisted of 1753 base pair nucleotides encod ...
DOI:: 10.1016/j.fsi.2011.09.008
: https://doi.org/10.1016/j.fsi.2011.09.008

71. Bioinformatic studies of the wheat glutaredoxin gene family and functional analysis of the ROXY1 orthologues

Author:: Ziemann, Mark; Bhave, Mrinal; Zachgo, Sabine
Source:: Functional plant biology 2011 v.38 no.1 pp. 25-34
ISSN:: 1445-4408
Subject:: Triticum aestivum; wheat; oxidoreductases; multigene family; proteome; proteomics; bioinformatics; polymerase chain reaction; alleles; sequence homology; genetic complementation; isozymes; transcription factors; protein binding; binding sites; protein-protein interactions; gene expression regulation; protein synthesis; nucleotide sequences; cell proliferation; root tips; apical meristems
Abstract:: ... CC-type glutaredoxins comprise a large land plant-specific class of oxidoreductases. Previous research shows roles for two such proteins in developmental processes in Arabidopsis; ROXY1 mediates petal initiation and morphogenesis, and ROXY1 and ROXY2 are required for normal anther development. In the present work, the broader glutaredoxin family was investigated in hexaploid wheat with bioinformat ...
DOI:: 10.1071/FP10185
: https://doi.org/10.1071/FP10185

72. Comprehensive analysis of localization of 78 solute carrier genes throughout the subsections of the rat gastrointestinal tract

Author:: Jonathan Cedernaes; Pawel K. Olszewski; Markus Sällman Almén; Olga Stephansson; Allen S. Levine; Robert Fredriksson; Olof Nylander; Helgi B. Schiöth
Source:: Biochemical and biophysical research communications 2011 v.411 no.4 pp. 702-707
ISSN:: 0006-291X
Subject:: absorption; amino acids; bioinformatics; cecum; colon; databases; drugs; duodenum; esophagus; fatty acids; gene expression regulation; gene pool; genes; humans; ileum; inorganic ions; jejunum; membrane proteins; metals; molecular biology; quantitative polymerase chain reaction; rats; solutes; stomach; sugars
Abstract:: ... Solute carriers (SLCs), the second largest super-family of membrane proteins in the human genome, transport amino acids, sugars, fatty acids, inorganic ions, essential metals and drugs over membranes. To date no study has provided a comprehensive analysis of SLC localization along the entire GI tract. The aim of the present study was to provide a comprehensive, segment-specific description of the ...
DOI:: 10.1016/j.bbrc.2011.07.005
: https://doi.org/10.1016/j.bbrc.2011.07.005

73. Development and assessment of oligonucleotide microarrays for Atlantic salmon (Salmo salar L.)

Author:: Aleksei Krasnov; Gerrit Timmerhaus; Sergey Afanasyev; Sven Martin Jørgensen
Source:: Comparative biochemistry and physiology 2011 v.6 no.1 pp. 31-38
ISSN:: 1744-117X
Subject:: Salmo salar; aquaculture; bioinformatics; complementary DNA; cost effectiveness; diagnostic techniques; gene expression; gene expression regulation; genes; genome mining; hybridization; leukocytes; microarray technology; nucleotide sequences; oligonucleotides; protein products; salmon; tissues; transcriptome
Abstract:: ... The cDNA microarrays have played a major role in functional genomics of fish and contributed substantially to different areas of aquaculture research. However at present these platforms are gradually substituted with oligonucleotide microarrays (ONM), which represent the most cost-efficient, flexible, powerful and accurate tool for multiple gene expression profiling, especially in species with ric ...
DOI:: 10.1016/j.cbd.2010.04.006
: https://doi.org/10.1016/j.cbd.2010.04.006

74. Dietary Supplementation of Selenium in Inorganic and Organic Forms Differentially and Commonly Alters Blood and Liver Selenium Concentrations and Liver Gene Expression Profiles of Growing Beef Heifers

Author:: Shengfa F. Liao; Kelly R. Brown; Arnold J. Stromberg; Walter R. Burris; James A. Boling; James C. Matthews
Source:: Biological trace element research 2011 v.140 no.2 pp. 151-169
ISSN:: 0163-4984
Subject:: Angus; beef cattle; bioinformatics; body weight; cattle feeds; cell communication; corn; cottonseed; dietary supplements; erythrocytes; forage crops; forage grasses; gene expression; gene expression regulation; genes; heifers; immune response; liver; messenger RNA; microarray technology; oxidative stress; protein synthesis; proteins; selenium; selenomethionine; sodium selenite; soil
Abstract:: ... In geographic regions where selenium (Se) soil concentrations are naturally low, the addition of Se to animal feed is necessary. Even though it is known that Se in grass and forage crops is primarily present in organic forms (especially as L-selenomethionine, L-selenocystine, and L-selenocystathionine), the feeding of Se in the naturally occurring organic selenium (OSe) compounds produces higher b ...
DOI:: 10.1007/s12011-010-8685-2
PubMed:: 20387001
: https://doi.org/10.1007/s12011-010-8685-2

75. Differential expression of porcine sperm microRNAs and their association with sperm morphology and motility

Author:: Erin Curry; Timothy J. Safranski; Scott L. Pratt
Source:: Theriogenology 2011 v.76 no.8 pp. 1532-1539
ISSN:: 0093-691X
Subject:: bioinformatics; embryogenesis; gene expression regulation; genes; male fertility; messenger RNA; metabolism; microRNA; proteins; sperm motility; spermatogenesis; spermatozoa; swine
Abstract:: ... MicroRNAs (miRNAs) are involved in nearly every biological process examined to date, but little is known of the identity or function of miRNA in sperm cells or their potential involvement in spermatogenesis. The objective was to identify differences in miRNA expression between normal porcine sperm samples and those exhibiting high percentages of morphological abnormalities or low motility. Quantit ...
DOI:: 10.1016/j.theriogenology.2011.06.025
PubMed:: 21872314
: https://doi.org/10.1016/j.theriogenology.2011.06.025

76. Estrogen-responsive genes in macrophages of the bony fish gilthead seabream: A transcriptomic approach

Author:: S. Liarte; E. Chaves-Pozo; E. Abellán; J. Meseguer; V. Mulero; A.V.M. Canario; A. García-Ayala
Source:: Developmental and comparative immunology 2011 v.35 no.8 pp. 840-849
ISSN:: 0145-305X
Subject:: Sparus aurata; bioinformatics; complementary DNA; estradiol; fish; gene expression regulation; genes; immune response; leukocytes; macrophages; pathogens; reverse transcriptase polymerase chain reaction; suppression subtractive hybridization; transcriptome; transcriptomics
Abstract:: ... The role of sex steroids in the modulation of fish immune responses has received little attention. Previous studies have demonstrated that 17β-estradiol (E₂) is able to alter the response of gilthead seabream leukocytes to infectious agents. We have used suppression subtractive hybridization to identify genes upregulated by E₂ (50ng/ml) in macrophage cultures from gilthead seabream. We isolated 39 ...
DOI:: 10.1016/j.dci.2011.03.015
: https://doi.org/10.1016/j.dci.2011.03.015

77. Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR

Author:: Ferraz, Lúcio F. C.; Verde, Leandro C. L.; Vicentini, Renato; Felício, Ana P.; Ribeiro, Marcelo L.; Alexandrino, Fabiana; Novo, Maria T. M.; Garcia, Oswaldo Jr; Rigden, Daniel J.; Ottoboni, Laura M. M.
Source:: Antonie van Leeuwenhoek 2011 v.99 no.3 pp. 609-617
ISSN:: 0003-6072
Subject:: Acidithiobacillus ferrooxidans; DNA; bioinformatics; copper; energy; fur; gel electrophoresis; gene expression; gene expression regulation; genes; genomics; iron; microorganisms; models; quantitative polymerase chain reaction; sulfides; transcription factors
Abstract:: ... Acidithiobacillus ferrooxidans is one of the most widely used microorganisms in bioleaching operations to recover copper from low-grade copper sulfide ores. This work aimed to investigate the relative expression of genes related to the iron uptake system when A. ferrooxidans LR was maintained in contact with chalcopyrite or bornite as the sole energy source. Real-time quantitative PCR analysis rev ...
DOI:: 10.1007/s10482-010-9533-2
: https://doi.org/10.1007/s10482-010-9533-2

78. Gene expression in placentation of farm animals: An overview of gene function during development

Author:: R.S.N. Barreto; F.F. Bressan; L.J. Oliveira; F.T.V. Pereira; F. Perecin; C.E. Ambrósio; F.V. Meirelles; M.A. Miglino
Source:: Theriogenology 2011 v.76 no.4 pp. 589-597
ISSN:: 0093-691X
Subject:: Danio rerio; assisted reproductive technologies; bioinformatics; cattle; cluster analysis; databases; gene expression; gene expression regulation; genes; glycoproteins; humans; mice; microarray technology; models; phylogeny; placenta; pregnancy; risk; women
Abstract:: ... Eutherian mammals share a common ancestor that evolved into two main placental types, i.e., hemotrophic (e.g., human and mouse) and histiotrophic (e.g., farm animals), which differ in invasiveness. Pregnancies initiated with assisted reproductive techniques (ART) in farm animals are at increased risk of failure; these losses were associated with placental defects, perhaps due to altered gene expre ...
DOI:: 10.1016/j.theriogenology.2011.03.001
PubMed:: 21550103
: https://doi.org/10.1016/j.theriogenology.2011.03.001

79. Haemocyte protein expression profiling of scallop Chlamys farreri response to acute viral necrosis virus (AVNV) infection

Author:: Guofu Chen; Chunyun Zhang; Chenghua Li; Chongming Wang; Zhong Xu; Peisheng Yan
Source:: Developmental and comparative immunology 2011 v.35 no.11 pp. 1135-1145
ISSN:: 0145-305X
Subject:: Chlamys; adults; bioinformatics; biomarkers; calcium; coasts; cytoskeleton; databases; desorption; digestion; gene expression regulation; genes; hemocytes; homeostasis; immune response; ionization; matrix-assisted laser desorption-ionization mass spectrometry; mortality; necrosis; pathogenesis; protein synthesis; proteins; scallops; signal transduction; specific pathogen-free animals; transcription (genetics); trypsin; two-dimensional gel electrophoresis; viruses
Abstract:: ... Acute viral necrosis virus (AVNV) was newly reported as one causative agent responsible for mass mortality of adult Chinese scallop Chlamys farreri, which is widely cultured on northern China coast. Unfortunately, the interaction between virus and host is largely unknown. According to these, this study was undertaken to deeply explore the immune response of haemocyte against AVNV. Two-dimensional ...
DOI:: 10.1016/j.dci.2011.03.022
: https://doi.org/10.1016/j.dci.2011.03.022

80. Identification and characterization of putative CIPK genes in maize

Author:: Xifeng Chen; Zhimin Gu; Dedong Xin; Liang Hao; Chengjie Liu; Ji Huang; Bojun Ma; Hongsheng Zhang
Source:: Journal of genetics and genomics 2011 v.38 no.2 pp. 77-87
ISSN:: 1673-8527
Subject:: Zea mays; bioinformatics; calcium; cold stress; corn; drought; gene expression regulation; genes; heat; inbred lines; microarray technology; phylogeny; plant stress; protein kinases; proteins; rice; salts; second messengers; stress response
Abstract:: ... Calcium (Ca) plays a crucial role as a second messenger in intracellular signaling elicited by developmental and environmental cues. Calcineurin B-like proteins (CBLs) and their target proteins, CBL-interacting protein kinases (CIPKs) have emerged as a key Ca²⁺-mediated signaling network in response to stresses in plants. Bioinformatic analysis was used to identify 43 putative ZmCIPK (Zea mays CIP ...
DOI:: 10.1016/j.jcg.2011.01.005
PubMed:: 21356527
: https://doi.org/10.1016/j.jcg.2011.01.005

81. Identification of Differentially Expressed Sequence Tags in Rapidly Elongating Phyllostachys pubescens Internodes by Suppressive Subtractive Hybridization

Author:: Zhou, Ming-bing; Yang, Ping; Gao, Pei-jun; Tang, Ding-Qin
Source:: Plant molecular biology reporter 2011 v.29 no.1 pp. 224-231
ISSN:: 0735-9640
Subject:: Phyllostachys edulis; protein synthesis; biosynthesis; brassinosteroids; cell walls; meristems; bioinformatics; internodes; expressed sequence tags; signal transduction; cell respiration; bamboo shoots; suppression subtractive hybridization; gibberellins; gene expression regulation
Abstract:: ... Bamboo shoots grow quickly through the rapid elongation of internodes, but the precise molecular mechanisms underlying this process remain unknown. We used a combination of suppressive subtractive hybridization (SSH), dot blotting, sequencing and bioinformatics to identify Phyllostachys pubescens genes that are differentially expressed in rapidly elongating vs. static internodes (SIs). We isolated ...
DOI:: 10.1007/s11105-010-0222-0
: https://doi.org/10.1007/s11105-010-0222-0

82. Identification of McbR as transcription regulator of aecD and genes involved in methionine and cysteine biosynthesis in Corynebacterium jeikeium K411

Author:: Iris Brune; Helena Barzantny; Marianne KlÃ¶tzel; Janette Jones; Gordon James; Andreas Tauch
Source:: Journal of biotechnology 2011 v.151 no.1 pp. 22-29
ISSN:: 0168-1656
Subject:: Corynebacterium jeikeium; DNA; DNA microarrays; affinity chromatography; aspartic acid; bioinformatics; biosynthesis; biotechnology; cysteine; gene expression regulation; humans; methionine; odors; promoter regions; regulon; transcription factors
Abstract:: ... The CâS lyase aecD (MetC) from skin corynebacteria plays an important role in body odour formation by releasing odoriferous sulfanylalkanols from cysteine conjugates in human axilla secretions. The expression of the aecD gene from Corynebacterium jeikeium K411, a strain originally isolated from the human axilla, was down-regulated in cells grown in minimal medium supplemented with methionine. A ...
DOI:: 10.1016/j.jbiotec.2010.11.005
: https://doi.org/10.1016/j.jbiotec.2010.11.005

83. Identification of a Mastigoneme Protein from Phytophthora nicotianae

Author:: Leila M. Blackman; Mikihiko Arikawa; Shuhei Yamada; Toshinobu Suzaki; Adrienne R. Hardham
Source:: Protist 2011 v.162 no.1 pp. 100-114
ISSN:: 1434-4610
Subject:: Phytophthora nicotianae; antibodies; bioinformatics; cell movement; epidermal growth factor; flagellum; gels; gene expression; gene expression regulation; hairs; molecular cloning; precipitin tests; proteins; secretion; sequence analysis; sporulation; zoospores
Abstract:: ... Tripartite tubular hairs (mastigonemes) on the anterior flagellum of protists in the stramenopile taxon are responsible for reversing the thrust of flagellar beat and for cell motility. Immunoprecipitation experiments using antibodies directed towards mastigonemes on the flagella of zoospores ofPhytophthora nicotianaehave facilitated the cloning of a gene encoding a mastigoneme shaft protein in th ...
DOI:: 10.1016/j.protis.2010.01.005
: https://doi.org/10.1016/j.protis.2010.01.005

84. Identification of a new cartilage-specific S100-like protein up-regulated during endo/perichondral mineralization in gilthead seabream

Author:: Vera G. Fonseca; Joana Rosa; Vincent Laizé; Paulo J. Gavaia; M. Leonor Cancela
Source:: Gene expression patterns 2011 v.11 no.7 pp. 448-455
ISSN:: 1567-133X
Subject:: Sparus aurata; adulthood; bioinformatics; bone formation; cDNA libraries; calcium; calcium-binding proteins; cartilage; chondrocytes; complementary DNA; fish; gene expression; gene expression regulation; genes; ions; juveniles; larvae; mineralization; phylogeny; signal peptide
Abstract:: ... Calcium ions and calcium-binding proteins play a major role in many cellular processes, in particular skeletogenesis and bone formation. We report here the discovery of a novel S100 protein in fish and the analysis of its gene expression patterns. A 648-bp full-length cDNA encoding an 86-amino acid S100-like calcium-binding protein was identified through the subtractive hybridization of a gilthead ...
DOI:: 10.1016/j.gep.2011.07.003
: https://doi.org/10.1016/j.gep.2011.07.003

85. Identification of differentially expressed genes in the heart precursor cells of the chick embryo

Author:: Margaret Bento; Elizabeth Correia; Ana T. Tavares; Jörg D. Becker; José A. Belo
Source:: Gene expression patterns 2011 v.11 no.7 pp. 437-447
ISSN:: 1567-133X
Subject:: bioinformatics; blood; chickens; chicks; embryo (animal); gene expression; gene expression regulation; genes; heart; in situ hybridization; promoter regions; screening
Abstract:: ... Genetic evidence has implicated several genes as being critical for heart development. However, the inducers of these genes as well as their targets and pathways they are involved with, remain largely unknown. Previous studies in the avian embryo showed that at HH4 Cerberus (cCer) transcripts are detected in the anterior endomesoderm including the heart precursor cells and later in the left latera ...
DOI:: 10.1016/j.gep.2011.07.002
: https://doi.org/10.1016/j.gep.2011.07.002

86. Identification of novel serum biomarkers in child nephroblastoma using proteomics technology

Author:: Qian Zhang; Jiaxiang Wang; Rui Dong; Shaobo Yang; Shu Zheng
Source:: Molecular biology reports 2011 v.38 no.1 pp. 631-638
ISSN:: 0301-4851
Subject:: apolipoprotein C-I; bioinformatics; biomarkers; blood serum; children; desorption; gender; gene expression regulation; haptoglobins; high performance liquid chromatography; ionization; mass spectrometry; molecular weight; patients; prognosis; proteomics
Abstract:: ... To screen and identify serum biomarkers for nephroblastoma in children using surface-enhanced laser desorption/ionization (SELDI) and other proteomics technologies. The surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI–TOF-MS) was used to identify biomarkers in 100 children with nephroblastoma and 30 gender and age-matched normal healthy children. There were 30 c ...
DOI:: 10.1007/s11033-010-0149-4
: https://doi.org/10.1007/s11033-010-0149-4

87. MicroRNAs expression in ox-LDL treated HUVECs: MiR-365 modulates apoptosis and Bcl-2 expression

Author:: Bing Qin; Bo Xiao; Desheng Liang; Jian Xia; Ye Li; Huan Yang
Source:: Biochemical and biophysical research communications 2011 v.410 no.1 pp. 127-133
ISSN:: 0006-291X
Subject:: B-lymphocytes; Internet; apoptosis; atherosclerosis; bioinformatics; gene expression; gene expression regulation; genes; human umbilical vein endothelial cells; low density lipoprotein; lymphoma; messenger RNA; microRNA; microarray technology; non-coding RNA; reverse transcriptase polymerase chain reaction; transfection
Abstract:: ... Endothelial cells (ECs) apoptosis induced by oxidized low-density lipoprotein (ox-LDL) is thought to play a critical role in atherosclerosis. MicroRNAs (miRNAs) are a class of noncoding RNAs that posttranscriptionally regulate the expression of genes involved in diverse cell functions, including differentiation, growth, proliferation, and apoptosis. However, whether miRNAs are associated with ox-L ...
DOI:: 10.1016/j.bbrc.2011.05.118
: https://doi.org/10.1016/j.bbrc.2011.05.118

88. Oct4-related cytokine effects regulate tumorigenic properties of colorectal cancer cells

Author:: Charn-Jung Chang; Yueh Chien; Kai-Hsi Lu; Shih-Ching Chang; Yueh-Ching Chou; Chi-Shuan Huang; Chin-Hong Chang; Kuan-Hsuan Chen; Yuh-Lih Chang; Ling-Ming Tseng; Wen-Shin Song; Jhi-Joung Wang; Jen-Kou Lin; Pin-I Huang; Yuan-Tzu Lan
Source:: Biochemical and biophysical research communications 2011 v.415 no.2 pp. 245-251
ISSN:: 0006-291X
Subject:: antibodies; bioinformatics; carcinogenesis; cell movement; colorectal neoplasms; drug resistance; gene expression regulation; gene overexpression; genes; inflammation; interleukin-8; microarray technology; neoplasm cells; neutralization; stem cells; transcription factors
Abstract:: ... Oct4, a member of the POU-domain transcription factor family, has been implicated in the cancer stem cell (CSC)-like properties of various cancers. However, the precise role of Oct4 in colorectal CSC initiation remains uncertain. Numerous studies have demonstrated a strong link between inflammation and tumorigenesis in colorectal cancers. In this study, we demonstrated that Oct4 overexpression enh ...
DOI:: 10.1016/j.bbrc.2011.10.024
: https://doi.org/10.1016/j.bbrc.2011.10.024

89. Overexpression of microRNA-29b induces apoptosis of multiple myeloma cells through down regulating Mcl-1

Author:: Yi-Kun Zhang; Hua Wang; Yun Leng; Ze-Liang Li; Yue-Feng Yang; Feng-Jun Xiao; Qing-Fang Li; Xie-Qun Chen; Li-Sheng Wang
Source:: Biochemical and biophysical research communications 2011 v.414 no.1 pp. 233-239
ISSN:: 0006-291X
Subject:: 3' untranslated regions; Western blotting; apoptosis; bioinformatics; bone marrow; caspase-3; gene expression; gene expression regulation; humans; interleukin-6; microRNA; microarray technology; myeloma; oncogenes; pathogenesis; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; translation (genetics)
Abstract:: ... MicroRNAs (miRNAs) are small, noncoding ribonucleic acids (ncRNAs), which regulate gene expression by targeting mRNAs for translational repression and degradation. Several lines of evidences have indicated that miRNAs act as tumor suppressors and oncogenes. However, the role of miRNAs in pathogenesis of multiple myeloma (MM) remains unclear. In this study, we examined the profile of miRNA expressi ...
DOI:: 10.1016/j.bbrc.2011.09.063
: https://doi.org/10.1016/j.bbrc.2011.09.063

90. Profiling Differential Gene Expression of Symbiotic and Aposymbiotic Corals Using a High Coverage Gene Expression Profiling (HiCEP) Analysis

Author:: Yuyama, Ikuko; Watanabe, Toshiki; Takei, Yoshio
Source:: Marine biotechnology 2011 v.13 no.1 pp. 32-40
ISSN:: 1436-2228
Subject:: Acropora tenuis; Symbiodinium; bioinformatics; corals; gene expression; gene expression regulation; genes; ions; juveniles; lipid metabolism; nutrient utilization; quantitative polymerase chain reaction; signal transduction; stress response; symbionts; symbiosis; transcriptomics
Abstract:: ... Coral generally harbors zooxanthellae (genus Symbiodinium) in the body for mutualistic symbiosis, which favors the host through effects on growth, stress response, and nutrient utilization. However, little is known about the molecular mechanisms by which the partners establish and regulate the endosymbiosis. In this study, we conducted a comprehensive transcriptome analysis in the coral Acropora t ...
DOI:: 10.1007/s10126-010-9265-3
: https://doi.org/10.1007/s10126-010-9265-3

91. Proteomic analysis of the interleukin-4 (IL-4) response in hepatitis B virus-positive human hepatocelluar carcinoma cell line HepG2.2.15

Author:: Yao, Yuqin; Li, Jiong; Lu, Zejun; Tong, Aiping; Wang, Wei; Su, Xiaolan; Zhou, Yan; Mu, Bo; Zhou, Shijie; Li, Xiaoan; Chen, Lijuan; Gou, Lantu; Song, Hongbing; Yang, Jinliang; Wei, Yuquan
Source:: Electrophoresis 2011 v.32 no.15 pp. 2004-2012
ISSN:: 0173-0835
Subject:: Hepatitis B virus; bioinformatics; carcinoma; electrophoresis; gene expression regulation; hepatitis B; hepatitis B antigens; hepatoma; humans; interleukin-4; liver cirrhosis; pathogenesis; people; protein synthesis; proteins; proteolysis; proteomics; virology
Abstract:: ... Hepatitis B virus (HBV) infection is the leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. In recent decades, significant progress toward understanding the molecular virology and pathogenesis of HBV infection has been made. In addition, multiple treatment modalities have been developed for persons with HBV infection. In the present study, we demonstrated that IL-4 inhibits t ...
DOI:: 10.1002/elps.201100147
: https://doi.org/10.1002/elps.201100147

92. Small RNA transcriptome investigation based on next-generation sequencing technology

Author:: Linglin Zhou; Xueying Li; Qi Liu; Fangqing Zhao; Jinyu Wu
Source:: Journal of genetics and genomics 2011 v.38 no.11 pp. 505-513
ISSN:: 1673-8527
Subject:: RNA; bioinformatics; databases; gene expression regulation; mining; transcriptome
Abstract:: ... Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a reduced cost, next-generation sequencing technology has provided an unprecedented opportunity to measure the extent and complexity of small RNA transcriptome. Meanwhile, the large amount ...
DOI:: 10.1016/j.jgg.2011.08.006
PubMed:: 22133681
: https://doi.org/10.1016/j.jgg.2011.08.006

93. Teladorsagia circumcincta: The transcriptomic response of a multi-drug-resistant isolate to ivermectin exposure in vitro

Author:: Alison J. Dicker; Mintu Nath; Raja Yaga; Alasdair J. Nisbet; F. Alex Lainson; John S. Gilleard; Philip J. Skuce
Source:: Experimental parasitology 2011 v.127 no.2 pp. 351-356
ISSN:: 0014-4894
Subject:: livestock and meat industry; carbohydrate metabolism; parasites; ivermectin; transcriptomics; genetic resistance; vitellogenin; multiple drug resistance; bioinformatics; data collection; expressed sequence tags; gene expression regulation; cytochrome P-450; cytochrome-c oxidase; anthelmintics; parasitology; Teladorsagia circumcincta; amino acid metabolism
Abstract:: ... The emergence and spread of anthelmintic resistance in parasitic nematodes is a serious threat to the sustainability of the livestock industry. Resistance has a genetic component but the underlying mechanisms and the means by which resistant parasites survive anthelmintic treatment are still poorly understood. Differential gene expression may be implicated, especially in multi-drug resistant paras ...
DOI:: 10.1016/j.exppara.2010.08.019
: https://doi.org/10.1016/j.exppara.2010.08.019

94. The laccase multigene family in Arabidopsis thaliana: towards addressing the mystery of their gene function(s)

Author:: Turlapati, Phanikanth V.; Kim, Kye-Won; Davin, Laurence B.; Lewis, Norman G.
Source:: Planta 2011 v.233 no.3 pp. 439-470
ISSN:: 0032-0935
Subject:: Arabidopsis thaliana; DNA methylation; amines; bioinformatics; cell walls; developmental stages; gene expression; gene expression regulation; glycoproteins; histones; laccase; microRNA; multigene family; oxidation; phenols; phloem; pollen; reverse transcriptase polymerase chain reaction; root hairs; testa; transcription (genetics)
Abstract:: ... While laccases, multi-copper glycoprotein oxidases, are often able to catalyze oxidation of a broad range of substrates, such as phenols and amines in vitro, their precise physiological/biochemical roles in higher plants remain largely unclear, e.g., Arabidopsis thaliana contains 17 laccases with only 1 having a known physiological function. To begin to explore their roles in planta, spatial and t ...
DOI:: 10.1007/s00425-010-1298-3
: https://doi.org/10.1007/s00425-010-1298-3

95. The miRNA-targetome of KSHV and EBV in human B-cells

Author:: Georg Malterer; Lars Dölken; Jürgen Haas
Source:: RNA biology 2011 v.8 no.1 pp. 30-34
ISSN:: 1555-8584
Subject:: B-lymphocytes; Herpesviridae infections; Human gammaherpesvirus 4; Human gammaherpesvirus 8; binding sites; bioinformatics; gene expression; gene expression regulation; genes; hosts; human cell lines; humans; microRNA; microarray technology; non-coding RNA; precipitin tests; transcriptome; viruses
Abstract:: ... Micro-RNAs (miRNAs) are small non-coding RNA molecules which provide a subtle layer of regulation to thousands of cellular genes. The identification of virally encoded miRNAs added another layer of complexity to the dense interaction between viruses and their natural hosts. While it has been shown that viral miRNAs can regulate both cellular and viral gene expression, target identification has bee ...
DOI:: 10.4161/rna.8.1.13745
: https://doi.org/10.4161/rna.8.1.13745

96. Transcriptome analysis reveals differentially expressed genes associated with the mantled homeotic flowering abnormality in oil palm (Elaeis guineensis)

Author:: Beulé, Thierry; Camps, Céline; Debiesse, Ségolène; Tranchant, Christine; Dussert, Stéphane; Sabau, Xavier; Jaligot, Estelle; Alwee, Sharifah Shahrul Rabiah Syed; Tregear, James W.
Source:: Tree genetics & genomes 2011 v.7 no.1 pp. 169-182
ISSN:: 1614-2942
Subject:: Elaeis guineensis; androecium; bioinformatics; complementary DNA; epigenetics; females; flowering; flowers; gene expression; gene expression regulation; genes; males; micropropagation; oils; phenotype; plantations; proteins; proteolysis; somatic embryogenesis; suppression subtractive hybridization; transcriptome; transcriptomics
Abstract:: ... Micropropagation of oil palm by somatic embryogenesis produces a proportion of off-type individuals (approximately 5% overall) displaying a homeotically modified flower structure known as mantled. Transformation of the fertile or sterile androecium into carpel-like structures is observed in staminate and pistillate mantled flowers, respectively, resulting in lower oil yields in affected plantation ...
DOI:: 10.1007/s11295-010-0323-9
: https://doi.org/10.1007/s11295-010-0323-9

97. A comparison of subcutaneous adipose tissue proteomes in juvenile piglets with a contrasted adiposity underscored similarities with human obesity

Author:: Florence Gondret; Blandine Guével; Emmanuelle Com; Annie Vincent; Bénédicte Lebret
Source:: Journal of proteomics 2012 v.75 no.3 pp. 949-961
ISSN:: 1874-3919
Subject:: subcutaneous fat; proteins; malic enzyme; NADP-glucose-6-phosphate dehydrogenase; humans; adipose tissue; bioinformatics; inflammation; human health; interleukin-6; models; nutrition; tumor necrosis factor-alpha; genes; obesity; adiposity; rodents; gene expression regulation; piglets; apoptosis
Abstract:: ... Subcutaneous fat tissues from an indigenous fat-type breed and an intensively-lean selected breed were studied in juvenile pigs. Combining DIGE with bioinformatics and target analyses of key genes, enzymes or terminal routes, this study identifies metabolic and homeostatic processes, response to organic substances, and acute-phase responses as the main pathways whose proteins were regulated in ass ...
DOI:: 10.1016/j.jprot.2011.10.012
PubMed:: 22061664
: https://doi.org/10.1016/j.jprot.2011.10.012

98. A novel high-throughput B1H-ChIP method for efficiently validating and screening specific regulator–target promoter interactions

Author:: Jumei Zeng; Yuqing Li; Shuguang Zhang; Zheng-Guo He
Source:: Applied microbiology and biotechnology 2012 v.93 no.3 pp. 1257-1269
ISSN:: 0175-7598
Subject:: prokaryotic cells; regulator genes; cell walls; hosts; multiple drug resistance; bioinformatics; eukaryotic cells; gene expression regulation; gene targeting; tuberculosis; screening; Mycobacterium tuberculosis; pathogens
Abstract:: ... Confident protein–DNA interaction (PDI) data could significantly improve our understanding of transcriptional regulation network in both prokaryotes and eukaryotes. New methods need to be established for validating and mining the protein–DNA interaction data produced by bioinformatic tools and large-scale screening assays. In this study, we integrated bacterial one-hybrid technique (B1H) with clas ...
DOI:: 10.1007/s00253-011-3748-7
PubMed:: 22189860
: https://doi.org/10.1007/s00253-011-3748-7

99. Alteration of the kidney membrane proteome of Mizuhopecten yessoensis induced by low-level methyl parathion exposure

Author:: Xiang Huang; He-Qing Huang
Source:: Aquatic toxicology 2012 v.114-115 no. pp. 189-199
ISSN:: 0166-445X
Subject:: Western blotting; bioinformatics; biomarkers; chronic toxicity; electrophoresis; environmental impact; environmental monitoring; gas chromatography; gene expression; gene expression regulation; human health; kidneys; messenger RNA; parathion-methyl; polymerase chain reaction; protein synthesis; proteins; proteome; scallops
Abstract:: ... Methyl parathion (MP) is a widely used organophosphorus pesticide that causes severe health and environmental effects. We investigated the alteration of the proteomic profile in the membrane enriched fraction of the kidneys of the scallop Mizuhopecten yessoensis exposed to low-level MP. Gas chromatography analysis showed that MP residues were significantly accumulated in the kidneys and the digest ...
DOI:: 10.1016/j.aquatox.2012.01.025
PubMed:: 22446831
: https://doi.org/10.1016/j.aquatox.2012.01.025

100. Analysis of putative miRNA function using a novel approach, GAPPS-miRTarGE

Author:: Seung Gu Park; Kyung-Hoon Kwon; Sun Shim Choi
Source:: Genes & genomics 2012 v.34 no.2 pp. 205-216
ISSN:: 1976-9571
Subject:: messenger RNA; developmental stages; bioinformatics; brain; gene expression; mice; heart; genes; microRNA; genetic techniques and protocols; embryogenesis; gene expression regulation; prediction
Abstract:: ... Deciphering the function of miRNA is one of the most important research subjects directed toward understanding the regulation of gene expression. Several experimental methodologies and bioinformatics programs have been developed, however, elucidating miRNA function has not been an easy task. Herein, we suggest a new method, GAPPS-miRTarGE, which is a novel methodology for predicting miRNA function ...
DOI:: 10.1007/s13258-011-0233-8
: https://doi.org/10.1007/s13258-011-0233-8

PubAg

Main content area

Limit your search

Text Availability

Journal

Publication Year

Subject

Search

1,367 Search Results

Search Results

1. Microarray data analysis using machine learning methods

2. Plant bZIP Gâbox binding factors.â: Modular structure and activation mechanisms

3. Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data

4. Inferring cellular networks using probabilistic graphical models

5. Structure, circadian regulation and bioinformatic analysis of the unique sigma factor gene in Chlamydomonas reinhardtii

6. Low temperature promotes intron retention in two e-cor genes of durum wheat

7. Bioinformatic analysis of expressed sequence tags derived from a compatible Alternaria brassicicola-Brassica oleracea interaction

8. Characterization of five microRNA families in maize

9. Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana

10. Identification and characterization of an Arabidopsis homogentisate phytyltransferase paralog

11. Putative fasciclin-like arabinogalactan-proteins (FLA) in wheat (Triticum aestivum) and rice (Oryza sativa): identification and bioinformatic analyses

12. The MYB Transcription Factor Superfamily of Arabidopsis: Expression Analysis and Phylogenetic Comparison with the Rice MYB Family

13. Transcription factor families in Arabidopsis: major progress and outstanding issues for future research

14. Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling

15. A translocation signal for delivery of oomycete effector proteins into host plant cells

16. Analysis of expression profile of selected genes expressed during auxin-induced somatic embryogenesis in leaf base system of wheat (Triticum aestivum) and their possible interactions

17. Global functional analyses of rice promoters by genomics approaches

18. Identification of differentially expressed genes in female Culex pipiens pallens

19. Identification of functional candidate genes for drought tolerance in rice

20. Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens

21. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses

22. A Novel Gene Involved in Lesion Formation in Magnaporthe grisea

23. Characterization of a profilin-like protein from Schistosoma japonicum, a potential new vaccine candidate

24. Do two mutually exclusive gene modules define the phenotypic diversity of mammalian smooth muscle

25. Eimeria tenella: Analysis of differentially expressed genes in the monensin- and maduramicin-resistant lines using cDNA array

26. Expression profiles of the organic acid metabolism-associated genes during rat liver regeneration

27. Grapevine habituation: Understanding of factors that contribute to neoplastic transformation and somaclonal variation

28. A Key Enzyme of the Leloir Pathway Is Involved in Pathogenicity of Leptosphaeria maculans Toward Oilseed Rape

29. BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis: bioinformatics and gene expression

30. Changes in microRNAs associated with hepatic stellate cell activation status identify signaling pathways

31. Characterization of the Mesorhizobium loti MAFF303099 Type-Three Protein Secretion System

32. Differential expression of ubiquitin-conjugating enzyme E2r in the developing ovary and testis of penaeid shrimp Marsupenaeus japonicus

33. Emerging technologies for amino acid nutrition research in the post-genome era

34. Glycoproteomic analysis of WGA-bound glycoprotein biomarkers in sera from patients with lung adenocarcinoma

35. Identification of a novel gene K23 over-expressed in fish cross-subfamily cloned embryos

36. Individuality and epigenetics in obesity

37. Malate dehydrogenase is negatively regulated by miR-1 in Trichomonas vaginalis

38. Noninvasive imaging of microRNA124a-mediated repression of the chromosome 14 ORF 24 gene during neurogenesis

39. Serial Expression Analysis of Liver Regeneration-Related Genes in Rat Regenerating Liver

40. Structural and bioinformatic analysis of the Roman snail Cd-Metallothionein gene uncovers molecular adaptation towards plasticity in coping with multifarious environmental stress

41. The gene road to royalty - differential expression of hydroxylating genes in the mandibular glands of the honeybee

42. The ionic effects of NaCl on physiology and gene expression in rice genotypes differing in salt tolerance

43. Transcript Profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR Arrhythmic Triple Mutant Reveals a Role for the Circadian Clock in Cold Stress Response

44. cis-Regulatory elements in plant cell signaling

45. A multidimensional electrophoretic system of separation for the analysis of gene expression (MESSAGE)

46. Alpha-1 antitrypsin variants in plasma from HIV-infected patients revealed by proteomic and glycoproteomic analysis

47. Cloning and Characterization of Functional Trehalose-6-Phosphate Synthase Gene in Maize

48. Cloning and Characterization of a Maize cDNA Encoding Glutamate Decarboxylase

49. Cloning and analysis of fetal ovary microRNAs in cattle

50. Cloning and characterization of HbJAZ1 from the laticifer cells in rubber tree (Hevea brasiliensis Muell. Arg.)

51. Design and Performance of a Turbot (Scophthalmus maximus) Oligo-microarray Based on ESTs from Immune Tissues

52. Differentially expressed genes associated with Staphylococcus aureus mastitis in dairy goats

53. Disrupting the Amblyomma americanum (L.) CD147 receptor homolog prevents ticks from feeding to repletion and blocks spontaneous detachment of ticks from their host

54. GIGANTEA is a component of a regulatory pathway determining wall ingrowth deposition in phloem parenchyma transfer cells of Arabidopsis thaliana

55. Gene Expression Atlas at the European Bioinformatics Institute

56. Genomics of metabolic adaptations in the peripartal cow

57. Histamine signalling in Schistosoma mansoni: Immunolocalisation and characterisation of a new histamine-responsive receptor (SmGPR-2)

58. Methodological framework for functional characterization of plant microRNAs

59. Proteome changes of lungs artificially infected with H-PRRSV and N-PRRSV by two-dimensional fluorescence difference gel electrophoresis

60. Seasonal effect on sperm messenger RNA profile of domestic swine (Sus Scrofa)

61. Systems genetics, bioinformatics and eQTL mapping

62. The tyrosyl-DNA phosphodiesterase gene family in Medicago truncatula Gaertn.: bioinformatic investigation and expression profiles in response to copper- and PEG-mediated stress

63. Toxicogenomics using yeast DNA microarrays

64. Transcription of LINE‐derived sequences in exercise‐induced stress in horses

65. 454 Genome Sequencing of Pseudoperonospora cubensis Reveals Effector Proteins with a QXLR Translocation Motif

66. A cross-species compendium of proteins/gene products related to cold stress identified by bioinformatic approaches

67. A novel gene with a vWD domain and three Kazal-type domains: Molecular cloning and expression in the ovary of the oriental river prawn, Macrobrachium nipponense

68. Application of Proteomic and Bioinformatic Techniques for Studying the Hepatoprotective Effect of Dioscin against CCl4-induced Liver Damage in Mice

69. Application of digital gene expression tag profiling on differential gene expression of two developmental stages in bulbs of Lycoris sprengeri

70. Bioinformatic characterization and gene expression pattern of apoptosis inhibitor from Macrobrachium rosenbergii challenged with infectious hypodermal and hematopoietic necrosis virus

2. Plant bZIP Gâbox binding factors.â: Modular structure and activation mechanisms