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Identification and analysis of the germin-like gene family in soybean
Mo Lu, Ying-Peng Han, Ji-Guo Gao, Xiang-Jing Wang, Wen-Bin Li
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-620
Abstract: In the present study, twenty-one germin gene members in soybean cultivar 'Maple Arrow' (partial resistance to Sclerotinia stem rot of soybean) were identified by in silico identification and RACE method (GmGER 1 to GmGER 21). A genome-wide analyses of these germin-like protein genes using a bioinformatics approach showed that the genes located on chromosomes 8, 1, 15, 20, 16, 19, 7, 3 and 10, on which more disease-resistant genes were located on. Sequence comparison revealed that the genes encoded three germin-like domains. The phylogenetic relationships and functional diversity of the germin gene family of soybean were analyzed among diverse genera. The expression of the GmGER genes treated with exogenous IAA suggested that GmGER genes might be regulated by auxin. Transgenic tobacco that expressed the GmGER 9 gene exhibited high tolerance to the salt stress. In addition, the GmGER mRNA increased transiently at darkness and peaked at a time that corresponded approximately to the critical night length. The mRNA did not accumulate significantly under the constant light condition, and did not change greatly under the SD and LD treatments.This study provides a complex overview of the GmGER genes in soybean. Phylogenetic analysis suggested that the germin and germin-like genes of the plant species that had been founded might be evolved by independent gene duplication events. The experiment indicated that germin genes exhibited diverse expression patterns during soybean development. The different time courses of the mRNAs accumulation of GmGER genes in soybean leaves appeared to have a regular photoperiodic reaction in darkness. Also the GmGER genes were proved to response to abiotic stress (such as auxin and salt), suggesting that these paralogous genes were likely involved in complex biological processes in soybean.Germin is a protein marker that was first discovered in the germination of wheat seeds [1]. Subsequently, germin and germin-like proteins (GLPs) were found i
CLONING, SEQUENCING AND IN SILICO ANALYSIS OF GERMIN-LIKE PROTEIN GENE 1 PROMOTER FROM ORYZA SATIVA L. SSP. INDICA
TAYYABA YASMIN,TARIQ MAHMOOD,M. ZEESHAN HYDER,SAMINA AKBAR
Pakistan Journal of Botany , 2008,
Abstract: Germin and germin-like proteins constitute a large family of plant proteins which are also considered as germination markers due to their high expression levels during germination/early growth. These proteins are known to be involved in many stress related processes as well, but their biochemical functions and physiological roles have not been fully described. In order to gain insight into the functions and regulation of a rice germin-like protein gene 1, about 1.2 kb of its upstream region was amplified, cloned, sequenced and analyzed. Analysis showed that this promoter has a very little homology with the promoters of other GLP genes within rice genome. The promoter contains putative regulatory elements of diverse functions and has distinct copy number, location and clustering pattern of regulatory elements in its sequence. This promoter being unique requires further characterization to explore its regulatory role.
IN SILICO ANALYSIS OF SOME MICROBIAL AMIDASES FOR THEIR AMINO ACID AND PHYSIOCHEMICAL PARAMETERS  [cached]
Krishan Gopal,Nikhil Sharma,Tek Chand Bhalla
International Journal of Bioassays , 2013,
Abstract: Amino acid sequences of amidases were retrieved from respective databases and in silico analysis for different physiochemical properties and substrate specificity has been done. Multiple Sequence Alignment (MSA) and statistical analysis of amino acid sequences has revealed significant differences among aliphatic and signature amidases in terms of conserved motif that plays a vital role in substrate binding and catalytic function. MSA has revealed that aliphatic amidases the conserved amino acid residues involved in catalytic function are position specific which remains within catalytic traid of Cys-166, Glu-59, Lys-134, while signature amidase contains signature motif GGSS(S/G)GS and catalytic traid of Ser-171, Ser-195, Lys-96 which too are position specific. Statistical analysis has revealed that these two groups also differ in physiochemical properties. In contrast to aliphatic amidases, signature amidase have significantly higher number of amino acid residues & molecular mass, theoretical pI, charged (negative and positive) residues, aliphatic index and grand average of hydropathicity. Present investigation revealed that the amino acid residues i.e. Cys, Met, Tyr, Asn, Ile, Trp, Glu and Gly in aliphatic amidases while in case of signature amidases amino acids i.e Leu, Pro, Ser, Ala and Val has been found to play an important and significant role both in enzyme catalysis, substrate specificity as well as in structural stability.
Cu and Zn tolerance and responses of the Biochemical and Physiochemical system of Wheat  [PDF]
Kumar Vinod,G. Awasthi,P.K. Chauchan
Journal of Stress Physiology & Biochemistry , 2012,
Abstract: The concentrations of heavy metals such as Zinc and copper in the environment are currently increasing, due mainly to human activities. Zinc and copper are essential elements for several biochemical processes in plants. Any of these metals, at high concentrations in soil, can cause severe damage to physiological and biochemical activities of plants. Plant growth, pigment concentration, biochemical parameters, uptake of heavy metals were investigated in 30-days old wheat (Triticum aestivum L.) in response to Cu and Zn stress. The plant exhibited a decline in growth, chlorophyll content, protein and DNA, RNA content carbohydrate, but proline, total phenol and H2O2 content increased at high concentration of Cu and Zn.
In silico prediction of gene expression patterns in Citrus flavedo
Berger, Irving J.;Freitas-Astúa, Juliana;Reis, Marcelo S.;Targon, Maria Luísa P.N.;Machado, Marcos A.;
Genetics and Molecular Biology , 2007, DOI: 10.1590/S1415-47572007000500004
Abstract: out of the 18,942 flavedo expressed sequences (clusters plus singletons) in citrus sinensis from the citrus est project (citest), 25 were statistically supported to be differentially expressed in this tissue after a double in silico hybridization strategy against leaf-, flower-, and bark-derived ests. five of them, two terpene synthases and three o-methyltransferases, are absent in the other citrus tissues with concomitant 2x2 statistics, supporting the hypothesis that they are putative flavedo-specific expressed sequences. the pattern of these differentially expressed sequences during fruit development suggests that most of them are developmentally regulated. some expressed gene products, including a putative germin-like protein highly expressed in flavedo, are shown to be promising candidates for further characterization. in addition to promoter seeking, this kind of analysis can lead to gene discovery, tissue-specific and tissue-enriched expression pattern predictions (as shown herein) and can also be adopted as an in silico first, and probably reliable approach, for detecting expression profiles from est sequencing efforts before experimental validation is available or for heuristically guiding that validation.
Wheat Yield Dynamics: A Structural Econometric Analysis  [PDF]
Afsin Sahin,Yilmaz Akdi,Fahrettin Arslan
Pakistan Journal of Biological Sciences , 2007,
Abstract: In this study we initially have tried to explore the wheat situation in Turkey, which has a small-open economy and in the member countries of European Union (EU). We have observed that increasing the wheat yield is fundamental to obtain comparative advantage among countries by depressing domestic prices. Also the changing structure of supporting schemes in Turkey makes it necessary to increase its wheat yield level. For this purpose, we have used available data to determine the dynamics of wheat yield by Ordinary Least Square Regression methods. In order to find out whether there is a linear relationship among these series we have checked each series whether they are integrated at the same order or not. Consequently, we have pointed out that fertilizer usage and precipitation level are substantial inputs for producing high wheat yield. Furthermore, in respect for our model, fertilizer usage affects wheat yield more than precipitation level.
Structural Modeling and In Silico Analysis of Human Superoxide Dismutase 2  [PDF]
Mariana Dias Castela de Carvalho, Joelma Freire De Mesquita
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065558
Abstract: Aging in the world population has increased every year. Superoxide dismutase 2 (Mn-SOD or SOD2) protects against oxidative stress, a main factor influencing cellular longevity. Polymorphisms in SOD2 have been associated with the development of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease, as well as psychiatric disorders, such as schizophrenia, depression and bipolar disorder. In this study, all of the described natural variants (S10I, A16V, E66V, G76R, I82T and R156W) of SOD2 were subjected to in silico analysis using eight different algorithms: SNPeffect, PolyPhen-2, PhD-SNP, PMUT, SIFT, SNAP, SNPs&GO and nsSNPAnalyzer. This analysis revealed disparate results for a few of the algorithms. The results showed that, from at least one algorithm, each amino acid substitution appears to harmfully affect the protein. Structural theoretical models were created for variants through comparative modelling performed using the MHOLline server (which includes MODELLER and PROCHECK) and ab initio modelling, using the I-Tasser server. The predicted models were evaluated using TM-align, and the results show that the models were constructed with high accuracy. The RMSD values of the modelled mutants indicated likely pathogenicity for all missense mutations. Structural phylogenetic analysis using ConSurf revealed that human SOD2 is highly conserved. As a result, a human-curated database was generated that enables biologists and clinicians to explore SOD2 nsSNPs, including predictions of their effects and visualisation of the alignment of both the wild-type and mutant structures. The database is freely available at http://bioinfogroup.com/database and will be regularly updated.
Structural basis of wheat hardness and technological consequences
Abecassis J.,Chaurand M.,Autran J-C.
International Agrophysics , 1997,
Abstract: The concept of grain hardness still remains to be fully elucidated. It was often mistaken for vitreousness and even for strength of a flour. In fact, hardness essentially depends on genetic origine of wheats and is defined as the more or less friable characteristics of endosperm. Consequently, hardness strongly influences the milling behaviour of wheats as well as the yield in each milling fraction, although the yield in total flour is not associated with kernel hardness. By acting on the degree of disaggregation of particles, granulometry and starch damage, hardness primarily affects flour hydration, especially in low-hydration doughs. However, hardness does not influence flour strength, which remains mainly determined by the composition in storage proteins. Taking into account the world-wide market, it is highly recommended to include hardness in the system of wheat grading.
germin基因的克隆及其在烟草中的表达  [PDF]
王冰山,窦道龙,张猛,王志兴,贾士荣
农业生物技术学报 , 2003,
Abstract: ?:克隆了具有草酸氧化酶活性的小麦(triticumaestivum)germin蛋白的基因,构建了植物表达载体并用根癌农杆菌(agrobacteriumtumefaciens)介导法转化烟草。southern杂交和酶活性检测表明,germin基因在转基因烟草(nicotianatabacum)中得到整合、表达,并正确组合成具有草酸氧化酶活性的同源六聚体蛋白。离体实验表明,外源germin基因的表达提高了转基因烟草离体叶片对草酸的耐受性。
A Comprehensive in silico Analysis of Functional and Structural Impact SNPS in the MC1R Gene
Chuan-Sheng Zhang,Li-Ying Geng,Zheng-Zhu Liu,Zhi-Xin Fu,Yuan-Fang Gong,Min-Shan Feng,Chen Juan,Qing-Hui Jia,Qiu-Yue Wang,Xie-Rong Liu,Su-Min Pan
Journal of Animal and Veterinary Advances , 2012, DOI: 10.3923/javaa.2011.928.931
Abstract: The aim of this study was to analyze the genetic variation that can alter the expression and the function of the MC1R gene using computational methods. Out of the total 222 SNPs, 22 were found to be non-synonymous (ns) SNPs, 9 were found in the 5' upstream and 7 were found in the 3'UTR. It was found that these 6 nsSNPs rs3212366, rs11547464, rs1805009, rs1805008 and rs1805007 were damaging by both the SIFT and the Poly Phen servers. We identified, a mutation from Phe to Leu at positions 196 (rs3212366) on the surface of the protein caused the greatest impact on stability. The rs3212362, rs3212379 and rs35025176 in the 5' upstream were suggested might change the MC1R gene expression levels by FastSNP. Based on the in silico search, the rs3212369 located in the putative Hsa-miR-421 target sequences might have some effect on MC1R gene expression.
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