Displaying publications 1 - 20 of 333 in total

  1. Kumar S
    Bioinformation, 2015;11(1):11-6.
    PMID: 25780274 DOI: 10.6026/97320630011011
    Rubisco is a very large, complex and one of the most abundant proteins in the world and comprises up to 50% of all soluble protein in plants. The activity of Rubisco, the enzyme that catalyzes CO2 assimilation in photosynthesis, is regulated by Rubisco activase (Rca). In the present study, we searched for hypothetical protein of Vitis vinifera which has putative Rubisco activase function. The Arabidopsis and tobacco Rubisco activase protein sequences were used as seed sequences to search against Vitis vinifera in UniprotKB database. The selected hypothetical proteins of Vitis vinifera were subjected to sequence, structural and functional annotation. Subcellular localization predictions suggested it to be cytoplasmic protein. Homology modelling was used to define the three-dimensional (3D) structure of selected hypothetical proteins of Vitis vinifera. Template search revealed that all the hypothetical proteins share more than 80% sequence identity with structure of green-type Rubisco activase from tobacco, indicating proteins are evolutionary conserved. The homology modelling was generated using SWISS-MODEL. Several quality assessment and validation parameters computed indicated that homology models are reliable. Further, functional annotation through PFAM, CATH, SUPERFAMILY, CDART suggested that selected hypothetical proteins of Vitis vinifera contain ATPase family associated with various cellular activities (AAA) and belong to the AAA+ super family of ring-shaped P-loop containing nucleoside triphosphate hydrolases. This study will lead to research in the optimization of the functionality of Rubisco which has large implication in the improvement of plant productivity and resource use efficiency.
  2. Kumar S
    BMC Res Notes, 2015;8:9.
    PMID: 25595103 DOI: 10.1186/s13104-015-0976-4
    Cytochrome P450s (CYPs) are important heme-containing proteins, well known for their monooxygenase reaction. The human cytochrome P450 4X1 (CYP4X1) is categorized as "orphan" CYP because of its unknown function. In recent studies it is found that this enzyme is expressed in neurovascular functions of the brain. Also, various studies have found the expression and activity of orphan human cytochrome P450 4X1 in cancer. It is found to be a potential drug target for cancer therapy. However, three-dimensional structure, the active site topology and substrate specificity of CYP4X1 remain unclear.
  3. Bilodi, Arun Kumar .S, Gangadhar, M R
    Anomaly is a congenital disorder. It is a medical condition that is present since birth. But the word congenital neither applies nor excludes genetic disorder. Congenital anomalies due to environmental factors are called as Teratogens. Infections, deficiency in the diet and toxins are environmental causes. Maternal folic acid deficiency may cause spina bifida. Intake of alcohol, and certain prescribed drugs like phenytoin may cause congenital anomalies or defects. Apart from physical anomalies, other types of congenital disorders are inborn errors of metabolism (Kumar, Abbas and Fausto, 2005). About 15% to 25% of anomalies are due to chromosomal factors or single gene factors, 8% to 12% anomalies are said to be due to environmental factors, 25% are said to be due to multifactorial inheritance 40% to 60% of anomalies are of unknown origin (Stevenson, 1993 ; Nelson and Holmes, 1984). Congenital anomalies are present since birth with structural deformity found immediately after birth or their presence may be detected by signs and symptoms later on (Holland and Brew, 1991). Congenital Anomalies are seen in 2% of population as major abnormality. There are two types of abnormalities, namely malformations where growth disturbances occur during embryogenesis and the other is deformation. It is late change that appears in a structure which was normal earlier (Roizen and Patterson, 2003).
  4. Kumar S
    Genomics Inform, 2017 Dec;15(4):162-169.
    PMID: 29307143 DOI: 10.5808/GI.2017.15.4.162
    Metal binding proteins or metallo-proteins are important for the stability of the protein and also serve as co-factors in various functions like controlling metabolism, regulating signal transport, and metal homeostasis. In structural genomics, prediction of metal binding proteins help in the selection of suitable growth medium for overexpression's studies and also help in obtaining the functional protein. Computational prediction using machine learning approach has been widely used in various fields of bioinformatics based on the fact all the information contains in amino acid sequence. In this study, random forest machine learning prediction systems were deployed with simplified amino acid for prediction of individual major metal ion binding sites like copper, calcium, cobalt, iron, magnesium, manganese, nickel, and zinc.
  5. Yusof A, Kumar S
    Parasitol. Res., 2012 May;110(5):1823-8.
    PMID: 22076052 DOI: 10.1007/s00436-011-2705-9
    Trichomonas vaginalis, a flagellated protozoan parasite, is commonly found in the genitourinary tract of humans. Its mode of reproduction has always been reported to be binary fission. The high parasite numbers seen in a relatively short period in in vitro cultures led us to believe that there must be other modes of reproduction. The present study for the first time provides transformational evidence at the ultrastructural level seen in tropohozoites of T. vaginalis undergoing a multiple asexual mode of reproduction. The findings show that the single cell with a nucleus is capable of dividing to as many as eight nuclei within the cytoplasmic body. Before the commencement of division, the nucleus remained round or ovoid in shape with condensed chromatin masses and only a few endoplasmic reticula surrounding the nucleus. During the division, the nucleus started to elongate and become irregular in shape with visible chromatin masses condensing with the accumulation of numerous endoplasmic reticula. Nuclear division gave rise to as many as eight nuclei within a cell, which could be seen to be connected by numerous endoplasmic reticula. In addition, a high number of hydrogenosomes and vacuoles can be seen in multinucleated T. vaginalis compared with single nucleated T. vaginalis. This study confirms that multiple modes of nuclear division do exist in T. vaginalis and are a precursor to progeny formation.
  6. Anil Kumar, S., Saif, S.A., Oothuman, P., Mustafa, M.I.A.
    Introduction: Reduced cerebral blood fl ow is associated with neurodegenerative disorders and dementia, in particular. Experimental evidence has demonstrated the initiating role of chronic cerebral hypoperfusion in neuronal damage to the hippocampus, the cerebral cortex, the white matter areas and the visual system. Permanent, bilateral occlusion of the common carotid arteries of rats (two vessel occlusion - 2VO) has been introduced for the reproduction of chronic cerebral hypoperfusion as it occurs in Alzheimer’s disease and human aging. Increased generation of free radicals through lipid peroxidation can damage neuronal cell membrane. Markers of lipid peroxidation have been found to be elevated in brain tissues and body fl uids in neurodegenerative diseases, including Alzheimer’s disease, Parkinson disease and amyotrophic lateral sclerosis. Materials and Methods: Malondialdehyde (MDA), fi nal product of lipid peroxidation, was estimated by thiobarbituric acid-reactive substances (TBARS) assay kit at eight weeks after induction of 2VO in the rats and control group. Results: Our study revealed a highly signifi cant (p
  7. Rodrigues, K. F., Yeoh, K. A., Kumar, S. V.
    Geographically isolated populations of endemic orchids have evolved and adapted to an existence within specifi c ecological niches. These populations are highly susceptible to anthropogenic
    infl uences on their microhabitats. The primary objective of conservation programs is the restoration of endangered populations to their ecologically sustainable levels, and the fi rst stage in the process of conservation involves estimation of molecular diversity at the level of the population. The approach described in this article involves the application of RAPD, Microsatellites and Chloroplast DNA markers for the characterization of the genetic structure of Paphiopedilum rothschildianum and Phalaenopsis gigantea, two endangered and endemic orchids of Sabah. This study has isolated a total of 96 microsatellite loci in P. rothschildianum and P. gigantea, 42 specifi c primer pairs have been designed for amplifi cation of microsatellite loci and are currently being applied to screen the breeding pools. The Chloroplast DNA regions amplifi ed by the primer pairs trnH-psbA and trnL-trnF exhibit distinct polymorphisms and can be used to establish phylogenetic
    relationships. The ability of microsatellite loci to cross-amplify selected varieties of orchids has been determined. The molecular markers developed will be applied to estimate population diversity
    levels and to formulate long-term management strategies for the conservation of endangered species of orchids of Sabah.
  8. Kumar S, Alagawadi KR
    Pharm Biol, 2013 May;51(5):607-13.
    PMID: 23363068 DOI: 10.3109/13880209.2012.757327
    Alpinia galanga Willd (Zingiberaceae) (AG) is a rhizomatous herb widely cultivated in shady regions of Malaysia, India, Indochina and Indonesia. It is used in southern India as a domestic remedy for the treatment of rheumatoid arthritis, cough, asthma, obesity, diabetes, etc. It was reported to have anti-obesity, hypoglycemic, hypolipidemic and antioxidant properties.
  9. Yusof AM, Kumar S
    Exp. Parasitol., 2012 Jul;131(3):267-73.
    PMID: 22525014 DOI: 10.1016/j.exppara.2012.03.015
    The protozoan Trichomonas vaginalis a sexually transmitted protozoan parasite causes vaginitis, urethritis and cervicitis in humans. The present study highlights phenotypic 'variant' forms of trophozoites isolated from patients suffering from cervical neoplasia condition. The growth curve of 10 isolates i.e., four non-cervical neoplasia (NCN) isolates (NCN1-NCN4) and six cervical neoplasia (CN) isolates (CN1-CN6) showed two distinct and different in vitro growth profiles. The parasite count and growth rates were significantly higher in trophozoites from CN isolates in cultures of day 2 up to day 8 (p<0.05, Mann-Whitney test). The average generation time was 1.84±0.40 and 3.38±0.55h for NCN and CN isolates respectively. The nucleus of trophozoites in CN isolates using acridine orange and DAPI showed more intense staining revealing higher nuclear content. The FITC-labeled Concanavalin A stained stronger green fluorescence with surface of trophozoites in CN isolates showing more rough and creased surface with numerous deep micropores. Transmission electron microscopy studies revealed that there was higher numbers of vacuoles and hydrogenosomes in these forms. The study mounted staining techniques, growth profiles, morphology, morphometry studies using scanning and transmission electron microscopy and confirms that the trophozoites from cervical neoplasia proliferates at a higher rate, shows higher FITC-labeled Concanavalin A binding with rough and creased surface implying that these are virulent forms which can aggravate or exacerbate cervical neoplasia conditions. The large numbers of hyrogenosomes and vacuoles implies that these forms are active and implicates a possible role in such conditions.
  10. Kumar S, Ratnavelu K
    PLoS ONE, 2016;11(6):e0157633.
    PMID: 27322645 DOI: 10.1371/journal.pone.0157633
    Scholars (n = 580) from 69 countries who had contributed articles in the field of Economics during the year 2015 participated in a survey that gauged their perceptions of various aspects of co-authorship, including its benefits, motivations, working relationships, order of authorship and association preferences. Among the main findings, significant differences emerged in the proportion of co-authored papers based on age, gender and number of years the researchers had spent in their present institution. Female scholars had a greater proportion of co-authored papers than male scholars. Respondents considered improved quality of paper, contribution of mutual expertise, and division of labor as the biggest benefits of and motivation for co-authorship. Contrary to common perceptions that Economics researchers used a predominantly alphabetical order of authorship, our study found that a considerable percentage of respondents (34.5%) had practiced an order of authorship based on the significance of the authors' contribution to the work. The relative importance of tasks differed significantly according to whether researchers co-authored as mentors or co-authored as colleagues. Lastly, researchers were found to associate, to varying degrees, with other researchers based on socio-academic parameters, such as nationality, ethnicity, gender, professional position and friendship. The study indicates that Economics authors perceive co-authorship as a rewarding endeavor. Nonetheless, the level of contribution and even the choice of association itself as a co-author depends to a great extent on the type of working relationship and socio-academic factors.
  11. Prasannan S, Kumar S, Gul YA
    Acta Chir. Belg., 2005 1 25;104(6):739-41.
    PMID: 15663288
    Pneumoperitoneum is almost always pathognomonic of a perforated abdominal viscus requiring urgent surgical intervention. Spontaneous or non-surgical pneumoperitoneum is a rare clinical condition arising secondary to abdominal, thoracic, gynaecologic or idiopathic causes. In addition to good clinical judgement, an important component in the management process is to rule out other causes of pneumoperitoneum by performing appropriate investigations. We describe a 60-year-old man who presented with clinical features of pseudo-obstruction, following an injury to his back which was compounded by hypokalaemia. Roentgenography revealed massive pneumoperitoneum and colonic distension. As there were no overt clinical features of peritonitis, the patient was managed conservatively with parenteral nutrition and close observation. A water-soluble contrast enema and computed tomography of the abdomen were of no help in identifying the cause of his pneumoperitoneum but were helpful in eliminating the presence of hollow viscus perforation or an obvious inflammatory focus. The aetiology of pneumoperitoneum in our patient was most likely due to dissection of air through the distended colonic wall, secondary to large bowel pseudo-obstruction. The diagnosis of spontaneous or non-surgical pneumoperitoneum is one of exclusion and we stress the importance of relying on clinical parameters when managing such patients conservatively.
  12. Yadav M, Arivananthan M, Kumar S
    Clin Diagn Virol, 1996 Oct;7(1):23-33.
    PMID: 9077427
    BACKGROUND: Human herpesvirus type 6 (HHV-6), an ubiquitous virus, is the causative agent for exanthem subitum. The virus is frequently associated with lymphoproliferative disorders and other diseases. Recently, we have reported the frequent presence of HHV-6 in oral carcinoma and the present study extends the observation to cervical carcinoma.

    OBJECTIVE: To examine the presence of HHV-6 in cervical carcinoma.

    STUDY DESIGN: Formalin-fixed, paraffin-embedded cervical carcinoma tissues were examined for the presence of HHV-6 by immunohistochemistry using two monoclonal antibodies that react to HHV-6-encoded p41/38 and gp116/64/54. In situ hybridization with variant-specific probes were used to type the HHV-6 DNA sequences present.

    RESULTS: A total of 14/26 (53.9%) carcinoma tissue specimens and 5/8 (62.5%) normal tissue specimens were positive for viral antigens. In situ hybridization studies revealed the presence of HHV-6 DNA sequences in 10/26 (38.5%) carcinoma tissue specimens and 1/8 (12.5%) normal tissue specimens. In the normal tissue, the HHV-6 was present in the endocervical ciliated columnar-epithelial cells and some cells in the subepithelial mucosa but in the carcinoma, the transformed cells were positive for the virus.

    CONCLUSIONS: HHV-6 viral proteins and DNA were found in more than one third of the cervical tissue examined suggesting possible viral expression in these tumours. The significance of the distribution and role of the HHV-6 in cervical tissue remains unclear. Since HHV-6 has an oncogenic potential, the virus may cooperate with other transforming agents for the progression of the disease.

  13. Arivananthan M, Yadav M, Kumar S
    J. Virol. Methods, 1997 Jun;66(1):5-14.
    PMID: 9220385
    Human herpesvirus-6 exists in two forms, HHV-6A which has not been clearly associated with any disease, and HHV-6B, the causative agent of exanthem subitum. The two variants have been distinguished by techniques such as dot blotting and restriction fragment length polymorphism of PCR products. This study aims to establish the prevalence of HHV-6A and HHV-6B in carcinoma tissues using variant-specific oligonucleotide probes. A total of 73 archived carcinoma biopsies from the oral, salivary gland, larynx, breast and cervix were obtained with seven histologically normal controls. In situ hybridization was carried out with nonradioactively labelled variant-specific probes. Samples that hybridized with both variant A and B probes were subjected further to nested PCR and digested with HindIII to distinguish the variants. A hybridization signal was observed in 76.2% of oral carcinoma tissue and 75.0% of salivary gland carcinoma tissue. In contrast, only 33.3% of cervical carcinoma tissue were positive for HHV-6 DNA. A hybridization signal was noted in all 4 laryngeal carcinoma tissues studied. However, the 10 breast carcinoma tissues studied were negative, as was the histologically normal tissue. The virus possesses tumourigenic potential and demonstrates virus transactivating properties. The frequency of HHV-6 variants in certain tumours suggest a cofactorial role in multistep carcinogenesis. While PCR amplifies selectively the predominant variant in a sample, this was not seen by in situ hybridization. The in situ hybridization technique allowed the localization of both HHV-6A and HHV-6B in the nuclei of transformed regions.
  14. Ruchi, K., Anil Kumar, S., Sunil, G., Bashir, A., Prabhat, S.
    Introduction: Attention deficit hyperactivity disorder (ADHD) is a frequently encountered clinical condition in children. Based on DSM IV-TR criteria it can be sub-classified into three distinct types namely hyperactiveimpulsive, inattentive and combined. Materials and Methods: In the present study, salivary antioxidant activity (AOA) in children with ADHD was compared with age-matched normal control subjects, both as a whole and also with regard to the three subtypes. Additionally, the effect of therapy on the altered AOA levels was investigated following short term (
  15. Bera H, Kumar S
    Int. J. Biol. Macromol., 2018 Mar;108:1053-1062.
    PMID: 29122714 DOI: 10.1016/j.ijbiomac.2017.11.019
    The current study aimed at developing diethonolamine-modified high-methoxyl pectin (DMP)-alginate (ALG) based core-shell composites for controlled intragastric delivery of metformin HCl (MFM) by combined approach of floating and bioadhesion. DMP with degree of amidation of 48.72% was initially accomplished and characterized by FTIR, DSC and XRD analyses. MFM-loaded core matrices were then fabricated by ionotropic gelation technique employing zinc acetate as cross-linker. The core matrices were further coated by fenugreek gum (FG)-ALG gel membrane via diffusion-controlled interfacial complexation method. Various formulations demonstrated excellent drug encapsulation efficiency (DEE, 51-70%) and sustained drug eluting behavior (Q8h, 72-96%), which were extremely influenced by polymer-blend (ALG:DMP) ratios, low density additives (olive oil/magnesium stearate) and FG-ALG coating inclusion. The drug release profile of the core-shell matrices (F-7) was best fitted in zero-order kinetic model with case-II transport driven mechanism. It also portrayed outstanding gastroretentive characteristics. Moreover, the composites were analyzed for surface morphology, drug-excipients compatibility, thermal behavior and drug crystallinity. Thus, the developed composites are appropriate for controlled stomach-specific delivery of MFM for type 2 diabetes management.
  16. Kumar S, Markscheffel B
    Scientometrics, 2016;109(1):533-550.
    PMID: 32287514 DOI: 10.1007/s11192-016-1942-1
    Hantavirus, one of the deadliest viruses known to humans, hospitalizes tens of thousands of people each year in Asia, Europe and the Americas. Transmitted by infected rodents and their excreta, Hantavirus are identified as etiologic agents of two main types of diseases-Hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome, the latter having a fatality rate of above 40 %. Although considerable research for over two decades has been going on in this area, bibliometric studies to gauge the state of research of this field have been rare. An analysis of 2631 articles, extracted from WoS databases on Hantavirus between 1980 and 2014, indicated a progressive increase (R2 = 0.93) in the number of papers over the years, with the majority of papers being published in the USA and Europe. About 95 % papers were co-authored and the most common arrangement was 4-6 authors per paper. Co-authorship has seen a steady increase (R2 = 0.57) over the years. We apply research collaboration network analysis to investigate the best-connected authors in the field. The author-based networks have 49 components (connected clump of nodes) with 7373 vertices (authors) and 49,747 edges (co-author associations) between them. The giant component (the largest component) is healthy, occupying 84.19 % or 6208 vertices with 47,117 edges between them. By using edge-weight threshold, we drill down into the network to reveal bonded communities. We find three communities' hotspots-one, led by researchers at University of Helsinki, Finland; a second, led by the Centers of Disease Control and Prevention, USA; and a third, led by Hokkaido University, Japan. Significant correlation was found between author's structural position in the network and research performance, thus further supporting a well-studied phenomenon that centrality effects research productivity. However, it was the PageRank centrality that out-performed degree and betweenness centrality in its strength of correlation with research performance.
  17. Jain S, Kumar S, Kaushal A
    Med. J. Malaysia, 2011 Oct;66(4):376-8.
    PMID: 22299566
    We report a case of rhinocerebral mucormycosis in a 31 year old immunocompetent female presenting initially like acute rhinosinusitis with nasal stuffiness, severe headache, vomiting who soon developed isolated right lateral rectus palsy. Computed tomography (CT) scan of the Post-Nasal Spaces(PNS) showed an ill defined expansile heterogenous density mass in the sphenoid with extension into the ethmoids, nasal cavity, optic canal, superior orbital fissure, clivus and right temporal lobe with signal void in Magnetic Resonance Imaging (MRI). The debris and polypoid mucosa obtained on nasal endoscopy revealed mucormycosis on histopathologic examination. The patient was managed with urgent surgical debridement and medical management.
  18. Yew CW, Kumar SV
    Mol. Biol. Rep., 2012 Feb;39(2):1783-90.
    PMID: 21625851 DOI: 10.1007/s11033-011-0919-7
    MicroRNAs (miRNAs) are small RNAs (sRNAs) with approximately 21-24 nucleotides in length. They regulate the expression of target genes through the mechanism of RNA silencing. Conventional isolation and cloning of miRNAs methods are usually technical demanding and inefficient. These limitations include the requirement for high amounts of starting total RNA, inefficient ligation of linkers, high amount of PCR artifacts and bias in the formation of short miRNA-concatamers. Here we describe in detail a method that uses 80 μg of total RNA as the starting material. Enhancement of the ligation of sRNAs and linkers with the use of polyethylene glycol (PEG8000) was described. PCR artifacts from the amplification of reverse-transcribed sRNAs were greatly decreased by using lower concentrations of primers and reducing the number of amplification cycles. Large concatamers with up to 1 kb in size with around 20 sRNAs/concatamer were obtained by using an optimized reaction condition. This protocol provide researchers with a rapid, efficient and cost-effective method for the construction of miRNA profiles from plant tissues containing low amounts of total RNA, such as fruit flesh and senescent leaves.
  19. Nithyamathi K, Chandramathi S, Kumar S
    PLoS ONE, 2016;11(2):e0136709.
    PMID: 26914483 DOI: 10.1371/journal.pone.0136709
    BACKGROUND: One of the largest cross-sectional study in recent years was carried out to investigate the prevalence of intestinal parasitic infections among urban and rural school children from five states namely Selangor, Perak, Pahang, Kedah and Johor in Peninsula Malaysia. This information would be vital for school authorities to influence strategies for providing better health especially in terms of reducing intestinal parasitism.

    METHODS AND PRINCIPAL FINDINGS: A total of 3776 stool cups was distributed to 26 schools throughout the country. 1760 (46.61%) responded. The overall prevalence of intestinal parasitic infection in both rural and urban areas was 13.3%, with Blastocystis sp (10.6%) being the most predominant, followed by Trichuris trichiura (3.4%), Ascaris lumbricoides (1.5%) and hook worm infection (0.9%). Only rural school children had helminthic infection. In general Perak had the highest infection (37.2%, total, n = 317), followed by Selangor (10.4%, total, n = 729), Pahang (8.6%, total, n = 221), Kedah (6.2%, total, n = 195) and Johor (3.4%, total, n = 298). School children from rural schools had higher infection (13.7%, total, n = 922) than urban school children (7.2%, total, n = 838). Subtype (ST) 3 (54.3%) is the most predominant ST with persons infected with only ST1 and ST3 showing symptoms. Blastocystis sp infection significantly associated with low household income, low parent's education and presence of symptoms (p<0.05).

    CONCLUSION: It is critical that we institute deworming and treatment to eradicate the parasite especially in rural school children.

  20. Girish S, Kumar S, Aminudin N
    Parasit Vectors, 2015;8:332.
    PMID: 26082155 DOI: 10.1186/s13071-015-0942-y
    In the local Malaysian context, herbal plants such as Eurycoma longifolia (Tongkat Ali), Orthosiphon stamineus (MisaiKucing), Ficus deltoidea (Mas Cotek), Zingiber officinale (Halia Bara) and Barringtonia racemosa (Putat) are known and widely used for its therapeutic properties. The first part of this study aims to screen for the anti-protozoal activity of these herbal plant extracts against Blastocystis sp. isolate subtype (ST) 3. Herbal extract with the highest efficacy was further fractionized into water and ethyl acetate fractions and tested against ST1, ST3 and ST5 Blastocystis sp. isolates. These isolates were also exposed to allopathic drugs, Metronidazole (MTZ), Tinidazole, Trimethoprim-sulfamethoxazole(TMP-SMX), Ketoconazole and Nitazoxanide for comparison purpose.
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