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1. Aldehyde dehydrogenase protein superfamily in maize

Author:
Zhou, Mei-Liang; Zhang, Qian; Zhou, Ming; Qi, Lei-Peng; Yang, Xiong-Bang; Zhang, Kai-Xuan; Pang, Jun-Feng; Zhu, Xue-Mei; Shao, Ji-Rong; Tang, Yi-Xiong; Wu, Yan-Min
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 683-691
ISSN:
1438-793X
Subject:
Arabidopsis; NAD (coenzyme); Zea mays subsp. mays; acid tolerance; agricultural biotechnology; aldehyde dehydrogenase; aldehydes; amino acid sequences; cold; corn; databases; genes; genetic improvement; heat stress; metabolism; microarray technology; pathogens; phylogeny; quantitative polymerase chain reaction; rice; salinity; water stress
Abstract:
... Maize (Zea mays ssp. mays L.) is an important model organism for fundamental research in the agro-biotechnology field. Aldehydes were generated in response to a suite of environmental stresses that perturb metabolism including salinity, dehydration, desiccation, and cold and heat shock. Many biologically important aldehydes are metabolized by the superfamily of NAD(P)⁺-dependent aldehyde dehydroge ...
DOI:
10.1007/s10142-012-0290-3
PubMed:
22983498

2. Co-expression of soybean Dicer-like genes in response to stress and development

Author:
Curtin, Shaun J.; Kantar, Michael B.; Yoon, Han W.; Whaley, Adam M.; Schlueter, Jessica A.; Stupar, Robert M.
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 671-682
ISSN:
1438-793X
Subject:
DNA methylation; RNA interference; abiotic stress; genes; microRNA; quantitative polymerase chain reaction; soybeans; stress response; transcription (genetics)
Abstract:
... Regulation of gene transcription and post-transcriptional processes is critical for proper development, genome integrity, and stress responses in plants. Many genes involved in the key processes of transcriptional and post-transcriptional regulation have been well studied in model diploid organisms. However, gene and genome duplication may alter the function of the genes involved in these processe ...
DOI:
10.1007/s10142-012-0278-z
PubMed:
22527487

3. Comparative genomic analysis of eutherian interferon-γ-inducible GTPases

Author:
Premzl, Marko
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 599-607
ISSN:
1438-793X
Subject:
genes; genomics; guanosinetriphosphatase; immune response; phylogeny; proteins
Abstract:
... The interferon-γ-inducible GTPases, IFGGs, are intracellular proteins involved in immune response against pathogens. A comprehensive comparative genomic review and analysis of eutherian IFGGs was carried out using public genomic sequences. The 64 eutherian IFGG genes were examined in detail and annotated. The eutherian IFGG promoter types were first catalogued followed by a phylogenetic analysis o ...
DOI:
10.1007/s10142-012-0291-2
PubMed:
22892676

4. Genome-wide identification of rice class I metallothionein gene: tissue expression patterns and induction in response to heavy metal stress

Author:
Gautam, Neelam; Verma, Pankaj Kumar; Verma, Shikha; Tripathi, Rudra Deo; Trivedi, Prabodh Kumar; Adhikari, Bijan; Chakrabarty, Debasis
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 635-647
ISSN:
1438-793X
Subject:
abiotic stress; alternative splicing; amino acid sequences; arsenic; cultivars; genes; growth and development; heavy metals; homeostasis; metal ions; metallothionein; molecular weight; polypeptides; rice; transcription (genetics)
Abstract:
... Metallothioneins (MTs) are members of a family of cysteine-rich low molecular weight polypeptides which play an important role in heavy metal detoxification and homeostasis of intracellular metal ions in plant. Though MT genes from some selected plants have been characterized with respect to their protein sequences, kinetic properties and tissue-specific localization, no detailed study has been ca ...
DOI:
10.1007/s10142-012-0297-9
PubMed:
23053198

5. Identification of novel members reveals the structural and functional divergence of lepidopteran-specific Lipoprotein_11 family

Author:
Zhang, Yan; Dong, Zhaoming; Liu, Shiping; Yang, Qiang; Zhao, Ping; Xia, Qingyou
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 705-715
ISSN:
1438-793X
Subject:
pupae; silkworms; phylogeny; Pseudomonas putida; Manduca sexta; data collection; cytokines; binding proteins; fat body; testes; embryogenesis; energy; immune response; larvae; integument; microarray technology; surveys; expressed sequence tags; reverse transcriptase polymerase chain reaction; Bombyx mori
Abstract:
... 30K proteins (30KPs) are classified into the lepidopteran-specific Lipoprotein_11 family. They are involved in various physiological processes such as energy storage, embryonic development, and immune response in the silkworm. To date, 30KPs were only found in Bombyx mori and Manduca sexta. Moreover, the C-termini of ENF peptide binding proteins (ENF-BPs) show similarity to 30KPs. ENF peptides are ...
DOI:
10.1007/s10142-012-0281-4
PubMed:
22534768

6. Increased resistance to late leaf spot disease in transgenic peanut using a combination of PR genes

Author:
Vasavirama, K.; Kirti, P. B.
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 625-634
ISSN:
1438-793X
Subject:
Arachis hypogaea; Cercospora; Phaeoisariopsis; Raphanus sativus; Solanum nigrum; Southern blotting; antifungal proteins; disease resistance; genes; genetic engineering; genetic resistance; genetically modified organisms; leaf spot; leaves; oilseed crops; pathogens; peanuts; plant proteins; reverse transcriptase polymerase chain reaction
Abstract:
... Peanut (Arachis hypogaea L.) is the sixth most important oil seed crop in the world. Yield loss due to Cercospora leaf spot (early and late leaf spots) is a serious problem in cultivating this crop. Non-availability of resistant genes within crossable germplasms of peanut necessitates the use of a genetic engineering strategy to develop genetic resistance against various biotic stresses. The patho ...
DOI:
10.1007/s10142-012-0298-8
PubMed:
23053199

7. Integrating cereal genomics to support innovation in the Triticeae

Author:
Feuillet, C.; Stein, N.; Rossini, L.; Praud, S.; Mayer, K.; Schulman, A.; Eversole, K.; Appels, R.
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 573-583
ISSN:
1438-793X
Subject:
barley; crops; genomics; rye; wheat
Abstract:
... The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain ref ...
DOI:
10.1007/s10142-012-0300-5
PubMed:
23161406
PubMed Central:
PMC3508266

8. Labellum transcriptome reveals alkene biosynthetic genes involved in orchid sexual deception and pollination-induced senescence

Author:
Monteiro, Filipa; Sebastiana, Mónica; Figueiredo, Andreia; Sousa, Lisete; Cotrim, Helena C.; Pais, Maria Salomé
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 693-703
ISSN:
1438-793X
Subject:
protein synthesis; sex pheromones; pollinators; trichomes; gene expression; genes; color; transcriptome; nutrients; pollination; Ophrys; odors
Abstract:
... One of the most remarkable pollination strategy in orchids biology is pollination by sexual deception, in which the modified petal labellum lures pollinators by mimicking the chemical (e.g. sex pheromones), visual (e.g. colour and shape/size) and tactile (e.g. labellum trichomes) cues of the receptive female insect species. The present study aimed to characterize the transcriptional changes occurr ...
DOI:
10.1007/s10142-012-0288-x
PubMed:
22706647

9. Novel miRNAs in the control of arsenite levels in rice

Author:
Liu, Qingpo
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 649-658
ISSN:
1438-793X
Subject:
DNA; arsenites; exons; gene expression; high-throughput nucleotide sequencing; leaves; microRNA; plant adaptation; promoter regions; protein kinases; proteins; reverse transcriptase polymerase chain reaction; rice; roots; seedlings; stress response; transcriptome
Abstract:
... In a species, the miRNA repertoire comprises many lineage- or species-specific miRNAs. Using deep sequencing, the whole transcriptome of seedling roots was studied and a total of 18 novel miRNAs in indica rice Minghui 86 were identified. Among these novel miRNAs six were up-regulated and two were down-regulated under arsenite stress. Quantitative real-time RT-PCR analysis revealed that miR6254 was ...
DOI:
10.1007/s10142-012-0282-3
PubMed:
22585409

10. Small RNA profiling of virus-infected grapevines: evidences for virus infection-associated and variety-specific miRNAs

Author:
Singh, Kashmir; Talla, Aarthi; Qiu, Wenping
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 659-669
ISSN:
1438-793X
Subject:
Badnavirus; DNA viruses; Vitis; cDNA libraries; cell division; complementary DNA; double-stranded RNA; fruit crops; gene expression regulation; genes; growth and development; microRNA; plant development; small interfering RNA; transcription (genetics); transcription factors; virus replication; viruses
Abstract:
... Grapevine is one of the economically and culturally important perennial fruit crops. More than 60 viruses infect grapevines and adversely affect their growth and development. Latent infection of most viruses in grapevines leads to chronic modulation of gene expression at transcriptional and post-transcriptional levels. Plant small RNAs (sRNAs) consist of microRNA (miRNA) and small interfering RNA ...
DOI:
10.1007/s10142-012-0292-1
PubMed:
22903235

11. The epitopes in wheat proteins for defining toxic units relevant to human health

Author:
Juhász, Angéla; Gell, Gyöngyvér; Békés, Frank; Balázs, Ervin
Source:
Functional & integrative genomics 2012 v.12 no.4 pp. 585-598
ISSN:
1438-793X
Subject:
cultivars; data collection; databases; epitopes; food industry; human health; nucleotide sequences; prediction; protein synthesis; proteins; toxicity; wheat; wheat flour
Abstract:
... Wheat-related disorders are well-studied health problems. Knowledge of the composition and amounts of epitopes present in a single wheat sample represents a significant gap, and the detailed wheat proteome datasets now available can provide the necessary information to carry out an estimation of allergen prediction for a single cultivar. The combined use of genome sequence and allergen databases, ...
DOI:
10.1007/s10142-012-0302-3
PubMed:
23179564

12. A shared response of thaumatin like protein, chitinase, and late embryogenesis abundant protein3 to environmental stresses in tea [Camellia sinensis (L.) O. Kuntze]

Author:
Muoki, Richard Chalo; Paul, Asosii; Kumar, Sanjay
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 565-571
ISSN:
1438-793X
Subject:
Camellia sinensis; beverages; cDNA libraries; chitinase; complementary DNA; drought; embryogenesis; gene expression; genes; heat; salt stress; tea; trees; water stress
Abstract:
... Drought poses a significant threat to tree plants including tea [Camellia sinensis (L.) O. Kuntze] that yields a popular beverage “tea.” Consequence of drought is heat and salt stress, for which data on molecular response in tree species are not available. The present work analyzed drought-responsive subtracted cDNA libraries of tea to identify drought-responsive genes. Temporal and spatial gene e ...
DOI:
10.1007/s10142-012-0279-y
PubMed:
22543414

13. Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense)

Author:
Anderson, James V.; Doğramacı, Münevver; Horvath, David P.; Foley, Michael E.; Chao, Wun S.; Suttle, Jeffrey C.; Thimmapuram, Jyothi; Hernandez, Alvaro G.; Ali, Shahjahan; Mikel, Mark A.
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 515-531
ISSN:
1438-793X
Subject:
Arabidopsis; Cirsium arvense; RNA; abscisic acid; auxins; biosynthesis; buds; cDNA libraries; cell division; complementary DNA; control methods; cytokinins; databases; dormancy; expressed sequence tags; gibberellic acid; greenhouses; hormones; metabolites; models; perennial weeds; roots; sequence analysis; shoots; transcriptome; unigenes
Abstract:
... Dormancy in underground vegetative buds of Canada thistle, an herbaceous perennial weed, allows escape from current control methods and contributes to its invasive nature. In this study, ∼65 % of root sections obtained from greenhouse propagated Canada thistle produced new vegetative shoots by 14 days post-sectioning. RNA samples obtained from sectioned roots incubated 0, 24, 48, and 72 h at 25°C ...
DOI:
10.1007/s10142-012-0280-5
PubMed:
22580957

14. Brachypodium distachyon as a model for defining the allergen potential of non-prolamin proteins

Author:
Juhász, A.; Gell, Gy; Sebestyén, E.; Haraszi, R.; Tamás, L.; Balázs, E.
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 439-446
ISSN:
1438-793X
Subject:
Brachypodium distachyon; allergens; amino acid sequences; barley; celiac disease; databases; diploidy; epitopes; food allergies; genes; grasses; models; nucleotide sequences; proteinases; proteins; wheat
Abstract:
... Epitope databases and the protein sequences of published plant genomes are suitable to identify some of the proteins causing food allergies and sensitivities. Brachypodium distachyon, a diploid wild grass with a sequenced genome and low prolamin content, is the closest relative of the allergen cereals, such as wheat or barley. Using the Brachypodium genome sequence, a workflow has been developed t ...
DOI:
10.1007/s10142-012-0294-z
PubMed:
22933233
PubMed Central:
PMC3431475

15. Chromosomes in the flow to simplify genome analysis

Author:
Doležel, Jaroslav; Vrána, Jan; Šafář, Jan; Bartoš, Jan; Kubaláková, Marie; Šimková, Hana
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 397-416
ISSN:
1438-793X
Subject:
DNA; animals; chromosome number; chromosomes; flow cytometry; fluorescence; fluorescence in situ hybridization; karyotyping; nuclear genome; nucleotide sequences; proteins; sequence analysis; ultrastructure; wheat
Abstract:
... Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carr ...
DOI:
10.1007/s10142-012-0293-0
PubMed:
22895700
PubMed Central:
PMC3431466

16. Genomic associations for drought tolerance on the short arm of wheat chromosome 4B

Author:
Kadam, Suhas; Singh, Kalpana; Shukla, Sanyukta; Goel, Sonia; Vikram, Prashant; Pawar, Vasantrao; Gaikwad, Kishor; Khanna-Chopra, Renu; Singh, Nagendra
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 447-464
ISSN:
1438-793X
Subject:
barley; biomass; chromosome mapping; chromosomes; corn; drought; drought tolerance; gene expression regulation; genes; genetic improvement; genetic markers; grain yield; harvest index; inbred lines; irrigation; marker-assisted selection; parents; phenotype; rain; rice; shoots; transcriptomics; water stress; wheat
Abstract:
... Drought is a major constraint to maintaining yield stability of wheat in rain fed and limited irrigation agro-ecosystems. Genetic improvement for drought tolerance in wheat has been difficult due to quantitative nature of the trait involving multiple genes with variable effects and lack of effective selection strategies employing molecular markers. Here, a framework molecular linkage map was const ...
DOI:
10.1007/s10142-012-0276-1
PubMed:
22476619

17. Identification of drought tolerant progenies in tea by gene expression analysis

Author:
Gupta, Sushmita; Bharalee, Raju; Bhorali, Priyadarshini; Bandyopadhyay, Tirthankar; Gohain, Bornali; Agarwal, Niraj; Ahmed, Parveen; Saikia, Hemanta; Borchetia, Sangeeta; Kalita, M. C.; Handique, A. K.; Das, Sudripta
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 543-563
ISSN:
1438-793X
Subject:
Camellia sinensis; abscisic acid; aminocyclopropanecarboxylate oxidase; breeding; calmodulin; drought; drought tolerance; ethylene; gene expression; genes; glutathione peroxidase; hydrogen peroxide; tea; transcription factors; triacylglycerol lipase; water stress; water use efficiency; wilting; wilting point
Abstract:
... Understanding the genes that govern tea plant (Camellia sinensis) architecture and response to drought stress is urgently needed to enhance breeding in tea with improved water use efficiency. Field drought is a slow mechanism and the plants go through an adaptive process in contrast to the drastic changes of rapid dehydration in case of controlled experiments. We identified a set of drought respon ...
DOI:
10.1007/s10142-012-0277-0
PubMed:
22562548

18. New cis-regulatory elements in the Rht-D1b locus region of wheat

Author:
Duan, Jialei; Wu, Jiajie; Liu, Yue; Xiao, Jianhui; Zhao, Guangyao; Gu, Yongqiang; Jia, Jizeng; Kong, Xiuying
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 489-500
ISSN:
1438-793X
Subject:
bacterial artificial chromosomes; corn; genes; loci; nucleotide sequences; rice; sequence analysis; wheat
Abstract:
... Fifteen gene-containing BACs with accumulated length of 1.82-Mb from the Rht-D1b locus region were sequenced and compared in detail with the orthologous regions of rice, sorghum, and maize. Our results show that Rht-D1b represents a conserved genomic region as implied by high gene sequence identity, good maintenance of gene colinearity, and the presence of multiple conserved noncoding sequences (C ...
DOI:
10.1007/s10142-012-0283-2
PubMed:
22592657

19. Novel role of NADPH oxidase in ischemic myocardium: a study with Nox2 knockout mice

Author:
Thirunavukkarasu, Mahesh; Adluri, Ram Sudheer; Juhasz, Bela; Samuel, Samson Mathews; Zhan, Lijun; Kaur, Anupinder; Maulik, Gautam; Sanchez, Juan A; Hager, Janet; Maulik, Nilanjana
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 501-514
ISSN:
1438-793X
Subject:
NADP (coenzyme); gene expression; gene expression regulation; genes; mice; microarray technology; myocardium; quantitative polymerase chain reaction; reactive oxygen species
Abstract:
... Several potential sources of reactive oxygen species (ROS) in cells exist. One source is NADPH oxidase, which is especially important for superoxide radical production. Nox2 is a primary regulatory subunit of NADPH oxidase. In the present study, we examined the role of ROS and NADPH oxidase in ischemic preconditioning (IP)-mediated cardioprotection by using Nox2−/− mice. Both wild-type (WT) and No ...
DOI:
10.1007/s10142-011-0256-x
PubMed:
22038056

20. Overexpression of wheat lipid transfer protein gene TaLTP5 increases resistances to Cochliobolus sativus and Fusarium graminearum in transgenic wheat

Author:
Zhu, Xiuliang; Li, Zhao; Xu, Huijun; Zhou, Miaoping; Du, Lipu; Zhang, Zengyan
Source:
Functional & integrative genomics 2012 v.12 no.3 pp. 481-488
ISSN:
1438-793X
Subject:
Southern blotting; Fusarium graminearum; gene overexpression; reverse transcriptase polymerase chain reaction; wheat; fungi; Triticum aestivum; genes; Fusarium head blight; root rot; pathogens; Bipolaris sorokiniana
Abstract:
... The fungus Cochliobolus sativus is the main pathogen of common root rot, a serious soil-borne disease of wheat (Triticum aestivum L.). The fungus Fusarium graminearum is the primary pathogen of Fusarium head blight, a devastating disease of wheat worldwide. In this study, the wheat lipid transfer protein gene, TaLTP5, was cloned and evaluated for its ability to suppress disease development in tran ...
DOI:
10.1007/s10142-012-0286-z
PubMed:
22689341