Neha Malviya

Insights into structural and functional diversity of Dof (DNA binding with one finger) transcription factor.

AbstractMain conclusionThe structural, functional and in-silico studies of Dof transcription factor attempted so far reveals immense opportunity to analyze the plant genomes in terms of number of Dof genes and discuss in light of the evolution. The multiple functions of Dof genes needs to explored for crop improvement. Transcription factors play a very vital role in gene regulation at transcriptional level and are being extensively studied across phylas. In recent years, sequencing of plant genomes has led to genome-wide identification and characterizations of diverse types of plant-specific transcription factor gene family providing key insights into their structural and functional diversity. The DNA binding with one finger (Dof), a class belonging to C2H2-type zinc finger family proteins, is a plant-specific transcription factor having multiple roles such as seed maturation and germination, phytohormone and light-mediated regulation and plant responses to biotic and abiotic stresses. Dof proteins are present across plant lineage, from green algae to higher angiosperm, and represent a unique class of transcription factor having bifunctional binding activities, with both DNA and proteins, to regulate the complex transcriptional machinery in plant cells. The structural and functional diversity of the Dof transcription factor family along with the bioinformatics analysis highlighting the phylogeny of Dof families is reviewed in light of its importance in plant biotechnology for crop improvement.

Analysis of genetic diversity in cowpea (Vigna unguiculata L.Walp.) cultivars with random amplified polymorphic DNA markers

The genetic diversity among ten Indian cultivars of cowpea was analyzed using 18 sets of RAPD markers. A total of 181 bands with an average of 15 bands per primer were obtained. Out of 181 bands, 148 showed polymorphism (81.7%). The variation in genetic diversity among these cultivars ranged from 0.1742 to 0.4054. Cluster analysis based on Jaccard’s similarity coefficient using UPGMA with high bootstrap values revealed two distinct clusters I and II comprised of two and seven cultivars, respectively. Cluster II was further differentiated into various subclusters. Cultivar IC-9883 was found to be unique based on its altogether distinct position in the dendrogram and two-dimensional space projections.

Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.)

The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.

Insights to Sequence Information of Polyphenol Oxidase Enzyme from Different Source Organisms

Polyphenol oxidases (PPOs) are widely distributed enzymes among animals, plants, bacteria, and fungi. PPOs often have significant role in many biologically essential functions including pigmentation, sclerotization, primary immune response, and host defense mechanisms. In the present study, forty-seven full-length amino acid sequences of PPO from bacteria, fungi, and plants were collected and subjected to multiple sequence alignment (MSA), domain identification, and phylogenetic tree construction. MSA revealed that six histidine, two phenylalanine, two arginine, and two aspartic acid residues were highly conserved in all the analyzed species, while a single cysteine residue was conserved in all the plant and fungal PPOs. Two major sequence clusters were constructed by phylogenetic analysis. One cluster was of the plant origin, whereas the other one was of the fungal and bacterial origin. Motif GGGMMGDVPTANDPIFWLHHCNVDRLWAVWQ was found in all the species of bacterial and fungus sources. In addition, seven new motifs which were unique for their group were also identified.

Genome- wide characterization of Nuclear Factor Y (NF-Y) gene family of sorghum [Sorghum bicolor (L.) Moench]: a bioinformatics approach

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor (TF) complex with preferential binding to CCAAT elements of promoters, regulating gene expression in most of the higher eukaryotes. The availability of plant genome sequences have revealed multiple number of genes coding for the three subunits, namely NF-YA, NF-YB and NF-YC in contrast to single NF-Y gene for each subunit reported in yeast and animals. A total of 33 NF-YTF comprising of 8 NF-YA, 11 NF-YB and 14 NF-YC subunits were accessed from the sorghum genome. The bioinformatic characterization of NF-Y gene family of sorghum for gene structure, chromosome location, protein motif, phylogeny, gene duplication and in-silico expression under abiotic stresses have been attempted in the present study. The identified SbNF-Y genes are distributed on all the 10 chromosomes of sorghum with variability in the frequency and 18 out of 33 SbNF-Ys were found to be intronless. Segmental duplication event was found to be predominant feature based on gene duplication pattern study. Several orthologs and paralogs groups were disclosed through the comprehensive phylogenetic analysis of SbNF-Y proteins along with 36 Arabidopsis and 28 rice NF-Y proteins. In-silico expression analysis under abiotic stresses using rice transcriptome data revealed several of the sorghum NF-Y genes to be associated with salt, drought, cold and heat stresses.

Overview and Principles of Bioengineering: The Drivers of Omics Technologies

Abstract The science of “omics” reflects the innovations in diverse technologies leading to studies of life processes in totality. With the initial emergence of genomics, proteomics, and metabolomics associated with the comprehensive studies of genes, proteins, and metabolites of an organism, respectively, there has been a substantial growth in other branches of omics such as lipidomics, cytomics, phenomics, and transcriptomics. The omics-driven science has a potential application in crop-improvement program, human health sector, environmental sector, and industrial sector. The recent developments in genome sequencing have further expanded the scope of the omics technologies for elucidating the complexity of life processes and understanding the gene expression and regulation in diverse systems. The concept of bioengineering is more relevant to the human health and is often referred to as biomedical engineering. In general, it covers tools and technologies associated with the manipulation of life processes for the benefit of the humankind. In biological system, the central dogma of molecular biology, i.e., replication, transcription, and translation, is the main center of attraction for manipulation using appropriate tools of omics. This chapter highlights the basics of science of omics along with relevant tools and diverse applications.

Omics Approaches in In Vitro Fertilization

Abstract Reproductive biology has witnessed substantial technological developments to cure infertility, which is a major concern worldwide affecting more than 10% of the couples. The combined effort of basic and applied medical research led to the development of a technique popularly known as in vitro fertilization (IVF) to alleviate infertility. It is a technique by which an egg is fertilized by a sperm in in vitro conditions. It has emerged as a safe and effective technique that overcomes the limitation of other methods. In general, damage of fallopian tubes is the major reason for female infertility as it obstructs the contact between the egg and the sperm, whereas male infertility is mainly due to impaired sperm quality and quantity. In 1978 the technique of IVF was successfully adopted by Dr. Edwards and Dr. Steptoe resulting in a normal, healthy, and fit baby from a human oocyte. The technique is performed by collecting the contents of female fallopian tube after natural ovulation and mixing it with sperm followed by implantation. The ovarian hyperstimulation, transvaginal oocyte retrieval from ovary, egg and sperm preparation, and selection of resulting embryos before implantation are important considerations for IVF. By the application of applied reproductive technologies, the IVF success rate is now substantially improved. There are many potential factors that might influence the success or failure of pregnancy rate through IVF. Although IVF has proved to be a boon for many couples suffering from infertility, it poses serious moral, ethical, social, and religious controversies.

Molecular cloning and expression profiling of multiple Dof genes of Sorghum bicolor (L) Moench

DNA binding with one finger (Dof) proteins represent a family of plant specific transcription factors associated with diverse biological processes, such as seed maturation and germination, phytohormone and light mediated regulation, and plant responses to biotic and abiotic stresses. In present study, a total of 21 Dof genes from Sorghum bicolor were cloned, sequenced and in silico characterized for homology search, revealing their identity to Dof like proteins. The expression profiling of SbDof genes using quantitative RT-PCR in different tissue types and also under drought and salt stresses was attempted. The SbDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth condition. Two of the SbDof genes namely SbDof8 and SbDof12 showed comparatively high level of transcript abundance in all the tissue types tested; whereas some of the SbDof genes showed a distinct tissue specific expression pattern. Further a total of 13 SbDof genes showed differential expression when subjected to either of the abiotic stress i.e. drought or salinity. Three of the SbDof genes namely SbDof12, SbDof19 and SbDof24 were found to be up-regulated in response to drought and salt stress. Comparative analysis of SbDof genes expression revealed existence of a complex transcriptional and functional diversity across plant growth and developmental stages.

Application of Biotechnology and Bioinformatics Tools in Plant–Fungus Interactions

Fungi have been recognized to be a major cause of disease in immunocompromised hosts: moreover, the loss of food and fodder crops through fungi has been unmatched since the last decade. Fungi colonize the plant cell and organs by modulating the host defense response. A number of different methods have been recently used to understand host–fungus interactions. With the advent of HiSeq approaches, more fungal genomes and transcriptomes are now sequenced, and their bioinformatics analyses have enriched and assisted our knowledge of the interplay between plant and fungi. The present chapter reviews the current biotechnological and bioinformatics approaches for the study of plant–fungus interactions.