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Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.)
YouSheng Han,FuLei Luan,HongLiang Zhu,Yi Shao,AnJun Chen,ChengWen Lu,YunBo Luo,BenZhong Zhu
Science China Life Sciences , 2009, DOI: 10.1007/s11427-009-0144-y
Abstract: microRNAs (miRNAs) are a class of endogenous, non-coding, short (~21 nt) RNAs directly involved in regulating gene expression at the post-transcriptional level. Previous reports have noted that plant miRNAs in the plant kingdom are highly conserved, which provides the foundation for identification of conserved miRNAs in other plant species through homology alignment. Conserved miRNAs in wheat are identified using EST (Expressed Sequence Tags) and GSS analysis. All previously known miRNAs in other plant species were blasted against wheat EST and GSS sequences to select novel miRNAs in wheat by a series of filtering criteria. From a total of 37 conserved miRNAs belonging to 18 miRNA families 10 conserved miRNAs comprising 4 families were reported in wheat. MiR395 is found to be a special family, because three members belonging to the same miR395 family are clustered together, similar to animal miRNAs. MiRNA targets are transcription factors involved in wheat growth and development, metabolism,and stress responses.
Computational Identification of Conserved microRNAs and Their Targets in Tea (Camellia sinensis)  [PDF]
Akan Das, Tapan Kumar Mondal
American Journal of Plant Sciences (AJPS) , 2010, DOI: 10.4236/ajps.2010.12010
Abstract: MicroRNAs (miRNAs) are a class of ~22 nucleotides long non coding RNA molecules which play an important role in gene regulation at the post transcriptional level. The conserved nature of miRNAs provides the basis of new miRNA identification through homology search. In an attempt to identify new conserved miRNAs in tea, previously known plant miRNAs were used for searching their homolog in a tea Expressed Sequence Tags and full length nucleotide sequence database. The sequences showing homolog no more than four mismatches were predicted for their fold back structures and passed through a series of filtration criteria, finally led us to identify 13 conserved miRNAs in tea belonging to 9 miRNA families. A total of 37 potential target genes in Arabidopsis were identified subsequently for 7 miRNA families based on their sequence complementarity which encode transcription factors (8%), enzymes (30%) and transporters (14%) as well as other proteins involved in physiological and metabolic processes (48%). Overall, our findings will accelerate the way for further researches of miRNAs and their functions in tea.
Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets
Virginie Gébelin, Xavier Argout, Worrawat Engchuan, Bertrand Pitollat, Cuifang Duan, Pascal Montoro, Julie Leclercq
BMC Plant Biology , 2012, DOI: 10.1186/1471-2229-12-18
Abstract: Deep sequencing of small RNAs was carried out on plantlets subjected to severe abiotic stress using the Solexa technique. By combining the LeARN pipeline, data from the Plant microRNA database (PMRD) and Hevea EST sequences, we identified 48 conserved miRNA families already characterized in other plant species, and 10 putatively novel miRNA families. The results showed the most abundant size for miRNAs to be 24 nucleotides, except for seven families. Several MIR genes produced both 20-22 nucleotides and 23-27 nucleotides. The two miRNA class sizes were detected for both conserved and putative novel miRNA families, suggesting their functional duality. The EST databases were scanned with conserved and novel miRNA sequences. MiRNA targets were computationally predicted and analysed. The predicted targets involved in "responses to stimuli" and to "antioxidant" and "transcription activities" are presented.Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs when the complete genome is not yet available. Our study provided additional information for evolutionary studies and revealed potentially specific regulation of the control of redox status in Hevea.Hevea brasiliensis, the sole commercial source of natural rubber, is a tropical perennial species native to the Amazon basin. South-East Asian countries supplied 92% of the 10 million tons of natural rubber produced in 2010, but ever-growing worldwide demand calls for enhanced tree productivity. This goal is increasingly becoming a crucial challenge for the corresponding research activities in a context of global climate change and redistribution of land for food crops. Natural rubber is a cis-1,4 polyisoprene polymer biosynthesized in rubber particles located in specialized latex cells. Latex cells are periodically emitted from the cambium and then anastomosed to form latificer mantels [1]. Natural rubber is harvested by tapping. The cytoplasm of lat
Computational Identification of microRNAs and Their Targets

GUO Zhi-yun,MAO Can-quan,XIONG Li-li,

中国生物工程杂志 , 2008,
Abstract: The discovery of microRNAs (miRNAs) has introduced a new paradigm into gene regulatory systems. Since inception, computational methods have been an invaluable tool complementing experimental approaches, and many discoveries have been obtained through combination of experimental and computational approaches. In this review, we summarize the knowledge that has been accumulated about the principles of miRNAs and target recognition. The currently available computational methodologies and software for prediction of miRNA and their target genes also have been discussed.
A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.)
Moreno Colaiacovo, Annalisa Subacchi, Paolo Bagnaresi, Antonella Lamontanara, Luigi Cattivelli, Primetta Faccioli
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-595
Abstract: One hundred-fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley. As expected on the basis of phylogenetic relations, miRNAs putatively orthologous to those of Triticum are significantly over-represented inside the set of identified barley microRNA mature sequences. Many previously known and several putatively new miRNA/target pairs have been identified. When the predicted microRNA targets were grouped into functional categories, biological processes previously known to be regulated by miRNAs, such as development and response to biotic and abiotic stress, have been highlighted and most of the target molecular functions were related to transcription regulation. Candidate microRNA coding genes have been reported and genetic variation (SNPs/indels) both in functional regions of putative miRNAs (mature sequence) and at miRNA target sites has been found.This study has provided an update of the information on barley miRNAs and their targets representing a foundation for future studies. Many of previously known plant microRNAs have homologues in barley with expected important roles during development, nutrient deprivation, biotic and abiotic stress response and other important physiological processes. Putative polymorphisms at miRNA target sites have been identified and they can represent an interesting source for the identification of functional genetic variability.MicroRNAs (miRNAs) are a class of non-coding small RNAs with fundamental roles in key plant biological processes such as development, signal transduction and environmental stress response [1]. miRNAs act on gene regulation at post-transcriptional level, a phenomenon known in plants as PTGS (Post Transcriptional Gene Silencing), through sequence-based interaction with target mRNAs.Many plant species have been investigated during recent years for miRNAs identification and characterization. The current information available on
Maisale A B,Patil M B,Jalalpure S S,Patil A M
Journal of Pharmaceutical and Scientific Innovation , 2012,
Abstract: Vigna unguiculata Linn belonging to family Fabaceae are used traditionally as appetizer, diuretic, laxative, anthelmintic. Seeds are coarse powdered and exhaustively with hot solvent (Soxhlet) extraction by ethanol and maceration with chloroform water I.P. Five concentrations (10-100 mg/ml) of ethanolic and aqueous extracts were studied for anthelmentic activity by using Eudrilus euginiae earthworms. Both aqueous and ethanolic extracts showed paralysis and death of worms in concentration (10-100 mg/ml) dependent manner. Alcoholic extract of Vigna unguiculata showed significant activity than aqueous extract. Piperazine citrate (10 mg/ml) and distilled water were included in the assay as standard drug and control respectively. The result showed seeds of vigna unguiculata possessed potential anthelmintic activity. The seeds extract also showed presence of flavonoids, and glycosides by preliminary phytochemical investigations.
Computational prediction of MicroRNAs targeting GABA receptors and experimental verification of miR-181, miR-216 and miR-203 targets in GABA-A receptor
Chunling Zhao, Chaoqun Huang, Tingting Weng, Xiao Xiao, Hong Ma, Lin Liu
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-91
Abstract: In this study, we used the online software, TargetScan and miRanda, to query the microRNAs that directly target GABA receptors and then selected some of them to verify experimentally using 3'-UTR reporter assays. Computational approaches predict many microRNA binding sites on the 3'-UTR of GABAA receptors, but not on GABAC receptors. 3'-UTR reporter assays only verified miR-181, miR-216, and miR-203 as the microRNAs that target GABA receptor α1-subunit among 10 microRNAs tested.Our studies reinforce that microRNA target prediction needs to be verified experimentally. The identification of microRNAs that target GABA receptors provides a basis for further studies of post-transcriptional regulation of GABA receptors.GABA receptors are well known as the inhibitory receptors in the central nervous system [1,2]. However, GABA receptors are also found in several peripheral tissues [3-6]. The functions of GABA receptors in peripheral tissues are less studied. They may be involved in ion homeostasis [7], cell proliferation and differentiation [8], development [1], and hormone secretion [5,9].We have initially identified GABA receptor π-subunit as a specific alveolar epithelial type II cell marker through DNA microarray analysis [10]. The expression pattern of the GABA receptor π-subunit is regulated by various culture conditions and is consistent with the type II cell phenotypes [11]. We have further identified 19 subunits of the ionotropic GABA receptors in alveolar epithelial cells [6]. Their expression is dynamically changed during lung development [12]. Functionally, GABA receptors play important roles in fluid homeostasis in the adult lung and fetal lung development [6,13].GABA receptors can be classified into two major types: GABAA and GABAC as ligand-gated Cl- channels, and GABAB receptor as a metabotropic receptor coupled to a heterotrimeric G-protein. GABAA and GABAC receptors share a conserved structure that contains a long extracellular N-terminal region, 4 transm
Induced mutations in cowpea, Vigna unguiculata (Leguminosae)
Odeigah,P.G.C.; Osanyinpeju,A.O.; Myers,G.O.;
Revista de Biología Tropical , 1998,
Abstract: two cowpea (vigna unguiculata l. walp) varieties, it84e-124 and vita 7 of the international institute of tropical agriculture, ibadan, were exposed to varying doses of chemical and physical mutagens. optimum doses of 10mm ems for 6hr and 0.1mm and 1.0mm nan3 for 2hr, determined from seeding growth tests and 100r and 200r gamma radiations were applied to 2000 seed samples of each genotype. screening of the m2 generation revealed that the mutagenic treatments induced morphological, physiological and biochemical changes in the genotypes. a spectrum of mutations which included variants with respect to anthocyanin pigmentation, leaf morphology, maturity date, male sterility and insect pest resistance qualities were observed. lines with significant increases in yield parameters such as number of seeds per pod, peduncles per plant, 100 seed weight and seed storage proteins were selected.
Induced mutations in cowpea, Vigna unguiculata (Leguminosae)
P.G.C. Odeigah,A.O. Osanyinpeju,G.O. Myers
Revista de Biología Tropical , 1998,
Abstract: Two cowpea (Vigna unguiculata L. Walp) varieties, IT84E-124 and Vita 7 of the International Institute of Tropical Agriculture, Ibadan, were exposed to varying doses of chemical and physical mutagens. Optimum doses of 10mM EMS for 6hr and 0.1mM and 1.0mM NaN3 for 2hr, determined from seeding growth tests and 100R and 200R gamma radiations were applied to 2000 seed samples of each genotype. Screening of the M2 generation revealed that the mutagenic treatments induced morphological, physiological and biochemical changes in the genotypes. A spectrum of mutations which included variants with respect to anthocyanin pigmentation, leaf morphology, maturity date, male sterility and insect pest resistance qualities were observed. Lines with significant increases in yield parameters such as number of seeds per pod, peduncles per plant, 100 seed weight and seed storage proteins were selected.
Salt Stress responses on Protein Profile in Vigna unguiculata L.  [PDF]
Johnson M,Dooslin Mary D,Babu A
Journal of Stress Physiology & Biochemistry , 2011,
Abstract: The present study was aimed to elucidate the salt tolerant, salt inducible and salt sensitive protein of the Vigna unguiculata by Sodium Deodyl Sulphate – Poly Acrylamide Gel Electrophoresis. Seedlings of Vigna unguiculata exposed to different environmental conditions exhibited a plethora of physio-chemical responses. The seedlings treated with various concentrations of NaCl at third day showed maximum of 85 bands, with nine active regions and their MW-Rf values ranged from 0.012 to 0.891. The seedlings treated with same experimental set up at fifth day showed maximum number of 63 bands with eight active regions and their MW-Rf values ranged from 0.108 to 0.891. On 5th day seedlings showed the isoperoxidase expression with various sizes of bands. The soluble protein showed a gradual increase during the initial stage and after fifth day there was gradual decrease in their content.
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