Pooja Singh

Evaluation of Bioactive Potential of an Aloe vera Sterol Extract

We prepared a crude gel material from Aloe vera succulent leaf tissues. The ethanolic extract of lyophilized A. vera gel was used for the GC‐MS analysis. Hexadecanoic acid (22.22%) was identified as major compound. Sitosterol and stigmasterol were found to be 2.89% and 2.1% in the extract. HPLC analysis was carried out to confirm the presence of stigmasterol. The concentration of sterol extract needed to scavenge DPPH free radical by 50% was calculated as 5.2u2009mgu2009mL−1. In the FRAP assay, the sterol extract showed significant hydroxyl radical scavenging in a dose‐dependent manner (IC50 value 1.17u2009µgu2009mL−1). Concentration of the sample required to reduce lipid peroxidation was found to be 4.18u2009µgu2009mL−1, and the extract also possessed acetylcholinesterase activity (IC50 ‐ 5.26u2009µgu2009mL−1). Catalase activity was 0.196u2009μM H2O2 decomposed min−1u2009µg−1 protein, whereas the peroxidase activity was 17.01u2009μM of pyragallol oxidized min−1u2009µg−1 protein. The extract recorded higher activity against growth of S. greseus and C. albicans in the experiments carried out to determine antibacterial and antifungal activity, respectively. Copyright

Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf.

The process of somatic embryogenesis and plant regeneration involve changes in gene expression and have been associated with changes in DNA methylation. Here, we report the expression and DNA methylation patterns of SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), BABY BOOM (BBM), LEAFY COTYLEDON 2 (LEC2) and WUSCHEL (WUS) in meristematic block of newly emerged shoots from rhizome, embryogenic and non-embryogenic calli, prolonged cell suspension culture, ex vitro leaf, and in vitro leaf of regenerated plants of Boesenbergia rotunda. Among all seven samples, based on qRT-PCR, the highest level of expression of SERK, BBM and LEC2 was in embryogenic callus, while WUS was most highly expressed in meristematic block tissue followed by embryogenic callus. Relatively lower expression was observed in cell suspension culture and watery callus for SERK, LEC2 and WUS and in in vitro leaf for BBM. For gene specific methylation determined by bisulfite sequencing data, embryogenic callus samples had the lowest levels of DNA methylation at CG, CHG and CHH contexts of SERK, LEC2 and WUS. We observed negative correlation between DNA methylation at the CG and CHG contexts and the expression levels of SERK, BBM, LEC2 and WUS. Based on our results, we suggest that relatively higher expression and lower level of DNA methylation of SERK, BBM, LEC2 and WUS are associated with somatic embryogenesis and plant regeneration in B. rotunda.

Responses of rice to Rhizoctonia solani and its toxic metabolite in relation to expression of Osmyb4 transcription factor

Pooja S., Babu S. (2017): Responses of rice to Rhizoctonia solani and its toxic metabolite in relation to expression of osmyb4 transcription factor. Plant Protect. Sci., 53: 208–215. The reaction of IR 50, TRY 3, and IR 36 cultivars of rice to R. solani challenge, the causal agent of sheath blight, and its toxic metabolite was studied. Differential response of these cultivars to the pathogen and/or toxin inoculation was observed in detached leaf sheaths and greenhouse-grown plants. The observations were based on disease scoring, electrolyte leakage, and also microscopic views of infection cushions. The osmyb4 gene expression was studied in the tissues from all these experiments and a correlation between the level of expression and disease response of the varieties was found at least in some experiments. The mechanisms regulated by osmyb4 might have a lower but significant contribution to the tolerance of rice cultivars to sheath blight.

Molecular Modeling and Dynamic Simulation of Arabidopsis thaliana Carotenoid Cleavage Dioxygenase Gene: A Comparison with Bixa orellana and Crocus sativus

Carotenoid cleavage dioxygenase (CCD) gene, ubiquitously found in numerous types of plants, are eminent in synthesizing the various volatile compounds (β‐ionone, C13‐norisoprenoid, geranylacetone) known as apocarotenoids. These apocarotenoids have various biological functions such as volatile signals, allelopathic interaction and plant defense. In Arabidopsis genome sequence, four potential CCD genes have been identified namely CCD1, CCD4, CCD7, and CCD8. These four genes give rise to diverse biological functions with almost similar sequence identity. In this investigation, an in silico analysis was proposed to study CCD proteins in Arabidopsis thaliana, aiming at constructing three‐dimensional (3D) structure for CCD1 proteins of Bixa orellana and Crocus sativus to observe the structural difference among AtCCD (A. thaliana CCD) proteins. The quality of modeled structures was evaluated using RAMPAGE, PSVS protein validation server and Q Mean server. Finally, we utilised molecular dynamics simulation to identify the stability of the predicted CCD protein structures. The molecular dynamic simulation also revealed that AtCCD4 protein showed lesser stability when compared to other CCD proteins. Overall results from molecular dynamics analysis predicted that BoCCD1, CsCCD1, and AtCCD1 show similar structural characteristics. J. Cell. Biochem. 118: 2712–2721, 2017.

Genome-Wide Regulatory Network Mapping of miRNA and Transcription Factors in Banana Roots

MicroRNA (miRNA) are important regulators of gene expression. Plant miRNA have been reported both to target and to be regulated by transcription factors, however, genomic distribution of miRNA, transcription factor targets for miRNA, transcription factor binding sites (TFBS) of miRNA promoters and their regulatory networks have not been systematically mapped in banana. In this study, genome-wide annotation of miRNA in the most recently published banana genome sequence was used to predict miRNA promoter regions and to map TFBS of miRNA genes. A total of 183 mature miRNAs, comprising 144 orthologous miRNA and 39 Musa-specific miRNA were predicted. Following this, banana root degradome data was used to confirm miRNA targets and the transcription factor targets were placed into a predicted network together with their targeting miRNA using cytoscape. Gene ontology of the 20 transcription factors among the predicted miRNA targets, showed predominance for auxin-activated signalling and developmental processes. Profiling of TFBS motifs across miRNA promoter regions showed that binding site motifs for TCP, AP2/ERF, GATA, NF-YB, DOF, B3, bZIP, trihelix, ZF-HD, bHLH and Dehydrin transcription factor families are abundant in the Musa acuminata genome. Finally, we propose a regulatory network for the miRNA families miR156, miR164, miR166, miR171, miR319, miR396, miR528, mac-miR-new14 and mac-miR-new20 and their respective transcription factor targets.

Prospects and progress in the production of valuable carotenoids: Insights from metabolic engineering, synthetic biology, and computational approaches

Carotenoids are isoprenoid pigments synthesized exclusively by plants and microorganisms and play critical roles in light harvesting, photoprotection, attracting pollinators and phytohormone production. In recent years, carotenoids have been used for their health benefits due to their high antioxidant activity and are extensively utilized in food, pharmaceutical, and nutraceutical industries. Regulation of carotenoid biosynthesis occurs throughout the life cycle of plants, with vibrant changes in composition based on developmental needs and responses to external environmental stimuli. With advancements in metabolic engineering techniques, there has been tremendous progress in the production of industrially valuable secondary metabolites such as carotenoids. Application of metabolic engineering and synthetic biology has become essential for the successful and improved production of carotenoids. Synthetic biology is an emerging discipline; metabolic engineering approaches may provide insights into novel ideas for biosynthetic pathways. In this review, we discuss the current knowledge on carotenoid biosynthetic pathways and genetic engineering of carotenoids to improve their nutritional value. In addition, we investigated synthetic biological approaches for the production of carotenoids. Theoretical biology approaches that may aid in understanding the biological sciences are discussed in this review. A combination of theoretical knowledge and experimental strategies may improve the production of industrially relevant secondary metabolites.

Genome-wide Analysis of the CCCH Zinc-Finger Gene Family in Banana (Musa acuminata): An Insight Into Motif and Gene Structure Arrangement, Evolution and Salt Stress Responses

The CCCH zinc finger proteins contain a signature motif comprising of three cysteine and one histidine residues. Increasing evidence suggests that members of this large family regulate the transcription of genes that participate in plant growth and development as well as responses to environmental stresses including salt stress in plants. However, little is known about this gene family in banana (Musa acuminata), a tropical crop that is globally consumed and is highly sensitive to salt stress conditions. Here, we present the genome-wide identification of the CCCH Zinc-Finger (CCCH-ZF) gene family in banana. We identified 89 CCCH-ZFP (MaZFP) genes and evaluated their phylogenetic relationships. Our analysis showed that this gene family encodes proteins with variable lengths and highly conserved motif structures. Distribution mapping of this gene family revealed that MaZFP genes are unevenly dispersed on the 11 chromosomes with segmental duplication in 15 gene pairs, suggesting an important contribution of duplication in expansion of this gene family in banana. Expression analysis of four selected MaZFP genes in leaf and root tissues of banana showed temporal and spatial expression in response to salt stress conditions with high transcript accumulation in root tissue. The highest level of transcript was measured for MaZFP88 in root tissues sampled 24xa0h after treatment with 100xa0mM NaCl. The analysis presented here provides a valuable reference for future functional studies of MaZFP genes with the potential for use in developing salt-tolerant banana varieties.

Use of dsRNA in Crop Improvement

Over recent years, many crops have benefited from the application of genetic transformation approaches to improve important agronomic and horticultural traits. The discovery of RNA-mediated gene silencing (RNA silencing) has allowed the application of precise approaches to inhibit plant pathogens and to alter plant metabolism and development. RNA silencing is initiated by double-stranded RNA (dsRNA) leading to sequence homology-dependent translational inhibition of a target mRNA or transcriptional repression of a target gene. RNA silencing was first described in plants as post-transcriptional gene silencing (PTGS), virus cross-protection and co-suppression. Activated by the presence of short dsRNA inside the cell, RNA silencing is a form of negative gene regulation lending itself towards the generation of loss-of-function genetic changes. Applications include reducing gene expression of a pathogen, such as a virus; reducing the expression of an endogenous plant gene to alter biosynthesis, such as that of an undesired allergen, toxin or flower or fruit pigment; reducing the expression of an endogenous plant gene to alter nutritional qualities, such as altered starch content and reducing the expression of endogenous genes to alter plant development. Alteration of plant phenotypes and inhibiting plant pathogens through the direct application of dsRNA to crop plants has provided a rapid and efficient method that is feasible for some situations and has the advantage of avoiding the steps in plant transformation and regeneration. In this chapter, we review examples that outline the technology for the application of dsRNA in crops, and discuss the role this has played in crop improvement.