CyclinPred: a SVM-based method for predicting cyclin protein sequences

Functional annotation of protein sequences with low similarity to well characterized protein sequences is a major challenge of computational biology in the post genomic era. The cyclin protein family is once such important family of proteins which consists of sequences with low sequence similarity making discovery of novel cyclins and establishing orthologous relationships amongst the cyclins, a difficult task. The currently identified cyclin motifs and cyclin associated domains do not represent all of the identified and characterized cyclin sequences. We describe a Support Vector Machine (SVM) based classifier, CyclinPred, which can predict cyclin sequences with high efficiency. The SVM classifier was trained with features of selected cyclin and non cyclin protein sequences. The training features of the protein sequences include amino acid composition, dipeptide composition, secondary structure composition and PSI-BLAST generated Position Specific Scoring Matrix (PSSM) profiles. Results obtained from Leave-One-Out cross validation or jackknife test, self consistency and holdout tests prove that the SVM classifier trained with features of PSSM profile was more accurate than the classifiers based on either of the other features alone or hybrids of these features. A cyclin prediction server--CyclinPred has been setup based on SVM model trained with PSSM profiles. CyclinPred prediction results prove that the method may be used as a cyclin prediction tool, complementing conventional cyclin prediction methods.     

<Emphasis Type="Italic">Agrobacterium</Emphasis> mediated genetic transformation of summer squash (<Emphasis Type="Italic">Cucurbita pepo</Emphasis> L. cv. Australian green) with <Emphasis Type="Italic">cbf-1</Emphasis> using a two vector system

Efficient plant regeneration via shoot tip provided a basis for the optimization of the genetic transformation protocol. Therefore, experiments were conducted to establish an efficient in vitro regeneration protocol in summer squash for genetic co-transformation. 6-benzylaminopurine at 0.05 mg l^−l was found to be optimum concentration of direct regeneration from shoot tip. Effective root system was induced in shootlets in indole-3-aceticacid 0.5 mg l^−l. Two vectors namely pCAMBIA 2200 harboring marker gene nptII and pCAMBIA 0390 harboring gene, encoding C-repeat binding factor (cbf1) were used for co-transformation taking shoot tips as explants from in vitro germinated seeds. Explants were selected after co-cultivation on kanamycin supplemented medium and shoots and roots were induced. The transgenic plants were confirmed by polymerase chain reaction (PCR) and further southern blot analysis confirmed the integration of nptII and cbf1 genes in genome of summer squash with co-transformation efficiency of 0.7 percent.     

Mechanistic Heterogeneity in Contractile Properties of α-Tropomyosin (TPM1) Mutants Associated with Inherited Cardiomyopathies

The most frequent known causes of primary cardiomyopathies are mutations in the genes encoding sarcomeric proteins. Among those are 30 single-residue mutations in TPM1, the gene encoding α-tropomyosin. We examined seven mutant tropomyosins, E62Q, D84N, I172T, L185R, S215L, D230N, and M281T, that were chosen based on their clinical severity and locations along the molecule. The goal of our study was to determine how the biochemical characteristics of each of these mutant proteins are altered, which in turn could provide a structural rationale for treatment of the cardiomyopathies they produce. Measurements of Ca²⁺ sensitivity of human β-cardiac myosin ATPase activity are consistent with the hypothesis that hypertrophic cardiomyopathies are hypersensitive to Ca²⁺ activation, and dilated cardiomyopathies are hyposensitive. We also report correlations between ATPase activity at maximum Ca²⁺ concentrations and conformational changes in TnC measured using a fluorescent probe, which provide evidence that different substitutions perturb the structure of the regulatory complex in different ways. Moreover, we observed changes in protein stability and protein-protein interactions in these mutants. Our results suggest multiple mechanistic pathways to hypertrophic and dilated cardiomyopathies. Finally, we examined a computationally designed mutant, E181K, that is hypersensitive, confirming predictions derived from in silico structural analysis.     

Latent larval cuticular phenoloxidase in the coconut pest,Oryctes rhinoceros

Cuticular phenoloxidase (Tyrosinase) in the larval stage of the coconut pest Oryctes rhinoceros has been extracted in the stable proform using cane sugar saline/borate buffer. The extracted prophenol oxidase can be activated by the addition of proteolytic enzymes such as trypsin, chymotrypsin, thermolysin, and subtilisin. Detergents such as SDS and Tween-80 also activated the enzyme. Electrophoretical analysis revealed dissociation of the enzyme into two molecular forms after its activation by proteolytic enzymes. The functional significance of the enzyme is suggested to involve the generation of quinone compounds in the wound healing process: most phenoloxidase inhibitors prevented melanization when applied topically to surgical wounds. © 1996 Wiley-Liss, Inc.     

RNA interference: evolutions and applications in plant disease management

Plant diseases are significant threats to modern agriculture and their control remains a challenge to the management of cultivation. Therefore, plant disease management has always been one of the main objectives of any crop improvement programme. To reduce the losses caused by plant diseases, plant biologists have adopted numerous methods to engineer resistant plants. Among them, RNA silencing-based resistance has been a powerful tool that has been used to engineer resistant crops during the last two decades. Engineered plants in particular plants expressing RNA-silencing nucleotides are becoming increasingly important and are likely to provide more effective strategies in future. The advantage of RNAi as a novel gene therapy against fungal, viral and bacterial infection in plants lies in the fact that it regulates gene expression via mRNA degradation, translation repression and chromatin remodelling through small non-coding RNAs. Mechanistically, the silencing processes are guided by processing products of the dsRNA trigger, which are known as small interfering RNAs and microRNAs. The application of tissue-specific or inducible gene silencing, with the use of appropriate promoters to silence several genes simultaneously should enhance researchers’ ability to protect crops against diseases. This reviews a general discussion on the development of RNAi and role of RNAi in plant disease management.