Structural Modeling and Validation of Rep protein of Begomovirus Strains (TLCBV and TYLCTHV)

Homology modeling involves taking a known sequence with an unknown structure and mapping it against a known structure of one or several similar (homologous) proteins. It would be expected that two proteins of similar origin and function would have reasonable structural similarity. Therefore it is possible to use the known structure as a template for modeling the structure of the unknown structure. Proteins that share the same function generally have similar structures. During alignment if two proteins show maximum sequence identity they also show a similar folding pattern. This principal has became the foundation of homology modeling. 
The Geminivirus taxonomic group of plant viruses is characterized by geminate particles and genomes consisting of single-stranded circular DNA molecules of about 2.5 to 2.8 kb in size. Agricultural plants are threatened by many diseases caused by whitefly-transmitted geminiviruses. Since these diseases are in a fast spreading phase, it is urgent to devise rapid diagnosis methods and to produce resistant plants. 
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In Silico Characterization of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A Proteins

We retrieved six protein sequences of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A [FJ345402] from GenBank-NCBI (ACJ03821, ACJ03822, ACJ03823, ACJ03824, ACJ03825 and ACJ03826) which were used for computational modeling structure prediction. Ramachandran plot of ACJ03826-AC4 had maximum 73.3% and ACJ03822-AV1 had 71% residues in core region therefore these models cannot be placed in a good quality category. ACJ03824-AC2 had only 18.6% residues in core and 13.6% residues in disallowed regions and therefore it was the least stable protein. Verify-3D graph profile scores for selected ToLCJV proteins were greater than zero. Therefore all the verify-3D graph corresponds to an acceptable environment for the model. Findings of the present study provide a base for docking and In-Silico anti-Begomoviral compound designing

Compensatory Phenolic Induction Dynamics in Aspen After Aphid Infestation

Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage

A comprehensive appraisal of mechanism of anti-CRISPR proteins: an advanced genome editor to amend the CRISPR gene editing

The development of precise and controlled CRISPR-Cas tools has been made possible by the discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs). The Acr protein has the ability to control off-targeted mutations and impede Cas protein–editing operations. Acr can help with selective breeding, which could help plants and animals improve their valuable features. In this review, the Acr protein–based inhibitory mechanisms that have been adopted by several Acrs, such as (a) the interruption of CRISPR-Cas complex assembly, (b) interference with target DNA binding, (c) blocking of target DNA/RNA cleavage, and (d) enzymatic modification or degradation of signalling molecules, were discussed. In addition, this review emphasizes the applications of Acr proteins in the plant research

Plant Viruses, Volume I : Detection Methods, Genetic Diversity, and Evolution

Non peer reviewe

Recursive Partitioning to Prioritize Morphometric Traits that Separate Aspen Specialist Chaitophorus Aphid by Species and Stage

Arthropod herbivore assemblages are used to gain insight into questions about evolution, ecology, diversity, and conservation. However, determination at the species level of small arthropods may be challenging risking underestimating diversity. Here we suggest morphometric analyses as a supplementary determination method, and we demonstrate its use for a study of Chaitophorus species collected from Aspen trees (Populus tremula). Although sampled as one colony, the aphids represented three species. Rearing the species separately allowed us to get estimates characteristic of the developmental stages from each of the three species for morphometric comparisons. Recursive partitioning (RP) was used to create a decision tree for choice of morphometric parameters that with significance (p \u3c 0.05) could determine the aphids by species and developmental stage; this insight could then be used as a key for determination. Eight of fifteen morphometric traits were selected by RP to be used in the key. Body length was responsible for nine splits and was consequently the more consistent morphometric trait used in the key