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  1. Fulltext Insights from the docking and molecular dynamics simulation of the Phosphopantetheinyl transferase (PptT) structural model from Mycobacterium tuberculosis
    Rohini K, Srikumar PS
    Bioinformation, 2013;9(13):685-9.
    PMID: 23930020 DOI: 10.6026/97320630009685
    A great challenge is posed to the treatment of tuberculosis due to the evolution of multidrug-resistant (MDR) and extensively drugresistant (XDR) strains of Mycobacterium tuberculosis in recent times. The complex cell envelope of the bacterium contains unusual structures of lipids which protects the bacterium from host enzymes and escape immune response. To overcome the drug resistance, targeting "drug targets" which have a critical role in growth and virulence factor is a novel approach for better tuberculosis treatment. The enzyme Phosphopantetheinyl transferase (PptT) is an attractive drug target as it is primarily involved in post translational modification of various types-I polyketide synthases and assembly of mycobactin, which is required for lipid virulence factors. Our in silico studies reported that the structural model of M.tuberculosis PptT characterizes the structure-function activity. The refinement of the model was carried out with molecular dynamics simulations and was analyzed with root mean square deviation (RMSD), and radius of gyration (Rg). This confirmed the structural behavior of PptT in dynamic system. Molecular docking with substrate coenzyme A (CoA) identified the binding pocket and key residues His93, Asp114 and Arg169 involved in PptT-CoA binding. In conclusion, our results show that the M.tuberculosis PptT model and critical CoA binding pocket initiate the inhibitor design of PptT towards tuberculosis treatment.
  2. Exploring the structural insights on human laforin mutation K87A in Lafora disease--a molecular dynamics study
    Srikumar PS, Rohini K
    Appl Biochem Biotechnol, 2013 Oct;171(4):874-82.
    PMID: 23904258 DOI: 10.1007/s12010-013-0393-x
    Lafora disease (LD) is an autosomal recessive, progressive form of myoclonus epilepsy which affects worldwide. LD occurs mainly in countries like southern Europe, northern Africa, South India, and in the Middle East. LD occurs with its onset mainly in teenagers and leads to decline and death within 2 to 10 years. The genes EPM2A and EPM2B are commonly involved in 90 % of LD cases. EPM2A codes for protein laforin which contains an amino terminal carbohydrate binding module (CBM) belonging to the CBM20 family and a carboxy terminal dual specificity phosphatase domain. Mutations in laforin are found to abolish glycogen binding and have been reported in wet lab methods. In order to investigate on structural insights on laforin mutation K81A, we performed molecular dynamics (MD) simulation studies for native and mutant protein. MD simulation results showed loss of stability due to mutation K87A which confirmed the structural reason for conformational changes observed in laforin. The conformational change of mutant laforin was confirmed by analysis using root mean square deviation, root mean square fluctuation, solvent accessibility surface area, radius of gyration, hydrogen bond, and principle component analysis. Our results identified that the flexibility of K87A mutated laforin structure, with replacement of acidic amino acid to aliphatic amino acid in functional CBM domain, have more impact in abolishing glycogen binding that favors LD.
  3. Structural insights on Mycobacterium tuberculosis thiazole synthase--a molecular dynamics/docking approach
    Rohini K, Srikumar PS
    Appl Biochem Biotechnol, 2013 Mar;169(6):1790-8.
    PMID: 23340867 DOI: 10.1007/s12010-013-0110-9
    Tuberculosis (TB), an epidemic disease, affects the world with death rate of two million people every year. The bacterium Mycobacterium tuberculosis was found to be a more potent and disease-prolonged bacterium among the world due to multi-drug resistance. Emergence of new drug targets is needed to overcome the bacterial resistance that leads to control epidemic tuberculosis. The pathway thiamine biosynthesis was targeting M. tuberculosis due to its role in intracellular growth of the bacterium. The screening of enzymes involved in thiamin biosynthesis showed novel target thiazole synthase (ThiG) involved in catalysis of rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. We carried out homology modeling for ThiG to understand the structure-function relationship, and the model was refined with MD simulations. The results showed that the model predicted with (α + β)8-fold of synthase family proteins. Molecular docking of ThiG model with substrate DXP showed binding mode and key residues ARG46, ASN69, THR41, and LYS96 involved in the catalysis. First-line anti-tuberculosis drugs were docked with ThiG to identify the inhibition. The report showed the anti-tuberculosis drugs interact well with ThiG which may lead to block thiamin biosynthesis pathway.
  4. Fulltext Assessment of serum calcium and phosphorus in pulmonary tuberculosis patients before, during and after chemotherapy
    Rohini K, Bhat S, Srikumar PS, Mahesh Kumar A
    Indian J Clin Biochem, 2014 Jul;29(3):377-81.
    PMID: 24966490 DOI: 10.1007/s12291-013-0383-3
    Our study was aimed to assess the levels of serum calcium and phosphorus in pulmonary tuberculosis patients. Blood samples were collected from 40 patients with pulmonary tuberculosis before treatment (PTB-0), at the end of 2 months of intensive phase of treatment (PTB-2) and after 6 months of treatment (PTB-6). Age and weight matched normal healthy volunteers (n = 37) served as normal controls. Serum was analyzed for calcium and phosphorus. Serum calcium significantly decreased to hypocalcemic levels and serum phosphorus significantly decreased but was within normophosphatemic limits in pulmonary tuberculosis. Chemotherapy for tuberculosis managed to raise serum levels of both the ions, with hypocalcemia still persisting in majority of patients during treatment but getting resolved in a significant percentage of patients at the end of 6 months of treatment. Results indicate the need for calcium and phosphorus supplements in tuberculosis patients during chemotherapy. This study also warrants the need for regular monitoring of serum calcium and phosphorus in patients undergoing anti-tuberculosis treatment.
  5. Fulltext Serum PCT and its Relation to Body Weight Gain in Pulmonary Tuberculosis
    Rohini K, Bhat S, Srikumar PS, Mahesh Kumar A
    Indian J Clin Biochem, 2015 Jul;30(3):329-33.
    PMID: 26089621 DOI: 10.1007/s12291-014-0432-6
    The present study was aimed at assessing alterations in serum PCT in terms of its relation to body weight gain in pulmonary tuberculosis (PTB) patients undergoing treatment. Among patients (25-75 years) diagnosed with pulmonary tuberculosis, those that were new smear positive, showed sputum conversion at the end of 2 months and were declared clinically cured at the end of 6 months, were included in the study (n = 40). Serum procalcitonin was determined by BRAHMS PCT-Q kit. Patients were divided into two study groups-Group 1 (n = 21; serum PCT > 2 ng/ml at diagnosis), Group 2 (n = 19; serum PCT > 10 ng/ml at diagnosis). Body weights of all patients were obtained at three different time points, PTB-0 (at diagnosis), PTB-2 (after 2 months of intensive treatment) and PTB-6 (after 6 months of treatment). In both groups, mean body weights at PTB-2 and PTB-6 were significantly higher than those at PTB-0 and at PTB-6 were significantly higher than those at PTB-2. However, percentage body weight gain following 2 months of intensive treatment was higher in group 1 (4.05 % gain, p 
  6. Molecular dynamics simulations and principal component analysis on human laforin mutation W32G and W32G/K87A
    Srikumar PS, Rohini K, Rajesh PK
    Protein J, 2014 Jun;33(3):289-95.
    PMID: 24770803 DOI: 10.1007/s10930-014-9561-2
    Mutations in human laforin lead to an autosomal neurodegenerative disorder Lafora disease. In N-terminal carbohydrate binding domain of laforin, two mutations W32G and K87A are reported as highly disease causing laforin mutants. Experimental studies reported that mutations are responsible for the abolishment of glycogen binding which is a critical function of laforin. Our current computational study focused on the role of conformational changes in human laforin structure due to existing single mutation W32G and prepared double mutation W32G/K87A related to loss of glycogen binding. We performed 10 ns molecular dynamics (MD) simulation studies in the Gromacs package for both mutations and analyzed the trajectories. From the results, the global properties like root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessible surface area and hydrogen bonds showed structural changes in atomic level observed in W32G and W32G/K87A laforin mutants. The conformational change induced by mutants influenced the loss of the overall stability of the native laforin. Moreover, the change in overall motion of protein was analyzed by principal component analysis and results showed protein clusters expanded more than native and also change in direction in case of double mutant in conformational space. Overall, our report provides theoretical information on loss of structure-function relationship due to flexible nature of laforin mutants. In conclusion, comparative MD simulation studies support the experimental data on W32G and W32G/K87A related to the lafora disease mechanism on glycogen binding.
  7. Fulltext Assessment of Hematological Parameters in Pulmonary Tuberculosis Patients
    Rohini K, Surekha Bhat M, Srikumar PS, Mahesh Kumar A
    Indian J Clin Biochem, 2016 Jul;31(3):332-5.
    PMID: 27382206 DOI: 10.1007/s12291-015-0535-8
    The aim of the study was the assessment of hematological parameters in pulmonary tuberculosis patients. Forty patients diagnosed with tuberculosis were recruited from the Institute of Thoracic Medicine on the basis of history, clinical examination, chest radiography, sputum examination and related laboratory parameters and were compared with age and sex matched healthy volunteers (n = 40). Hematological parameters and CRP in tuberculosis patients were determined. The mean values for serum hemoglobin level, RBC count and platelet count in PTB was found to be less (p 
  8. Fulltext Ecotoxicological assessment and dermal layer interactions of nanoparticle and its routes of penetrations
    Thanigaivel S, Vickram AS, Anbarasu K, Gulothungan G, Nanmaran R, Vignesh D, et al.
    Saudi J Biol Sci, 2021 Sep;28(9):5168-5174.
    PMID: 34466094 DOI: 10.1016/j.sjbs.2021.05.048
    Our review focused on nanomaterials-based toxicity evaluation and its exposure to the human and aquatic animals when it was leached and contaminated in the environment. Ecotoxicological assessment and its mechanism mainly affect the skin covering layers and its preventive barriers that protect the foreign particles' skin. Nanoscale materials are essential in the medical field, especially in biomedical and commercial applications such as nanomedicine and drug delivery, mainly in therapeutic treatments. However, various commercial formulations of pharmaceutical drugs are manufactured through a series of clinical trials. The role of such drugs and their metabolites has not met the requirement of an individual's need at the early stage of the treatments except few drugs and medicines with minimal or no side effects. Therefore, biology and medicines are taken up the advantages of nano scaled drugs and formulations for the treatment of various diseases. The present study identifies and analyses the different nanoparticles and their chemical components on the skin and their effects due to penetration. There are advantageous factors available to facilitate positive and negative contact between dermal layers. It creates a new agenda for an established application that is mainly based on skin diseases.
  9. Fulltext Identification and Structure Prediction of Human Septin-4 as a Biomarker for Diagnosis of Asthenozoospermic Infertile Patients-Critical Finding Toward Personalized Medicine
    Vickram AS, Anbarasu K, Jeyanthi P, Gulothungan G, Nanmaran R, Thanigaivel S, et al.
    Front Med (Lausanne), 2021;8:723019.
    PMID: 34926486 DOI: 10.3389/fmed.2021.723019
    Semen parameters are been found as a key factor to evaluate the count and morphology in the given semen sample. The deep knowledge of male infertility will unravel with semen parameters correlated with molecular and biochemical parameters. The current research study is to identify the motility associated protein and its structure through the in-silico approach. Semen samples were collected and initial analysis including semen parameters was analyzed by using the World Health Organization protocol. Semen biochemical parameters, namely, seminal plasma protein concentration, fructose content, and glucosidase content were calculated and evaluated for correlation. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) were carried out for identification of Septin-4 presence in the semen sample. Mascot search was done for protein conformation and in-silico characterization of Septin-4 by structural modeling in Iterative Threading Assembly Refinement (I-TASSER). Twenty-five nanoseconds molecular dynamics (MD) simulations results showed the stable nature of Septin-4 in the dynamic system. Overall, our results showed the presence of motility-associated protein in normospermia and control samples and not in the case of asthenospermia and oligoasthenospermia. Molecular techniques characterized the presence of Septin-4 and as a novel biomarker for infertility diagnosis.
  10. Carbon-based nanomaterial intervention and efficient removal of various contaminants from effluents - A review
    Manimegalai S, Vickram S, Deena SR, Rohini K, Thanigaivel S, Manikandan S, et al.
    Chemosphere, 2023 Jan;312(Pt 1):137319.
    PMID: 36410505 DOI: 10.1016/j.chemosphere.2022.137319
    Water treatment is a worldwide issue. This review aims to present current problems and future challenges in water treatments with the existing methodologies. Carbon nanotube production, characterization, and prospective uses have been the subject of considerable and rigorous research around the world. They have a large number of technical uses because of their distinct physical characteristics. Various catalyst materials are used to make carbon nanotubes. This review's primary focus is on integrated and single-treatment technologies for all kinds of drinking water resources, including ground and surface water. Inorganic non-metallic matter, heavy metals, natural organic matter, endocrine-disrupting chemicals, disinfection by-products and microbiological pollutants are among the contaminants that these treatment systems can remediate in polluted drinking water resources. Significant advances in the antibacterial and adsorption capabilities of carbon-based nanomaterials have opened up new options for excluding organic/inorganic and biological contaminants from drinking water in recent years. The advancements in multifunctional nanocomposites synthesis pave the possibility for their use in enhanced wastewater purification system design. The adsorptive and antibacterial characteristics of six main kinds of carbon nanomaterials are single-walled carbon nanotubes, multi-walled carbon nanotubes, graphene, graphene oxide, fullerene and single-walled carbon nanohorns. This review potentially addressed the essential metallic and polymeric nanocomposites, are described and compared. Barriers to use these nanoparticles in long-term water treatment are also discussed.
  11. Fulltext Seminal exosomes - An important biological marker for various disorders and syndrome in human reproduction
    Vickram AS, Srikumar PS, Srinivasan S, Jeyanthi P, Anbarasu K, Thanigaivel S, et al.
    Saudi J Biol Sci, 2021 Jun;28(6):3607-3615.
    PMID: 34121904 DOI: 10.1016/j.sjbs.2021.03.038
    BACKGROUND: Exosomes are nano-sized membrane vesicles, secreted by different types of cells into the body's biological fluids. They are found in abundance in semen as compared to other fluids. Exosomes contain a cargo of lipid molecules, proteins, phospholipids, cholesterol, mRNAs, and miRNAs. Each molecule of seminal exosomes (SE) has a potential role in male reproduction for childbirth. Many potential candidates are available within the seminal exosomes that can be used as diagnostic markers for various diseases or syndromes associated with male reproduction. Also these seminal exospmes play a major role in female reproductive tract for effective fertilization.

    AIM: The aim of this review is to focus on the advancement of human seminal exosomal research and its various properties.

    METHODS: We used many databases like Scopus, Google scholar, NCBI-NLM and other sources to filter the articles of interest published in exosomes. We used phrases like "Exosomes in human semen", "Composition of exosomes in human semen" and other relevant words to filter the best articles.

    RESULTS: Seminal exosomes play a major role in sperm functions like cell-to-cell communication, motility of the sperm cells, maintaining survival capacity for the sperm in the female reproductive tract and spermatogenesis. Also, seminal exosomes are used as a carrier for many regulatory elements using small RNA molecules. miRNAs of the seminal exosomes can be used as a diagnostic marker for prostate cancer instead of prostate specific antigen (PSA). Epididymosomes can be used as a biomarker for reproductive diseases and male infertility.

    CONCLUSION: Seminal exosomes could be used as biological markers for various reproductive disorders, male infertility diagnosis, and it can be used in anti-retroviral research for the identification of novel therapeutics for HIV-1 infection and transmission.

  12. Fulltext Identification of key biomarkers and associated pathways of pancreatic cancer using integrated transcriptomic and gene network analysis
    Rambabu M, Konageni N, Vasudevan K, Dasegowda KR, Gokul A, Jayanthi S, et al.
    Saudi J Biol Sci, 2023 Nov;30(11):103819.
    PMID: 37860809 DOI: 10.1016/j.sjbs.2023.103819
    Pancreatic cancer shows malignancy around the world standing in 4th position for causing death globally. This cancer is majorly divided into exocrine and neuroendocrine where exocrine pancreatic ductal adenocarcinoma is observed to be nearly 85% of cases. The lack of diagnosis of pancreatic cancer is considered to be one of the major drawbacks to the prognosis and treatment of pancreatic cancer patients. The survival rate after diagnosis is very low, due to the higher incidence of drug resistance to cancer which leads to an increase in the mortality rate. The transcriptome analysis for pancreatic cancer involves dataset collection from the ENA database, incorporating them into quality control analysis to the quantification process to get the summarized read counts present in collected samples and used for further differential gene expression analysis using the DESeq2 package. Additionally, explore the enriched pathways using GSEA software and represented them by utilizing the enrichment map finally, the gene network has been constructed by Cytoscape software. Furthermore, explored the hub genes that are present in the particular pathways and how they are interconnected from one pathway to another has been analyzed. Finally, we identified the CDKN1A, IL6, and MYC genes and their associated pathways can be better biomarker for the clinical processes to increase the survival rate of of pancreatic cancer.
  13. Fulltext Role of Zinc (Zn) in Human Reproduction: A Journey from Initial Spermatogenesis to Childbirth
    Vickram S, Rohini K, Srinivasan S, Nancy Veenakumari D, Archana K, Anbarasu K, et al.
    Int J Mol Sci, 2021 Feb 22;22(4).
    PMID: 33671837 DOI: 10.3390/ijms22042188
    Zinc (Zn), the second-most necessary trace element, is abundant in the human body. The human body lacks the capacity to store Zn; hence, the dietary intake of Zn is essential for various functions and metabolism. The uptake of Zn during its transport through the body is important for proper development of the three major accessory sex glands: the testis, epididymis, and prostate. It plays key roles in the initial stages of germ cell development and spermatogenesis, sperm cell development and maturation, ejaculation, liquefaction, the binding of spermatozoa and prostasomes, capacitation, and fertilization. The prostate releases more Zn into the seminal plasma during ejaculation, and it plays a significant role in sperm release and motility. During the maternal, labor, perinatal, and neonatal periods, the part of Zn is vital. The average dietary intake of Zn is in the range of 8-12 mg/day in developing countries during the maternal period. Globally, the dietary intake of Zn varies for pregnant and lactating mothers, but the average Zn intake is in the range of 9.6-11.2 mg/day. The absence of Zn and the consequences of this have been discussed using critical evidence. The events and functions of Zn related to successful fertilization have been summarized in detail. Briefly, our current review emphasizes the role of Zn at each stage of human reproduction, from the spermatogenesis process to childbirth. The role of Zn and its supplementation in in vitro fertilization (IVF) opens opportunities for future studies on reproductive biology.
  14. Fulltext Cardiovascular diseases prediction by machine learning incorporation with deep learning
    Subramani S, Varshney N, Anand MV, Soudagar MEM, Al-Keridis LA, Upadhyay TK, et al.
    Front Med (Lausanne), 2023;10:1150933.
    PMID: 37138750 DOI: 10.3389/fmed.2023.1150933
    It is yet unknown what causes cardiovascular disease (CVD), but we do know that it is associated with a high risk of death, as well as severe morbidity and disability. There is an urgent need for AI-based technologies that are able to promptly and reliably predict the future outcomes of individuals who have cardiovascular disease. The Internet of Things (IoT) is serving as a driving force behind the development of CVD prediction. In order to analyse and make predictions based on the data that IoT devices receive, machine learning (ML) is used. Traditional machine learning algorithms are unable to take differences in the data into account and have a low level of accuracy in their model predictions. This research presents a collection of machine learning models that can be used to address this problem. These models take into account the data observation mechanisms and training procedures of a number of different algorithms. In order to verify the efficacy of our strategy, we combined the Heart Dataset with other classification models. The proposed method provides nearly 96 percent of accuracy result than other existing methods and the complete analysis over several metrics has been analysed and provided. Research in the field of deep learning will benefit from additional data from a large number of medical institutions, which may be used for the development of artificial neural network structures.
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