Entropy-driven global best selection in particle swarm optimization for many-objective software package restructuring

Many real-world optimization problems usually require a large number of conflicting objectives to be optimized simultaneously to obtain solution. It has been observed that these kinds of many-objective optimization problems (MaOPs) often pose several performance challenges to the traditional multi-objective optimization algorithms. To address the performance issue caused by the different types of MaOPs, recently, a variety of many-objective particle swarm optimization (MaOPSO) has been proposed. However, external archive maintenance and selection of leaders for designing the MaOPSO to real-world MaOPs are still challenging issues. This work presents a MaOPSO based on entropy-driven global best selection strategy (called EMPSO) to solve the many-objective software package restructuring (MaOSPR) problem. EMPSO makes use of the entropy and quality indicator for the selection of global best particle. To evaluate the performance of the proposed approach, we applied it over the five MaOSPR problems. We compared it with eight variants of MaOPSO, which are based on eight different global best selection strategies. The results indicate that the proposed EMPSO is competitive with respect to the existing global best selection strategies based on variants of MaOPSO approaches.publishedVersio

PP2C-like Promoter and Its Deletion Variants Are Induced by ABA but Not by MeJA and SA in Arabidopsis thaliana

Gene expression is mediated through interaction between cis regulatory elements and its cognate transcription factors. Cis regulatory elements are defined as non-coding DNA sequences that provide the binding sites for transcription factors and are clustered in the upstream region of genes. ACGT cis regulatory element is one of the important cis regulatory elements found to be involved in diverse biological processes like auxin response, salicylic acid response, UV light response, ABA response and jasmonic acid response .We identified through in silico analysis that the upstream region of protein phosphatase 2C (PP2C) gene has a distinct genetic architecture of ACGT elements. In the present study, the activation of the full length promoter and its deletion constructs like 900 base pair, 500 base pair, 400 base pair and NRM were examined by stable transformation in Arabidopsis thaliana using β glucuronidase as the reporter gene. Evaluation of deletion constructs of PP2C- like promoter was carried out in the presence of phytohormones like abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA). Our result indicated that the full length and 900 base pair promoter-reporter constructs of PP2C-like promoter was induced in response to ABA but not to methyl jasmonate and salicylic acid

Synergistic Enzyme Cocktail to Enhance Hydrolysis of Steam Exploded Wheat Straw at Pilot Scale

Multiple enzymes are required for efficient hydrolysis of lignocellulosic biomass and no wild type organism is capable of producing all enzymes in desired levels. In this study, steam explosion of wheat straw was carried out at pilot scale and a synthetic enzyme mixture (EnzMix) was developed by partially replacing the cellulase with critical dosages of commercially available accessory enzymes (β-glucosidase, xylanase and laccase) through central composite design. Highest degree of synergism (DS) was observed with β-glucosidase (1.68) followed by xylanase (1.36). Finally, benchmarking of EnzMix (Celluclast, β-glucosidase and xylanase in a protein ratio of 20.40: 38.43: 41.16, respectively) and other leading commercial enzymes was carried out. Interestingly, hydrolysis improved by 75% at 6 h and 30% at 24 h, respectively in comparison of control. By this approach, 25% reduction in enzyme dosage was observed for obtaining the same hydrolysis yield with opitimized enzyme cocktail. Thus, development of enzyme cocktail is an effective and sustainable approach for high hydrolysis efficiency

Compendium of Plant-Specific CRISPR Vectors and Their Technical Advantages

CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific gRNA, leader sequence, selectable marker gene, precise promoters, and other accessories. It has always been challenging to select the specific vector for each study due to a lack of comprehensive information on CRISPR vectors in one place. Herein, we have discussed every technical aspect of various important elements that will be highly useful in vector selection and efficient editing of the desired plant genome. Various factors such as the promoter regulating the expression of Cas and gRNA, gRNA size, Cas variants, multicistronic gRNA, and vector backbone, etc. influence transformation and editing frequency. For example, the use of polycistronic tRNA-gRNA, and Csy4-gRNA has been documented to enhance the editing efficiency. Similarly, the selection of an efficient selectable marker is also a very important factor. Information on the availability of numerous variants of Cas endonucleases, such as Cas9, Cas12a, Cas12b, Casɸ, and CasMINI, etc., with diverse recognition specificities further broadens the scope of editing. The development of chimeric proteins such as Cas fused to cytosine or adenosine deaminase domain and modified reverse transcriptase using protein engineering enabled base and prime editing, respectively. In addition, the newly discovered Casɸ and CasMINI would increase the scope of genetic engineering in plants by being smaller Cas variants. All advancements would contribute to the development of various tools required for gene editing, targeted gene insertion, transcriptional activation/suppression, multiplexing, prime editing, base editing, and gene tagging. This review will serve as an encyclopedia for plant-specific CRISPR vectors and will be useful for researchers

Investigation of Roles of TaTALE Genes during Development and Stress Response in Bread Wheat

The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and performed a comprehensive investigation for gene and protein structural properties, phylogeny, expression patterns, and multilevel gene regulations. The identified TaTALE proteins were further classified into two groups, TaBLHs and TaKNOXs, which were tightly clustered into the phylogeny. The negative Ka/Ks ratio of duplicated genes suggested purifying selection pressure with confined functional divergence. Various signature domains and motifs were found conserved in both groups of proteins. The occurrence of diverse cis-regulatory elements and modulated expression during various developmental stages and in the presence of abiotic (heat, drought, salt) and two different fungal stresses suggested their roles in development and stress response, as well. The interaction of TaTALEs with the miRNAs and other development-related homeobox proteins also suggested their roles in growth and development and stress response. The present study revealed several important aspects of TaTALEs that will be useful in further functional validation of these genes in future studies

Potential of engineering the myo-inositol oxidation pathway to increase stress resilience in plants

Myo-inositol is one of the most abundant form of inositol. The myo-inositol (MI) serves as substrate to diverse biosynthesis pathways and hence it is conserved across life forms. The biosynthesis of MI is well studied in animals. Beyond biosynthesis pathway, implications of MI pathway and enzymes hold potential implications in plant physiology and crop improvement. Myo-inositol oxygenase (MIOX) enzyme catabolize MI into D-glucuronic acid (D-GlcUA). The MIOX enzyme family is well studied across few plants. More recently, the MI associated pathway’s crosstalk with other important biosynthesis and stress responsive pathways in plants has drawn attention. The overall outcome from different plant species studied so far are very suggestive that MI derivatives and associated pathways could open new directions to explore stress responsive novel metabolic networks. There are evidences for upregulation of MI metabolic pathway genes, specially MIOX under different stress condition. We also found MIOX genes getting differentially expressed according to developmental and stress signals in Arabidopsis and wheat. In this review we try to highlight the missing links and put forward a tailored view over myo-inositol oxidation pathway and MIOX proteins