This page has only limited features, please log in for full access.
Dr. Muthuramalingam received his M. Sc., Biotechnology in the year 2015. He has secured the second rank in the final University examinations and subsequently joined for PhD in Biotechnology on 01st October 2015 under the guidance of Dr. M. Ramesh, Associate Professor, Department of Biotechnology, Alagappa University. He has recently earned his PhD in Biotechnology from Alagappa University with Highly commented Grade. He carried out his doctoral research in the field of Plant Biotechnology & Bioinformatics and Molecular Biology with special reference to identification and annotation of novel individual and combined abiotic stress responsible genes from rice through multi-omics approaches. During his study, he has identified 364 individual and combined abiotic stress responsible genes and published twelve research papers in SCI/SCOPUS indexed journals such as Frontiers in Plant Science, Scientific Reports, Genomics, International Journal of Biological Macromolecules, Journal of Biomolecular Structure and Dynamics, Biomolecules, Plants, Journal of Plant Biochemistry and Biotechnology Gene, Rice Science, Biocatalysis and Agricultural Biotechnology with cumulative impact factor 46.996. He also has six Book Chapters in reputed international publishers namely CRC Press (Taylor & Francis Group), Wiley and Springer Nature. He has also presented his research findings in many national/ intern
Abiotic stresses (AbS), such as drought, salinity, and thermal stresses, could highly affect the growth and development of plants. For decades, researchers have attempted to unravel the mechanisms of AbS for enhancing the corresponding tolerance of plants, especially for crop production in agriculture. In the present communication, we summarized the significant factors (atmosphere, soil and water) of AbS, their regulations, and integrated omics in the most important cereal crops in the world, especially rice, wheat, sorghum, and maize. It has been suggested that using systems biology and advanced sequencing approaches in genomics could help solve the AbS response in cereals. An emphasis was given to holistic approaches such as, bioinformatics and functional omics, gene mining and agronomic traits, genome-wide association studies (GWAS), and transcription factors (TFs) family with respect to AbS. In addition, the development of omics studies has improved to address the identification of AbS responsive genes and it enables the interaction between signaling pathways, molecular insights, novel traits and their significance in cereal crops. This review compares AbS mechanisms to omics and bioinformatics resources to provide a comprehensive view of the mechanisms. Moreover, further studies are needed to obtain the information from the integrated omics databases to understand the AbS mechanisms for the development of large spectrum AbS-tolerant crop production.
Rajendran Jeyasri; Pandiyan Muthuramalingam; Lakkakula Satish; Shunmugiah Pandian; Jen-Tsung Chen; Sunny Ahmar; Xiukang Wang; Freddy Mora-Poblete; Manikandan Ramesh. An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics. Plants 2021, 10, 1472 .
AMA StyleRajendran Jeyasri, Pandiyan Muthuramalingam, Lakkakula Satish, Shunmugiah Pandian, Jen-Tsung Chen, Sunny Ahmar, Xiukang Wang, Freddy Mora-Poblete, Manikandan Ramesh. An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics. Plants. 2021; 10 (7):1472.
Chicago/Turabian StyleRajendran Jeyasri; Pandiyan Muthuramalingam; Lakkakula Satish; Shunmugiah Pandian; Jen-Tsung Chen; Sunny Ahmar; Xiukang Wang; Freddy Mora-Poblete; Manikandan Ramesh. 2021. "An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics." Plants 10, no. 7: 1472.
Arbuscular mycorrhizal (AM) fungi have beneficial effects on host plants, but their growth is influenced by various factors. This study was carried out to analyze the variation of AM fungi in soils and roots of peach (Prunus persica L. var. Golden Honey 3, a yellow-flesh variety) trees in different soil layers (0–40 cm) and their correlation with soil properties. The peach tree could be colonized by indigenous AM fungi (2.2–8.7 spores/g soil and 1.63–3.57 cm hyphal length/g soil), achieving 79.50–93.55% of root AM fungal colonization degree. The mycorrhizal growth, root sugars, soil three glomalins, NH4+-N, NO3−-N, available P and K, and soil organic matter (SOM) had spatial heterogeneity. Soil spores, but not soil hyphae contributed to soil glomalin, and soil glomalin also contributed to SOM. There was a significant correlation of soil hyphae with spore density, soil NO3−-N, and SOM. Root mycorrhiza was positively correlated with spore density, NH4+-N, NO3−-N, and easily extractable glomalin-related soil protein. Notably, spore density positively correlated with NO3−-N, available K, SOM, and root fructose and glucose, while negatively correlated with available P and root sucrose. These findings concluded that mycorrhiza of peach showed spatial distribution, and soil properties mainly affected/altered based on the soil spore density.
Sheng-Min Liang; Feng-Ling Zheng; Elsayed Fathi Abd_Allah; Pandiyan Muthuramalingam; Qiang-Sheng Wu; Abeer Hashem. Spatial changes of arbuscular mycorrhizal fungi in peach and their correlation with soil properties. Saudi Journal of Biological Sciences 2021, 1 .
AMA StyleSheng-Min Liang, Feng-Ling Zheng, Elsayed Fathi Abd_Allah, Pandiyan Muthuramalingam, Qiang-Sheng Wu, Abeer Hashem. Spatial changes of arbuscular mycorrhizal fungi in peach and their correlation with soil properties. Saudi Journal of Biological Sciences. 2021; ():1.
Chicago/Turabian StyleSheng-Min Liang; Feng-Ling Zheng; Elsayed Fathi Abd_Allah; Pandiyan Muthuramalingam; Qiang-Sheng Wu; Abeer Hashem. 2021. "Spatial changes of arbuscular mycorrhizal fungi in peach and their correlation with soil properties." Saudi Journal of Biological Sciences , no. : 1.
The WRKY genes are one of the largest families of transcription factors (TFs) and play a crucial role in certain processes in plants including stress signaling, regulation of transcriptional reprogramming associated with stress responses, and other regulatory networks. This study aims to investigate the WRKY gene family in the C3 model plant, Oryza sativa L., using a genome-wide in silico expression analysis. Firstly, 104 WRKY TF family members were identified, and then their molecular properties and expression signatures were analyzed systematically. In silico spatio-temporal and hormonal expression profiling revealed the roles of OsWRKY genes and their dynamism in diverse developmental tissues and hormones, respectively. Comparative mapping between OsWRKY genes and their synteny with C4 panicoid genomes showed the evolutionary insights of the WRKY TF family. Interactions of OsWRKY coding gene sequences represented the complexity of abiotic stress (AbS) and their molecular cross-talks. The expression signature of 26 novel candidate genes in response to stresses exhibited the putative involvement of individual and combined AbS (CAbS) responses. These novel findings unravel the in-depth insights into OsWRKY TF genes and delineate the plant developmental metabolisms and their functional regulations in individual and CAbS conditions.
Rajendran Jeyasri; Pandiyan Muthuramalingam; Lakkakula Satish; Sivakumar Adarshan; Muthukannan Lakshmi; Shunmugiah Pandian; Jen-Tsung Chen; Sunny Ahmar; Xiukang Wang; Freddy Mora-Poblete; Manikandan Ramesh. The Role of OsWRKY Genes in Rice When Faced with Single and Multiple Abiotic Stresses. Agronomy 2021, 11, 1301 .
AMA StyleRajendran Jeyasri, Pandiyan Muthuramalingam, Lakkakula Satish, Sivakumar Adarshan, Muthukannan Lakshmi, Shunmugiah Pandian, Jen-Tsung Chen, Sunny Ahmar, Xiukang Wang, Freddy Mora-Poblete, Manikandan Ramesh. The Role of OsWRKY Genes in Rice When Faced with Single and Multiple Abiotic Stresses. Agronomy. 2021; 11 (7):1301.
Chicago/Turabian StyleRajendran Jeyasri; Pandiyan Muthuramalingam; Lakkakula Satish; Sivakumar Adarshan; Muthukannan Lakshmi; Shunmugiah Pandian; Jen-Tsung Chen; Sunny Ahmar; Xiukang Wang; Freddy Mora-Poblete; Manikandan Ramesh. 2021. "The Role of OsWRKY Genes in Rice When Faced with Single and Multiple Abiotic Stresses." Agronomy 11, no. 7: 1301.
Acinetobacter baumannii is a nosocomial-infection-causing bacterium and also possesses multidrug resistance to a wide range of conventional antibiotics. The biofilm-forming ability of A. baumannii plays a major role in its resistance and persistence. There is an alarming need for novel treatment strategies to control A. baumannii biofilm-associated issues. The present study demonstrated the strong antibiofilm and antivirulence efficacy of citral against A. baumannii . In addition, proteomic analysis revealed the multitarget potential of citral against A. baumannii . Furthermore, citral treatment enhances the susceptibility of A. baumannii to the host innate immune system and reactive oxygen species (ROS). Cytotoxicity analysis revealed the nonfatal effect of citral on human PBMCs. Therefore, citral could be the safest therapeutic compound and can be taken for further clinical evaluation for the treatment of biofilm-associated infections by A. baumannii .
Anthonymuthu Selvaraj; Alaguvel Valliammai; Pandiyan Muthuramalingam; Sivasamy Sethupathy; Ganapathy Ashwinkumar Subramenium; Manikandan Ramesh; Shunmugiah Karutha Pandian. Proteomic and Systematic Functional Profiling Unveils Citral Targeting Antibiotic Resistance, Antioxidant Defense, and Biofilm-Associated Two-Component Systems of Acinetobacter baumannii To Encumber Biofilm and Virulence Traits. mSystems 2020, 5, 1 .
AMA StyleAnthonymuthu Selvaraj, Alaguvel Valliammai, Pandiyan Muthuramalingam, Sivasamy Sethupathy, Ganapathy Ashwinkumar Subramenium, Manikandan Ramesh, Shunmugiah Karutha Pandian. Proteomic and Systematic Functional Profiling Unveils Citral Targeting Antibiotic Resistance, Antioxidant Defense, and Biofilm-Associated Two-Component Systems of Acinetobacter baumannii To Encumber Biofilm and Virulence Traits. mSystems. 2020; 5 (6):1.
Chicago/Turabian StyleAnthonymuthu Selvaraj; Alaguvel Valliammai; Pandiyan Muthuramalingam; Sivasamy Sethupathy; Ganapathy Ashwinkumar Subramenium; Manikandan Ramesh; Shunmugiah Karutha Pandian. 2020. "Proteomic and Systematic Functional Profiling Unveils Citral Targeting Antibiotic Resistance, Antioxidant Defense, and Biofilm-Associated Two-Component Systems of Acinetobacter baumannii To Encumber Biofilm and Virulence Traits." mSystems 5, no. 6: 1.
Drought and salinity are the major constraints on agricultural production worldwide and a remarkable attempt is being made to improve the plant yields in the direction of increasing water deficit. We have developed transgenic finger millet cultivars ‘CO(Ra)-14’ and ‘Paiyur-2’ overexpressing Erianthus arundinaceous DREB2 (EaDREB2) transcription factor confirmed by PCR and Southern stably expressed in T0 and T1. These transgenic lines were tolerant to high salinity and severe drought stress conditions without affecting the morphological or agronomic characters. Analysis of morpho-physiological characters revealed that overexpression of EaDREB2 gene was associated with maintenance of chlorophyll content, increased relative water content, improved accumulation of the osmotic substance such as proline and decreased electrolyte leakage, under both saline and drought stresses. After treating the plants to progressive drought and salinity stress, transgenic lines showed less chlorophyll reduction and moderate growth inhibition than the controls. The majority of the transformed lines showed prominent tolerance to salinity and drought with significant spikelet fertility and higher grain yield compared to the controls at stressed and unstressed conditions. This is the first holistic report on development of drought and saline tolerance in finger millet through transgenic modification and it is essential to benefit the farmers from seasonal stress.
Lakkakula Satish; Periyasamy Rathinapriya; Pandiyan Muthuramalingam; Subramani Pandian; Stanislaus Ceasar; Manikandan Ramesh. Overexpression of Erianthus arundinaceus DREB2 Transcription Factor Ameliorates the Salinity and Drought Tolerance in Eleusine coracana Cultivars. Biology and Life Sciences Forum 2020, 4, 8 .
AMA StyleLakkakula Satish, Periyasamy Rathinapriya, Pandiyan Muthuramalingam, Subramani Pandian, Stanislaus Ceasar, Manikandan Ramesh. Overexpression of Erianthus arundinaceus DREB2 Transcription Factor Ameliorates the Salinity and Drought Tolerance in Eleusine coracana Cultivars. Biology and Life Sciences Forum. 2020; 4 (1):8.
Chicago/Turabian StyleLakkakula Satish; Periyasamy Rathinapriya; Pandiyan Muthuramalingam; Subramani Pandian; Stanislaus Ceasar; Manikandan Ramesh. 2020. "Overexpression of Erianthus arundinaceus DREB2 Transcription Factor Ameliorates the Salinity and Drought Tolerance in Eleusine coracana Cultivars." Biology and Life Sciences Forum 4, no. 1: 8.
Carvacrol is an essential oil traditionally used in culinary processes as spice due to its aromatic nature and also known for various biological activities. In the present study, the antivirulence efficacy of carvacrol against methicillin-resistant Staphylococcus aureus (MRSA) is explored. MRSA is an opportunistic pathogen capable of causing various superficial and systemic infections in humans. Biofilm formation and virulence factors of MRSA are responsible for its pathogenesis and resistance. Hence, the aim of this study was to explore the antibiofilm and antivirulence efficacy of carvacrol against MRSA. Carvacrol at 75 μg/mL inhibited MRSA biofilm by 93%, and it also decreased the biofilm formation on polystyrene and glass surfaces. Further, microscopic analyses revealed the reduction in microcolony formation and collapsed structure of biofilm upon carvacrol treatment. The growth curve analysis and the Alamar blue assay showed the nonfatal effect of carvacrol on MRSA. Further, carvacrol significantly reduced the production of MRSA biofilm-associated slime and extracellular polysaccharide. In addition, carvacrol strongly inhibited the antioxidant pigment staphyloxanthin and its intermediates’ synthesis in MRSA. Inhibition of biofilm and staphyloxanthin by carvacrol enhanced the susceptibility of MRSA to oxidants and healthy human blood. Quantitative polymerase chain reaction (qPCR) analysis unveiled the downregulation of sarA-mediated biofilm gene expression and staphyloxanthin-associated crtM gene expression. The sarA-dependent antibiofilm potential of carvacrol was validated using S. aureus Newman wild-type and isogenic ΔsarA strains. In silico molecular docking analysis showed the high binding efficacy of carvacrol with staphylococcal accessory regulator A (SarA) and 4,4′-diapophytoene synthase (CrtM) when compared to positive controls. Furthermore, the in vivo efficacy of carvacrol against MRSA infection was demonstrated using the model organism Galleria mellonella. The results revealed the nontoxic nature of carvacrol to the larvae and the rescuing potential of carvacrol against MRSA infection. Finally, the current study reveals the potential of carvacrol in inhibiting the biofilm formation and staphyloxanthin synthesis of MRSA by targeting the global regulator SarA and a novel antivirulence target CrtM.
Anthonymuthu Selvaraj; Alaguvel Valliammai; Pandiyan Muthuramalingam; Arumugam Priya; Manokaran Suba; Manikandan Ramesh; Shunmugiah Karutha Pandian. Carvacrol Targets SarA and CrtM of Methicillin-Resistant Staphylococcus aureus to Mitigate Biofilm Formation and Staphyloxanthin Synthesis: An In Vitro and In Vivo Approach. ACS Omega 2020, 5, 31100 -31114.
AMA StyleAnthonymuthu Selvaraj, Alaguvel Valliammai, Pandiyan Muthuramalingam, Arumugam Priya, Manokaran Suba, Manikandan Ramesh, Shunmugiah Karutha Pandian. Carvacrol Targets SarA and CrtM of Methicillin-Resistant Staphylococcus aureus to Mitigate Biofilm Formation and Staphyloxanthin Synthesis: An In Vitro and In Vivo Approach. ACS Omega. 2020; 5 (48):31100-31114.
Chicago/Turabian StyleAnthonymuthu Selvaraj; Alaguvel Valliammai; Pandiyan Muthuramalingam; Arumugam Priya; Manokaran Suba; Manikandan Ramesh; Shunmugiah Karutha Pandian. 2020. "Carvacrol Targets SarA and CrtM of Methicillin-Resistant Staphylococcus aureus to Mitigate Biofilm Formation and Staphyloxanthin Synthesis: An In Vitro and In Vivo Approach." ACS Omega 5, no. 48: 31100-31114.
Understanding the immunological behavior of COVID-19 cases at molecular level is essential for therapeutic development. In this study, multi-omics and systems pharmacology analyses were performed to unravel the multi-targeted mechanisms of novel bioactives to combat COVID-19. Immuno-transcriptomic dataset of healthy controls and COVID-19 cases was retrieved from ArrayExpress. Phytocompounds from ethnobotanical plants were collected from PubChem. Differentially expressed 98 immune genes associated with COVID-19 were derived through NetworkAnalyst 3.0. Among 259 plant derived compounds, 154 compounds were targeting 13 COVID-19 immune genes involved in diverse signaling pathways. In addition, pharmacological properties of these phytocompounds were compared with COVID-19 drugs prescribed by WHO, and 25 novel phytocompounds were found to be more efficient with higher bioactive scores. The current study unravels the virogenomic signatures which can serve as therapeutic targets and identified phytocompounds with anti-COVID-19 efficacy. However, further experimental validation is essential to bring out these molecules as commercial drug candidates.
Pandiyan Muthuramalingam; Rajendran Jeyasri; Alaguvel Valliammai; Anthonymuthu Selvaraj; Chandrasekar Karthika; Shanmugaraj Gowrishankar; Shunmugiah Karutha Pandian; Manikandan Ramesh; Jen-Tsung Chen. Global multi-omics and systems pharmacological strategy unravel the multi-targeted therapeutic potential of natural bioactive molecules against COVID-19: An in silico approach. Genomics 2020, 112, 4486 -4504.
AMA StylePandiyan Muthuramalingam, Rajendran Jeyasri, Alaguvel Valliammai, Anthonymuthu Selvaraj, Chandrasekar Karthika, Shanmugaraj Gowrishankar, Shunmugiah Karutha Pandian, Manikandan Ramesh, Jen-Tsung Chen. Global multi-omics and systems pharmacological strategy unravel the multi-targeted therapeutic potential of natural bioactive molecules against COVID-19: An in silico approach. Genomics. 2020; 112 (6):4486-4504.
Chicago/Turabian StylePandiyan Muthuramalingam; Rajendran Jeyasri; Alaguvel Valliammai; Anthonymuthu Selvaraj; Chandrasekar Karthika; Shanmugaraj Gowrishankar; Shunmugiah Karutha Pandian; Manikandan Ramesh; Jen-Tsung Chen. 2020. "Global multi-omics and systems pharmacological strategy unravel the multi-targeted therapeutic potential of natural bioactive molecules against COVID-19: An in silico approach." Genomics 112, no. 6: 4486-4504.
Plants can be considered to biosynthesize the specialized metabolites to adapt to various environmental stressors mainly on abiotic stresses (AbS). Among specialized metabolites, glutamine (Gln) is an essential plant metabolite to achieve sustainable plant growth, yield and food security. In this pilot study, swe employed computational metabolomics genome wide association survey (cmGWAS) of Gln metabolite profiling in Oryza sativa, targeting at the identification of abiotic stress responsible (AbSR) – Gln metabolite producing genes (GlnMPG). Identified 5 AbSR-GlnMPG alter the metabolite levels and play a predominant role in delineating the physiological significance of rice. These genes were systematically analysed for their biological features via OryzaCyc. Spatio-temporal and plant hormonal expression pattern of AbSR-GlnMPG was analysed and their differential expression profiling were noted in 48 different tissues and hormones, respectively. Furthermore, comparative ideogram of these genes revealed the chromosomal synteny with C4 grass genomes. Molecular crosstalks of these proteins, unravelled the various metabolic interaction. The systems expression profiling of AbSR-GlnMPG will lead to unravel the metabolite signaling and putative responses in multiple AbS. On the whole, this holistic study provides deeper insights on biomolecular features of AbSR-GlnMPG, which could be analysed further to decipher their functional metabolisms in AbS dynamism.
Pandiyan Muthuramalingam; Rajendran Jeyasri; Anthonymuthu Selvaraj; Shunmugiah Karutha Pandian; Manikandan Ramesh. Integrated transcriptomic and metabolomic analyses of glutamine metabolism genes unveil key players in Oryza sativa (L.) to ameliorate the unique and combined abiotic stress tolerance. International Journal of Biological Macromolecules 2020, 164, 222 -231.
AMA StylePandiyan Muthuramalingam, Rajendran Jeyasri, Anthonymuthu Selvaraj, Shunmugiah Karutha Pandian, Manikandan Ramesh. Integrated transcriptomic and metabolomic analyses of glutamine metabolism genes unveil key players in Oryza sativa (L.) to ameliorate the unique and combined abiotic stress tolerance. International Journal of Biological Macromolecules. 2020; 164 ():222-231.
Chicago/Turabian StylePandiyan Muthuramalingam; Rajendran Jeyasri; Anthonymuthu Selvaraj; Shunmugiah Karutha Pandian; Manikandan Ramesh. 2020. "Integrated transcriptomic and metabolomic analyses of glutamine metabolism genes unveil key players in Oryza sativa (L.) to ameliorate the unique and combined abiotic stress tolerance." International Journal of Biological Macromolecules 164, no. : 222-231.
Genes encoding proteins with A20/AN1 zinc-finger domains, belonging to the stress associated protein (SAP) gene family, are present in all eukaryotes and play a decisive role in plant response to diverse physiological and molecular activities particularly on biotic and abiotic stresses (AbS). In this first and foremost study, global transcriptome analysis of members of the SAP gene family was carried out in C3 model- Oryza sativa (OsSAP) aiming at the identification of OsSAP genes activated in response to unique or Combined AbS (CAbS). Based on the available spatio-temporal and phytohormonal RNA-Seq expression profile datasets, nine OsSAP genes were filtered out and identified by a differential expression signature noted in various tissues as well as plant hormones. Comparative genome ideogram of OsSAP genes confirmed the orthologous collinearity with C4 panicoid genomes. Interactome of these genes, revealed the molecular cross-talks of OsSAP. Thus, the computational expression signature of OsSAP genes led to a better understanding of gene dynamism in diverse developmental tissues/organs. Transcriptional regulation analysis of key OsSAP genes in response to stress (drought and salinity) suggested the novel role of OsSAP1, OsSAP2, OsSAP5, OsSAP7, OsSAP8 and OsSAP11 in AbS. Altogether, the study provides deeper insights on molecular characteristics of OsSAP genes, which could be deployed further to decipher their precise functional roles in AbS responses.
Pandiyan Muthuramalingam; Rajendran Jeyasri; Anthonymuthu Selvaraj; Dhamodharan Kalaiyarasi; Wilson Aruni; Shunmugiah Thevar Karutha Pandian; Manikandan Ramesh. Global transcriptome analysis of novel stress associated protein (SAP) genes expression dynamism of combined abiotic stresses inOryza sativa(L.). Journal of Biomolecular Structure and Dynamics 2020, 1 -12.
AMA StylePandiyan Muthuramalingam, Rajendran Jeyasri, Anthonymuthu Selvaraj, Dhamodharan Kalaiyarasi, Wilson Aruni, Shunmugiah Thevar Karutha Pandian, Manikandan Ramesh. Global transcriptome analysis of novel stress associated protein (SAP) genes expression dynamism of combined abiotic stresses inOryza sativa(L.). Journal of Biomolecular Structure and Dynamics. 2020; ():1-12.
Chicago/Turabian StylePandiyan Muthuramalingam; Rajendran Jeyasri; Anthonymuthu Selvaraj; Dhamodharan Kalaiyarasi; Wilson Aruni; Shunmugiah Thevar Karutha Pandian; Manikandan Ramesh. 2020. "Global transcriptome analysis of novel stress associated protein (SAP) genes expression dynamism of combined abiotic stresses inOryza sativa(L.)." Journal of Biomolecular Structure and Dynamics , no. : 1-12.
Neurological diseases (NDs), especially Alzheimer’s and Spinocerebellar ataxia (SCA), can severely cause biochemical abnormalities in the brain, spinal cord and other nerves of human beings. Their ever-increasing prevalence has led to a demand for new drug development. Indian traditional and Ayurvedic medicine used to combat the complex diseases from a holistic and integrative point of view has shown efficiency and effectiveness in the treatment of NDs. Bacopa monnieri is a potent Indian medicinal herb used for multiple ailments, but is significantly known as a nootropic or brain tonic and memory enhancer. This annual herb has various active compounds and acts as an alternative and complementary medicine in various countries. However, system-level insights of the molecular mechanism of a multiscale treatment strategy for NDs is still a bottleneck. Considering its prominence, we used cheminformatics and system pharmacological approaches, with the aim to unravel the various molecular mechanisms represented by Bacopa-derived compounds in identifying the active human targets when treating NDs. First, using cheminformatics analysis combined with the drug target mining process, 52 active compounds and their corresponding 780 direct receptors were retrieved and computationally validated. Based on the molecular properties, bioactive scores and comparative analysis with commercially available drugs, novel and active compounds such as asiatic acid (ASTA) and loliolide (LLD) to treat the Alzheimer’s and SCA were identified. According to the interactions among the active compounds, the targets and diseases were further analyzed to decipher the deeper pharmacological actions of the drug. NDs consist of complex regulatory modules that are integrated to dissect the therapeutic effects of compounds derived from Bacopa in various pathological features and their encoding biological processes. All these revealed that Bacopa compounds have several curative activities in regulating the various biological processes of NDs and also pave the way for the treatment of various diseases in modern medicine.
Rajendran Jeyasri; Pandiyan Muthuramalingam; Vellaichami Suba; Manikandan Ramesh; Jen-Tsung Chen. Bacopa monnieri and Their Bioactive Compounds Inferred Multi-Target Treatment Strategy for Neurological Diseases: A Cheminformatics and System Pharmacology Approach. Biomolecules 2020, 10, 536 .
AMA StyleRajendran Jeyasri, Pandiyan Muthuramalingam, Vellaichami Suba, Manikandan Ramesh, Jen-Tsung Chen. Bacopa monnieri and Their Bioactive Compounds Inferred Multi-Target Treatment Strategy for Neurological Diseases: A Cheminformatics and System Pharmacology Approach. Biomolecules. 2020; 10 (4):536.
Chicago/Turabian StyleRajendran Jeyasri; Pandiyan Muthuramalingam; Vellaichami Suba; Manikandan Ramesh; Jen-Tsung Chen. 2020. "Bacopa monnieri and Their Bioactive Compounds Inferred Multi-Target Treatment Strategy for Neurological Diseases: A Cheminformatics and System Pharmacology Approach." Biomolecules 10, no. 4: 536.
Bacopa monnieri has been used as a reputed drug in the Indian traditional ayurvedic system for centuries. This medicinal herb with important phytopharmaceuticals has been popularly known as “Brahmi”. In recent years, B. monnieri has been extensively studied for its bioactive constituents, constituents responsible for memory enhancing effect, and also its diverse other useful effects. It possesses many pharmacological activities such as antioxidant, gastrointestinal, endocrine, antimicrobial, anti-inflammatory etc. The plant has been also used for the treatment of neurological and neuropsychiatric diseases. Due to its multipurpose therapeutic potential, micropropagation using axillary meristems and de novo organogenesis has been extensively studied in the species and is being reviewed. High frequency direct shoot organogenesis can be induced in excised leaf and internode explants in the absence of exogenous phytohormones and the rate of induction is enhanced in the presence of exogenous cytokinins, supplements, growth regulators, etc. Using explants from tissue culture raised plants, direct shoot regeneration leading to production of more than 100 rooted plants/explant within 8–12 weeks period with 85%–100% survival in the field after acclimatization can be expected following optimized protocols. Bioreactor based micropropagation was found to increase the multiplication rate of shoot cultures for the commercial propagation of B. monnieri plants. The maximum content of bacosides has been recorded in shoot biomass using an airlift bioreactor system. Further studies for the biosynthesis of bacosides and other secondary metabolites need to be conducted in the species utilizing untransformed shoot cultures in bioreactors.
Partha Sarathi Saha; Sayantika Sarkar; Rajendran Jeyasri; Pandiyan Muthuramalingam; Manikandan Ramesh; Sumita Jha. In Vitro Propagation, Phytochemical and Neuropharmacological Profiles of Bacopa monnieri (L.) Wettst.: A Review. Plants 2020, 9, 411 .
AMA StylePartha Sarathi Saha, Sayantika Sarkar, Rajendran Jeyasri, Pandiyan Muthuramalingam, Manikandan Ramesh, Sumita Jha. In Vitro Propagation, Phytochemical and Neuropharmacological Profiles of Bacopa monnieri (L.) Wettst.: A Review. Plants. 2020; 9 (4):411.
Chicago/Turabian StylePartha Sarathi Saha; Sayantika Sarkar; Rajendran Jeyasri; Pandiyan Muthuramalingam; Manikandan Ramesh; Sumita Jha. 2020. "In Vitro Propagation, Phytochemical and Neuropharmacological Profiles of Bacopa monnieri (L.) Wettst.: A Review." Plants 9, no. 4: 411.
Among the significant transcription factors (TFs), HSF proteins play pivotal roles in the regulation of hormonal signal transduction and different abiotic stress (AbS) responses. Hence considering its importance, global omics expression analysis of HSF candidates was performed in rice (OsHSF). The current study identified 25 HSF family members and physically plotted them against the rice genome. These proteins were systematically analyzed for their physicochemical features, organization and expression signatures. Further, heatmap of both spatio-temporal and global plant hormones revealed the developmental tissues and hormone specific expression profiling of these genes respectively. Comparative genome mapping between OsHSF players in interrelated C4 grass species revealed the chromosome level synteny. Signalome analysis revealed the protein - protein interactions of OsHSF. Expression profiling of key players in response to stresses exhibited the new involvement in combined AbS (CAbS) responses. Our results are significantly valuable to decipher their functional analysis of CAbS tolerant in rice.
Pandiyan Muthuramalingam; Rajendran Jeyasri; Ravichandran Kavitha Anbu Snega Bharathi; Vellaichami Suba; Shunmugiah Thevar Karutha Pandian; Manikandan Ramesh. Global integrated omics expression analyses of abiotic stress signaling HSF transcription factor genes in Oryza sativa L.: An in silico approach. Genomics 2020, 112, 908 -918.
AMA StylePandiyan Muthuramalingam, Rajendran Jeyasri, Ravichandran Kavitha Anbu Snega Bharathi, Vellaichami Suba, Shunmugiah Thevar Karutha Pandian, Manikandan Ramesh. Global integrated omics expression analyses of abiotic stress signaling HSF transcription factor genes in Oryza sativa L.: An in silico approach. Genomics. 2020; 112 (1):908-918.
Chicago/Turabian StylePandiyan Muthuramalingam; Rajendran Jeyasri; Ravichandran Kavitha Anbu Snega Bharathi; Vellaichami Suba; Shunmugiah Thevar Karutha Pandian; Manikandan Ramesh. 2020. "Global integrated omics expression analyses of abiotic stress signaling HSF transcription factor genes in Oryza sativa L.: An in silico approach." Genomics 112, no. 1: 908-918.
Abiotic stress can inflict limitations on plant growth, developmental processes and also crop productivity. Here we have portrayed advances in omics tools in the view of conservative and contemporary approaches that could be used to unravel abiotic stress tolerance in rice. Under stressful conditions, plants can develop diverse molecular mechanisms to combat stress challenges, while it is not sufficient to protect them. Hence, speculation of this study is essential for understanding how plants react to adverse environmental conditions with the hope of enhancing the tolerance of plants to abiotic stress. It could be addressed by computational biology (bioinformatics); invigorated sequencing approaches in genomics have paved the way for various analytical applications. Focusing on the technological advances, multiple new omics such as the transcriptome, metabolome, hormonome, epigenome, proteome and phenome have emerged. An emphasis was given to systems approaches with respect to abiotic stress. In addition, the availability of rice whole genome information, advancement and development of omics studies has improved to address the identification of unique and combined abiotic stress responsive cellular metabolisms and this enables the interaction between signalling pathways, molecular biological insights along with novel traits and their significance. Thus, this chapter provides the bioinformatics and systems biology aspects of abiotic stress responses by comparing it with the publically available omics and bioinformatics resources which could provide a base for detailed functional studies of stress tolerance in rice.
Pandiyan Muthuramalingam; Rajendran Jeyasri; Subramanian Radhesh Krishnan; Shunmugiah Thevar Karutha Pandian; Ramalingam Sathishkumar; Manikandan Ramesh. Integrating the Bioinformatics and Omics Tools for Systems Analysis of Abiotic Stress Tolerance in Oryza sativa (L.). Advances in Plant Transgenics: Methods and Applications 2019, 59 -77.
AMA StylePandiyan Muthuramalingam, Rajendran Jeyasri, Subramanian Radhesh Krishnan, Shunmugiah Thevar Karutha Pandian, Ramalingam Sathishkumar, Manikandan Ramesh. Integrating the Bioinformatics and Omics Tools for Systems Analysis of Abiotic Stress Tolerance in Oryza sativa (L.). Advances in Plant Transgenics: Methods and Applications. 2019; ():59-77.
Chicago/Turabian StylePandiyan Muthuramalingam; Rajendran Jeyasri; Subramanian Radhesh Krishnan; Shunmugiah Thevar Karutha Pandian; Ramalingam Sathishkumar; Manikandan Ramesh. 2019. "Integrating the Bioinformatics and Omics Tools for Systems Analysis of Abiotic Stress Tolerance in Oryza sativa (L.)." Advances in Plant Transgenics: Methods and Applications , no. : 59-77.
An easy, efficient and highly reproducible regeneration system was established through organogenesis from leaf base mediated callus of an ethnobotanical hairy shrub Abutilon indicum L. sweet, which is documented to possess pharmaceutically important phytochemicals. Among various explants, leaf bases produced significant callus induction (89%) with 140 mg fresh weight on Murashige and Skoog (MS) medium supplemented with 11.31 μM 2, 4-Dichlorophenoxyacetic acid (2, 4-D). Combinations of 2, 4-D and kinetin (KIN) increased the biomass (191 mg) of embryogenic calli. Regeneration medium with a combination of 8.88 μM of 6-amino benzyl purine (BAP) and 8.06 μM of naphthalene acetic acid in MS basal media significantly influenced the initiation of shoot primordium with 91% of regeneration. Proficiently regenerated shoot apical meristems (SAMs) produced higher frequency of multiple shoot induction on 4.10 μM of zeatin. The fully regenerated mature shootlets produced high root biomass (791.67 ± 48.05 mg) on half - strength MS with 4.54 μM indole-3-butyric acid (IBA) with an excellent mat root system for efficient acclimatization. In vitro established plantlets were successfully acclimatized under ex vitro conditions with high frequency. Presence of homologous DNA banding pattern with Single Primer Amplification Reaction markers confirmed the genetic similarity. FTIR and GC-MS spectrum showed similar metabolic profiles between wild and in vitro regenerated plantlets. Thus the protocol is reliable for in vitro regeneration through leaf base derived callus which could pave a way to the large scale production of secondary metabolite through biotechnological approaches.
Subramanian Radhesh Krishnan; Subramani Pandian; Ramachandradoss Banupriya; Pandiyan Muthuramalingam; Syed Jeritha Banu; Manikandan Arumugam; Manikandan Ramesh. Augmenting a competent in vitro organogenesis etiquette from leaf base of country mallow, Abutilon indicum L. sweet: An ethno-botanically valuable medicinal plant. Biocatalysis and Agricultural Biotechnology 2019, 19, 101125 .
AMA StyleSubramanian Radhesh Krishnan, Subramani Pandian, Ramachandradoss Banupriya, Pandiyan Muthuramalingam, Syed Jeritha Banu, Manikandan Arumugam, Manikandan Ramesh. Augmenting a competent in vitro organogenesis etiquette from leaf base of country mallow, Abutilon indicum L. sweet: An ethno-botanically valuable medicinal plant. Biocatalysis and Agricultural Biotechnology. 2019; 19 ():101125.
Chicago/Turabian StyleSubramanian Radhesh Krishnan; Subramani Pandian; Ramachandradoss Banupriya; Pandiyan Muthuramalingam; Syed Jeritha Banu; Manikandan Arumugam; Manikandan Ramesh. 2019. "Augmenting a competent in vitro organogenesis etiquette from leaf base of country mallow, Abutilon indicum L. sweet: An ethno-botanically valuable medicinal plant." Biocatalysis and Agricultural Biotechnology 19, no. : 101125.
The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) – Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser. A total of 1373 and 1028 SNPs were involved in complex traits and genomic variations. Comparative mapping of AbSR-ThrMPG revealed the chromosomal colinearity with C4 grass species. Further, computational expression pattern of these genes predicted a differential expression profiling in diverse developmental tissues. Protein interaction of protein coding gene sequences revealed that the abiotic stresses (AbS) are multigenic in nature. In silico expression of AbSR-ThrMPG determined the putative involvement in response to individual AbS. This is the first comprehensive genome wide study reporting on AbSR –ThrMPG analysis in rice. The results of this study provide a pivotal resource for further functional investigation of these key genes in the vital areas of manipulating AbS signaling in rice improvement.
Pandiyan Muthuramalingam; Subramanian Radhesh Krishnan; Subramani Pandian; Narayanan Mareeswaran; Wilson Aruni; Shunmugiah Karutha Pandian; Manikandan Ramesh. Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance. Scientific Reports 2018, 8, 9270 .
AMA StylePandiyan Muthuramalingam, Subramanian Radhesh Krishnan, Subramani Pandian, Narayanan Mareeswaran, Wilson Aruni, Shunmugiah Karutha Pandian, Manikandan Ramesh. Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance. Scientific Reports. 2018; 8 (1):9270.
Chicago/Turabian StylePandiyan Muthuramalingam; Subramanian Radhesh Krishnan; Subramani Pandian; Narayanan Mareeswaran; Wilson Aruni; Shunmugiah Karutha Pandian; Manikandan Ramesh. 2018. "Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance." Scientific Reports 8, no. 1: 9270.
Subramanian Radhesh Krishnan; Pandiyan Muthuramalingam; Subramani Pandian; Ramachandradoss Banupriya; Gunasekar Chithra; Manikandan Ramesh. Sprouted Sorghum Extract Elicits Coleoptile Emergence, Enhances Shoot and Root Acclimatization, and Maintains Genetic Fidelity in indica Rice. Rice Science 2018, 25, 61 -72.
AMA StyleSubramanian Radhesh Krishnan, Pandiyan Muthuramalingam, Subramani Pandian, Ramachandradoss Banupriya, Gunasekar Chithra, Manikandan Ramesh. Sprouted Sorghum Extract Elicits Coleoptile Emergence, Enhances Shoot and Root Acclimatization, and Maintains Genetic Fidelity in indica Rice. Rice Science. 2018; 25 (2):61-72.
Chicago/Turabian StyleSubramanian Radhesh Krishnan; Pandiyan Muthuramalingam; Subramani Pandian; Ramachandradoss Banupriya; Gunasekar Chithra; Manikandan Ramesh. 2018. "Sprouted Sorghum Extract Elicits Coleoptile Emergence, Enhances Shoot and Root Acclimatization, and Maintains Genetic Fidelity in indica Rice." Rice Science 25, no. 2: 61-72.
Finger millet (Eleusine coracana (L.) Geartn.) is one of the important small millets serves as a food security crop because of its high nutritional values. The complex tetraploid genome of finger millet requires a large number of informative, functional DNA markers for different applications in genetics and breeding. Yet, less number of simple sequence repeat (SSR) markers have been developed from expressed sequence tags in finger millet. In the present study, 56 new genic SSR markers were developed from publicly available drought related ESTs. The 43 polymorphic markers were used to evaluate polymorphism, revealed a range of PIC value 0.41 to 0.79. Our results suggest that, analyzed genotypes have high genetic diversity with an average gene diversity (h) of 0.176 and Shannon's information index (I) of 0.315. We conclude that there was a higher gene exchange within populations, by the value of overall gene flow (Nm) of 0.7721. The unweighted pair group method with arithmetic mean and neighbor joining dendrogram generated three main clusters to differentiate genotypes and these results were also confirmed by PCA and PCoA analysis. The high genetic diversity (77%) was found within the populations in the analysis of molecular variance. A Bayesian model-based cluster analysis evidenced a high extent of admixture between the gene pools from the different geographical origins. Population based cluster analyses pointed out a strong pattern of ‘isolation by distance’. Overall, these results underscored that this study showed a significantly high level of polymorphism, adequate genetic diversity and population structure which expand the modern genetic resources and its utility in various applications in genetics and genomics including association mapping and breeding.
Subramani Pandian; Lakkakula Satish; Ramakrishnan Rameshkumar; Pandiyan Muthuramalingam; Arockiam Sagina Rency; Periyasamy Rathinapriya; Manikandan Ramesh. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene 2018, 653, 80 -90.
AMA StyleSubramani Pandian, Lakkakula Satish, Ramakrishnan Rameshkumar, Pandiyan Muthuramalingam, Arockiam Sagina Rency, Periyasamy Rathinapriya, Manikandan Ramesh. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene. 2018; 653 ():80-90.
Chicago/Turabian StyleSubramani Pandian; Lakkakula Satish; Ramakrishnan Rameshkumar; Pandiyan Muthuramalingam; Arockiam Sagina Rency; Periyasamy Rathinapriya; Manikandan Ramesh. 2018. "Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers." Gene 653, no. : 80-90.
Transcription factors (TFs) are pivotal players in plant stress signaling and signal transduction pathways. Among the key TFs, NAC, ZF-HD, AP2-EREBP, WRKY and bHLH proteins play crucial roles in the regulation of reprogramming the transcriptome and associated responses in stress. Considering this, genome-wide identification of NAC, ZF-HD, AP2-EREBP, WRKY and bHLH TF families were performed in the C3 model plant, Oryza sativa. The computational study identified 144 NAC, 15 ZF-HD, 164 AP2-EREBP, 103 WRKY, and 135 bHLH proteins and their physicochemical properties and, expression profiling by computational analysis. Genome-wide in silico expression analysis of NAC, ZF-HD, AP2-EREBP, WRKY, bHLH genes showed their differential expression profiling in different tissues. Expression patterns, gene structure, subcellular localization, gene ontology of 17 NAC, 3 ZF-HD, 13 AP2-EREBP, 11 WRKY, 8 bHLH key genes suggested the putative novel variants in stress and signal transduction. These key players are needed to be studied in order to categorize and outline their functional roles in AbS signaling network.
Pandiyan Muthuramalingam; Subramanian Radhesh Krishnan; Kadarkarai Saravanan; Narayanan Mareeswaran; Reetesh Kumar; Manikandan Ramesh. Genome-wide identification of major transcription factor superfamilies in rice identifies key candidates involved in abiotic stress dynamism. Journal of Plant Biochemistry and Biotechnology 2018, 27, 300 -317.
AMA StylePandiyan Muthuramalingam, Subramanian Radhesh Krishnan, Kadarkarai Saravanan, Narayanan Mareeswaran, Reetesh Kumar, Manikandan Ramesh. Genome-wide identification of major transcription factor superfamilies in rice identifies key candidates involved in abiotic stress dynamism. Journal of Plant Biochemistry and Biotechnology. 2018; 27 (3):300-317.
Chicago/Turabian StylePandiyan Muthuramalingam; Subramanian Radhesh Krishnan; Kadarkarai Saravanan; Narayanan Mareeswaran; Reetesh Kumar; Manikandan Ramesh. 2018. "Genome-wide identification of major transcription factor superfamilies in rice identifies key candidates involved in abiotic stress dynamism." Journal of Plant Biochemistry and Biotechnology 27, no. 3: 300-317.
Combined abiotic stress (CAbS) affects the field grown plants simultaneously. The multigenic and quantitative nature of uncontrollable abiotic stresses complicates the process of understanding the stress response by plants. Considering this, we analyzed the CAbS response of C3 model plant, Oryza sativa by meta-analysis. The datasets of commonly expressed genes by drought, salinity, submergence, metal, natural expression, biotic and abiotic stresses were data mined through publically accessible transcriptomic abiotic stress (AbS) responsive datasets. Of which 1175, 12821 and 42877 genes were commonly expressed in meta differential, individual differential, and unchanged expressions respectively. Highly regulated 100 differentially expressed AbS genes were derived through integrative meta-analysis of expression data (INMEX). Of this 30 genes were identified from AbS gene families through expression atlas that were computationally analyzed for their physicochemical properties. All Abs genes were physically mapped against O. sativa genome. Comparative mapping of these genes demonstrated the orthologous relationship with related C4 panicoid genome. In silico expression analysis of these genes showed differential expression patterns in different developmental tissues. Protein-protein interaction of these genes, represented the complexity of AbS. Computational expression profiling of candidate genes in response to multiple stresses suggested the putative involvement of OS05G0350900, OS02G0612700, OS05G0104200, OS03G0596200, OS12G0225900, OS07G0152000, OS08G0119500, OS06G0594700, and Os01g0393100 in CAbS. These potential candidate genes need to be studied further to decipher their functional roles in AbS dynamics.
Pandiyan Muthuramalingam; Subramanian R. Krishnan; Ramanujam Pothiraj; Manikandan Ramesh. Global Transcriptome Analysis of Combined Abiotic Stress Signaling Genes Unravels Key Players in Oryza sativa L.: An In silico Approach. Frontiers in Plant Science 2017, 8, 759 .
AMA StylePandiyan Muthuramalingam, Subramanian R. Krishnan, Ramanujam Pothiraj, Manikandan Ramesh. Global Transcriptome Analysis of Combined Abiotic Stress Signaling Genes Unravels Key Players in Oryza sativa L.: An In silico Approach. Frontiers in Plant Science. 2017; 8 ():759.
Chicago/Turabian StylePandiyan Muthuramalingam; Subramanian R. Krishnan; Ramanujam Pothiraj; Manikandan Ramesh. 2017. "Global Transcriptome Analysis of Combined Abiotic Stress Signaling Genes Unravels Key Players in Oryza sativa L.: An In silico Approach." Frontiers in Plant Science 8, no. : 759.