Ramamoorthy Siva

Bio: Ramamoorthy Siva is an academic researcher from VIT University. The author has contributed to research in topics: Mutant & Mutation. The author has an hindex of 25, co-authored 102 publications receiving 2040 citations. Previous affiliations of Ramamoorthy Siva include Ben-Gurion University of the Negev.

The amazing potential of fungi: 50 ways we can exploit fungi industrially

Abstract: Fungi are an understudied, biotechnologically valuable group of organisms. Due to the immense range of habitats that fungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi have developed numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application in biotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. The search for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in which fungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable researchers. We also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi have provided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untapped resource with enormous industrial potential.

Status of natural dyes and dye-yielding plants in India

Abstract: Indians have been considered as forerunners in the art of natural dyeing. Natural dyes find use in the colouring of textiles, drugs, cosmetics, etc. Owing to their nontoxic effects, they are also used for colouring various food products. In India, there are more than 450 plants that can yield dyes. In addition to their dye-yielding characteristics, some of these plants also possess medicinal value. Though there is a large plant resource base, little has been exploited so far. Due to lack of availability of precise technical knowledge on the extracting and dyeing technique, it has not commercially succeeded like the synthetic dyes. Although indigenous knowledge system has been practised over the years in the past, the use of natural dyes has diminished over generations due to lack of documentation. Also there is not much information available on databases of either dye-yielding plants or their products. In this article we review the availability of natural dyes, their extraction, applications, mordant types, advantages and disadvantages.

Integrative Bioinformatics Approaches to Map Potential Novel Genes and Pathways Involved in Ovarian Cancer.

Abstract: Background and aims: Ovarian cancer (OC) is the seventh most commonly detected cancer among women. This study aimed to map the hub and core genes and potential pathways that might be involved in the molecular pathogenesis of OC. Methods: In the present work, we analyzed a microarray dataset (GSE126519) from the Gene Expression Omnibus (GEO) database and used the GEO2R tool to screen OC cells and ovarian SINE-resistant cancer cells for differentially expressed genes (DEGs). For the functional annotation of the DEGs, we conducted Gene Ontology (GO) and pathway enrichment analyses (KEGG) using the DAVID v6.8 online server and GenoGo Metacore™, Cortellis Solution software. Protein-protein interaction (PPI) networks were constructed using the STRING database, and Cytoscape software was used for visualization. The survival analysis was performed using the online platform GEPIA2 to determine the prognostic value of the expression of hub genes in cell lines from OC patients. Results: We identified a total of 809 upregulated and 700 downregulated DEGs. GO analysis revealed that the genes with statistically significant differences in expression were mainly associated with biological processes involved in the cell cycle, the mitotic cell cycle, mitotic nuclear division, organ morphogenesis, cell development, and cell morphogenesis. By using the Analyze Networks (AN) algorithm in GeneGo, we identified the most relevant biological networks involving DEGs that were mainly enriched in the cell cycle (in metaphase checkpoints) and revealed the role of APC in cell cycle regulation pathways. We found 10 hub genes and four core genes (FZD6, FZD8, CDK2, and RBBP8) that are strongly linked to OC. Conclusion: This study sheds light on the molecular pathogenesis of OC and is expected to provide potential molecular biomarkers that are beneficial for the treatment and clinical molecular diagnosis of OC.

Dysregulation of Signaling Pathways Due to Differentially Expressed Genes From the B-Cell Transcriptomes of Systemic Lupus Erythematosus Patients - A Bioinformatics Approach.

Abstract: Systemic lupus erythematosus (SLE) is an autoimmune inflammatory disorder that is clinically complex and has increased production of autoantibodies. Via emerging technologies, researchers have identified genetic variants, expression profiling of genes, animal models, and epigenetic findings that have paved the way for a better understanding of the molecular and genetic mechanisms of SLE. Our current study aimed to illustrate the essential genes and molecular pathways that are potentially involved in the pathogenesis of SLE. This study incorporates the gene expression profiling data of the microarray dataset GSE30153 from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between the B-cell transcriptomes of SLE patients and healthy controls were screened using the GEO2R web tool. The identified DEGs were subjected to STRING analysis and Cytoscape to explore the protein-protein interaction (PPI) networks between them. The MCODE (Molecular Complex Detection) plugin of Cytoscape was used to screen the cluster subnetworks that are highly interlinked between the DEGs. Subsequently, the clustered DEGs were subjected to functional annotation with ClueGO/CluePedia to identify the significant pathways that were enriched. For integrative analysis, we used GeneGo MetacoreTM, a Cortellis Solution software, to exhibit the Gene Ontology (GO) and enriched pathways between the datasets. Our study identified 4 upregulated and 13 downregulated genes. Analysis of GO and functional enrichment using ClueGO revealed the pathways that were statistically significant, including pathways involving T-cell costimulation, lymphocyte costimulation, negative regulation of vascular permeability, and B-cell receptor signaling. The DEGs were mainly enriched in metabolic networks such as the phosphatidylinositol-3,4,5-triphosphate pathway and the carnitine pathway. Additionally, potentially enriched pathways, such as the signaling pathways induced by oxidative stress and reactive oxygen species (ROS), chemotaxis and lysophosphatidic acid signaling induced via G protein-coupled receptors (GPCRs), and the androgen receptor activation pathway, were identified from the DEGs that were mainly associated with the immune system. Four genes (EGR1, CD38, CAV1, and AKT1) were identified to be strongly associated with SLE. Our integrative analysis using a multitude of bioinformatics tools might promote an understanding of the dysregulated pathways that are associated with SLE development and progression. The four DEGs in SLE patients might shed light on the pathogenesis of SLE and might serve as potential biomarkers in early diagnosis and as therapeutic targets for SLE.

Influence of V54M mutation in giant muscle protein titin: a computational screening and molecular dynamics approach

Abstract: Recent genetic studies have revealed the impact of mutations in associated genes for cardiac sarcomere components leading to dilated cardiomyopathy (DCM). The cardiac sarcomere is composed of thick and thin filaments and a giant muscle protein known as titin or connectin. Titin interacts with T-cap/telethonin in the Z-line region and plays a vital role in regulating sarcomere assembly. Initially, we screened all the variants associated with giant protein titin and analyzed their impact with the aid of pathogenicity and stability prediction methods. V54M mutation found in the hydrophobic core region of the protein associated with abnormal clinical phenotype leads to DCM was selected for further analysis. To address this issue, we mapped the deleterious mutant V54M, modeled the mutant protein complex, and deciphered the impact of mutation on binding with its partner telethonin in the titin crystal structure of PDB ID: 1YA5 with the aid of docking analysis. Furthermore, two run molecular dynamics simulation was initiated to understand the mechanistic action of V54M mutation in altering the protein structure, dynamics, and stability. According to the results obtained from the repeated 50 ns trajectory files, the overall effect of V54M mutation was destabilizing and transition of bend to coil in the secondary structure was observed. Furthermore, MMPBSA elucidated that V54M found in the Z-line region of titin decreases the binding affinity of titin to Z-line proteins T-cap/telethonin thereby hindering the protein-protein interaction.

Recent advancements in natural dye applications: a review

Abstract: A vast array of colorants obtained from natural sources such as plants, insects/animals and microbes have been scrutinized in recent past for their use in different kinds of applications. Research into new natural dyes sources along with eco-friendly, robust and cost-effective technologies for their processing and application have greatly aided in widening the scope of natural dyes in various traditional and advanced application disciplines. This review encompasses a summary of research performed in last 15 years (1998–2013) in different arenas of applications of natural dyes, with specific reference to technological development in natural textile dyeing and use of natural dyes in functional finishing of textiles, food coloration and dye-sensitized solar cells. In addition, some newly discovered applications of natural dyes have also been discussed.

A comprehensive review on tyrosinase inhibitors.

Abstract: Tyrosinase is a multi-copper enzyme which is widely distributed in different organisms and plays an important role in the melanogenesis and enzymatic browning. Therefore, its inhibitors can be attractive in cosmetics and medicinal industries as depigmentation agents and also in food and agriculture industries as antibrowning compounds. For this purpose, many natural, semi-synthetic and synthetic inhibitors have been developed by different screening methods to date. This review has focused on the tyrosinase inhibitors discovered from all sources and biochemically characterised in the last four decades.

Microalgae as versatile cellular factories for valued products

Abstract: As major part of the phytoplankton, microalgae are pivotal for the global food chain. Their exceptional capacity for CO2-fixation illustrates their indispensable significance to sustain earth's ecosystems. Further, they play a still underestimated role in eliminating contaminants from various environments. In addition to ecological benefit, many microalgal species exhibit high nutritional value and, at the same time, generate valued bio-products: Pigments, lipids, bioactive compounds, certain polysaccharides, bio-hydrogen and even biopolyesters with plastic-like properties have the potential for successful market penetration. Three substantial pigment groups, namely chlorophylls, carotenoids, and phycobilins, are essential for light harvesting and CO2 fixation. Those pigments will most likely undergo quick commercial success in “functional food”, cosmetics, aquaculture, pharmaceuticals, or food technology. Due to often high contents of polyunsaturated fatty acids essential for human metabolism, microalgal oils can be commercialized as health food and in the pharmaceutical and therapeutic field, creating much higher value than by converting them to biofuel. Finally, algal biomass remaining as residue after product recovery can be used as forage, biogas feedstock or biofertilizer. This utilization is needed for balancing the material- and energy cycles of the entire process. Thus, technology platforms following the principles of bio-refineries shall be established to enable the design of sustainable and economically feasible production of marketable microalgal products.

Carotenoids and their cleavage products: Biosynthesis and functions

Abstract: This review focuses on plant carotenoids, but it also includes progress made on microbial and animal carotenoid metabolism to better understand the functions and the evolution of these structurally diverse compounds with a common backbone. Plants have evolved isogenes for specific key steps of carotenoid biosynthesis with differential expression profiles, whose characteristic features will be compared. Perhaps the most exciting progress has been made in studies of carotenoid cleavage products (apocarotenoids) with an ever-expanding variety of novel functions being discovered. This review therefore covers structural, molecular genetic and functional aspects of carotenoids and apocarotenoids alike. Apocarotenoids are specifically tailored from carotenoids by a family of oxidative cleavage enzymes, but whether there are contributions to their generation from chemical oxidation, photooxidation or other mechanisms is largely unknown. Control of carotenoid homeostasis is discussed in the context of biosynthetic and degradative reactions but also in the context of subcellular environments for deposition and sequestration within and outside of plastids. Other aspects of carotenoid research, including metabolic engineering and synthetic biology approaches, will only be covered briefly.

Quinghaosu (artemisin): an antimalarial drug from china

Abstract: The herb Artemisia annua has been used for many centuries in Chinese traditional medicine as a treatment for fever and malaria. In 1971, Chinese chemists isolated from the leafy portions of the plant the substance responsible for its reputed medicinal action. This compound, called qinghaosu (QHS, artemisinin), is a sesquiterpene lactone that bears a peroxide grouping and, unlike most other antimalarials, lacks a nitrogen-containing heterocyclic ring system. The compound has been used successfully in several thousand malaria patients in China, including those with both chloroquine-sensitive and chloroquine-resistant strains of Plasmodium falciparum. Derivatives of QHS, such as dihydroqinghaosu, artemether, and the water-soluble sodium artesunate, appear to be more potent than QHS itself. Sodium artesunate acts rapidly in restoring to consciousness comatose patients with cerebral malaria. Thus QHS and its derivatives offer promise as a totally new class of antimalarials.