Displaying publications 1 - 20 of 30 in total

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  1. Wasito I, Hashim SZ, Sukmaningrum S
    Bioinformation, 2007 Dec 30;2(5):175-81.
    PMID: 18305825
    Gene expression profiling plays an important role in the identification of biological and clinical properties of human solid tumors such as colorectal carcinoma. Profiling is required to reveal underlying molecular features for diagnostic and therapeutic purposes. A non-parametric density-estimation-based approach called iterative local Gaussian clustering (ILGC), was used to identify clusters of expressed genes. We used experimental data from a previous study by Muro and others consisting of 1,536 genes in 100 colorectal cancer and 11 normal tissues. In this dataset, the ILGC finds three clusters, two large and one small gene clusters, similar to their results which used Gaussian mixture clustering. The correlation of each cluster of genes and clinical properties of malignancy of human colorectal cancer was analysed for the existence of tumor or normal, the existence of distant metastasis and the existence of lymph node metastasis.
  2. Wang E, Chinni S, Bhore SJ
    Bioinformation, 2014;10(3):130-7.
    PMID: 24748752 DOI: 10.6026/97320630010130
    The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken.
  3. Suresh A, Karthikraja V, Lulu S, Kangueane U, Kangueane P
    Bioinformation, 2009 Nov 17;4(5):197-205.
    PMID: 20461159
    The formation of protein homodimer complexes for molecular catalysis and regulation is fascinating. The homodimer formation through 2S (2 state), 3SMI (3 state with monomer intermediate) and 3SDI (3 state with dimer intermediate) folding mechanism is known for 47 homodimer structures. Our dataset of forty-seven homodimers consists of twenty-eight 2S, twelve 3SMI and seven 3SDI. The dataset is characterized using monomer length, interface area and interface/total (I/T) residue ratio. It is found that 2S are often small in size with large I/T ratio and 3SDI are frequently large in size with small I/T ratio. Nonetheless, 3SMI have a mixture of these features. Hence, we used these parameters to develop a decision tree model. The decision tree model produced positive predictive values (PPV) of 72% for 2S, 58% for 3SMI and 57% for 3SDI in cross validation. Thus, the method finds application in assigning homodimers with folding mechanism.
  4. Sekimoto O, Chiappelli F
    Bioinformation, 2024;20(1):1-3.
    PMID: 38352906 DOI: 10.6026/973206300200001
    First identified as a pathogen in Malaysia and Singapore in 1999, Nipah virus (NiV) caused nearly 300 human cases and over 100 fatalities. It also killed about 1 million pigs. Three years later (2002), it was reported in Pteropus bats in Malaysia, in Cambodia & Thailand, (2005), and as far as Madagascar (2007) and Ghana (2008). India (Kerala) reported its first human NiV-caused fatalities in September 2023. Taken together, these trends emphasize its public health threat. In humans, NiV infection initially leads to fever, headache, body aches and muscle pain, nausea and vomiting. The symptoms rapidly evolve into sore throat, cough and atypical pneumonia leading to severe respiratory distress. The cadre of NiV-induced pathology (Nipah disease, NiD) then includes severe dizziness and drowsiness, progressive alteration in cognition and consciousness, acute encephalitis and seizures. Public health protocols (e.g., mask-wearing, quarantine), essential to contain and control CoViD-19, seem insufficient to contain NiD spread because NiV transmission occurs primarily via direct contacts with body fluids of infected carriers, but presumably not by airborne transmission. As in the case of SARS-C0V2, health care providers (i.e., physicians, dentists, nurses, dental assistants) are greatest risks not only of contracting but of spreading NiV infection. NiV is a high-pathogenicity pathogen, against which, at present, we have no anti-viral medications or preventive vaccine. Taken together, the evidence to date heightens the threat of an upcoming NiD pandemic.
  5. Sabetian S, Shamsir MS
    Bioinformation, 2019;15(7):513-522.
    PMID: 31485137 DOI: 10.6026/97320630015513
    Proteins can interact in various ways, ranging from direct physical relationships to indirect interactions in a formation of protein-protein interaction network. Diagnosis of the protein connections is critical to identify various cellular pathways. Today constructing and analyzing the protein interaction network is being developed as a powerful approach to create network pharmacology toward detecting unknown genes and proteins associated with diseases. Discovery drug targets regarding therapeutic decisions are exciting outcomes of studying disease networks. Protein connections may be identified by experimental and recent new computational approaches. Due to difficulties in analyzing in-vivo proteins interactions, many researchers have encouraged improving computational methods to design protein interaction network. In this review, the experimental and computational approaches and also advantages and disadvantages of these methods regarding the identification of new interactions in a molecular mechanism have been reviewed. Systematic analysis of complex biological systems including network pharmacology and disease network has also been discussed in this review.
  6. 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.
  7. Razmara J, Deris SB, Illias RB, Parvizpour S
    Bioinformation, 2013;9(7):345-8.
    PMID: 23750078 DOI: 10.6026/97320630009345
    A hidden Markov model (HMM) has been utilized to predict and generate artificial secretory signal peptide sequences. The strength of signal peptides of proteins from different subcellular locations via Lactococcus lactis bacteria correlated with their HMM bit scores in the model. The results show that the HMM bit score +12 are determined as the threshold for discriminating secreteory signal sequences from the others. The model is used to generate artificial signal peptides with different bit scores for secretory proteins. The signal peptide with the maximum bit score strongly directs proteins secretion.
  8. Ramamoorthy K, Raghunandhakumar S, Anand RS, Paramasivam A, Kamaraj S, Nagaraj S, et al.
    Bioinformation, 2020;16(11):965-973.
    PMID: 34803274 DOI: 10.6026/97320630016965
    Astaxanthin (AXN) is known to have health benefits by epidemiological studies. Therefore, it is of interest to assess the effect of AXN (derived from indigenous unicellular green alga Haematococcus lacustris) to modulate cell cycle arrest, lysosomal acidification and eventually apoptosis using in vitro in A549 lung cancer cells. Natural extracts of astaxanthin were obtained by standardized methods as reported earlier and characterized by standard HPLC and MS. Treatment of A549 cells with AXN (purified fraction) showed significant reduction in cell viability (about 50%) as compared to crude extract at 50µM concentration. Thus, we show the anticancer effects and lysosomal acidification in A549 cells by Astaxanthin from Haematococcus lacustris for further consideration. Together, our results demonstrated the anticancer potential of AXN from Haematococcus lacustris, which is found to be mediated via its ability to induce cell cycle arrest, lysosomal acidification and apoptotic induction.
  9. Muthu N, Lee SY, Phua KK, Bhore SJ
    Bioinformation, 2016;12(12):420-424.
    PMID: 28405126 DOI: 10.6026/97320630012420
    Plants are very complex organisms that produce medicinally important natural products. The Star-fruit producing plant (Averrhoa carambola L.) is a species of woody plant in the family Oxalidaceae native to the Philippines, Indonesia, Malaysia, Vietnam, India, Bangladesh and Sri Lanka; but, cultivated in many parts of the world. Star-fruits are popular tropical fruits and used commonly in Ayurvedic and Traditional Chinese Medicines (TCM) in India, China, and Brazil to relieve ailments such as chronic headache, fever, cough, gastro-enteritis, diarrhoea, ringworm infections, and skin inflammations. However, this fruit contains high amount of oxalate, which is hazardous for uremic patients, and caramboxin (CBX), which is neurotoxic. The aim of this review is to highlight the nutritional, medicinal and toxicological traits of the star-fruits.
  10. Moorthy K, Mohamad MS
    Bioinformation, 2011;7(3):142-6.
    PMID: 22125385
    A random forest method has been selected to perform both gene selection and classification of the microarray data. In this embedded method, the selection of smallest possible sets of genes with lowest error rates is the key factor in achieving highest classification accuracy. Hence, improved gene selection method using random forest has been proposed to obtain the smallest subset of genes as well as biggest subset of genes prior to classification. The option for biggest subset selection is done to assist researchers who intend to use the informative genes for further research. Enhanced random forest gene selection has performed better in terms of selecting the smallest subset as well as biggest subset of informative genes with lowest out of bag error rates through gene selection. Furthermore, the classification performed on the selected subset of genes using random forest has lead to lower prediction error rates compared to existing method and other similar available methods.
  11. Mohamad SB, Ong AL, Ripen AM
    Bioinformation, 2008 Jun 18;2(9):369-72.
    PMID: 18795108
    Laccase belongs to the family of blue multi-copper oxidases and are capable of oxidizing a wide range of aromatic compounds. Laccases have industrial applications in paper pulping or bleaching and hydrocarbon bioremediation as a biocatalyst. We describe the design of a laccase with broader substrate spectrum in bioremediation. The application of evolutionary trace (ET) analysis of laccase at the ligand binding site for optimal design of the enzyme is described. In this attempt, class specific sites from ET analysis were mapped onto known crystal structure of laccase. The analysis revealed 162PHE as a critical residue in structure function relationship studies.
  12. Misman MF, Mohamad MS, Deris S, Abdullah A, Hashim SZ
    Bioinformation, 2011;7(4):169-75.
    PMID: 22102773
    Pathway analysis has lead to a new era in genomic research by providing further biological process information compared to traditional single gene analysis. Beside the advantage, pathway analysis provides some challenges to the researchers, one of which is the quality of pathway data itself. The pathway data usually defined from biological context free, when it comes to a specific biological context (e.g. lung cancer disease), typically only several genes within pathways are responsible for the corresponding cellular process. It also can be that some pathways may be included with uninformative genes or perhaps informative genes were excluded. Moreover, many algorithms in pathway analysis neglect these limitations by treating all the genes within pathways as significant. In previous study, a hybrid of support vector machines and smoothly clipped absolute deviation with groups-specific tuning parameters (gSVM-SCAD) was proposed in order to identify and select the informative genes before the pathway evaluation process. However, gSVM-SCAD had showed a limitation in terms of the performance of classification accuracy. In order to deal with this limitation, we made an enhancement to the tuning parameter method for gSVM-SCAD by applying the B-Type generalized approximate cross validation (BGACV). Experimental analyses using one simulated data and two gene expression data have shown that the proposed method obtains significant results in identifying biologically significant genes and pathways, and in classification accuracy.
  13. 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.
  14. Khairudin NB, Mazlan NS
    Bioinformation, 2013;9(16):813-7.
    PMID: 24143051 DOI: 10.6026/97320630009813
    Beta-glucosidase (3.2.1.21) plays an essential role in the removal of non-reducing terminal glucosyl residues from glycosides. Recently, beta-glucosidase has been of interest for biomass conversion that acts in synergy with two other enzymes, endoglucanase and exo-glucanase. However, there is not much information available on the catalytic interactions of beta-glucosidase with its substrates. Thus, this study reports on the binding modes between beta-glucosidase from glycoside hydrolase family 1 namely BglB with cellobiose, cellotetraose and cellotetriose via molecular docking simulation. From the results, the binding affinities of BglB-cellobiose, BglB-cellotetraose, and BglB-cellotetriose complexes were reported to be -6.2kJ/mol , -5.68 kJ/mol and -5.63 kJ/mol, respectively. The detail interactions were also been investigated that revealed the key residues involved in forming hydrogen bonds (h-bond) with the substrates. These findings may provide valuable insigths in designing beta-glucosidase with higher cellobiose-hydrolyzing efficiency.
  15. Karthik D, Majumder P, Palanisamy S, Khairunnisa K, Venugopal V
    Bioinformation, 2014;10(9):580-5.
    PMID: 25352726 DOI: 10.6026/97320630010580
    Kinase Suppressor of Ras (KSR) is a molecular scaffold that interacts with the core kinase components of the ERK cascade, Raf, MEK, ERK to provide spatial and temporal regulation of Ras-dependent ERK cascade signaling. Interruption of this mechanism can have a high influence in inhibiting the downstream signaling of the mutated tyrosine kinase receptor kinase upon ligand binding. Still none of the studies targeted to prevent the binding of Raf, MEK binding on kinase suppressor of RAS. In that perspective the cysteine rich C1 domain of scaffold proteins kinase suppressor of Ras-1 was targeted rather than its ATP binding site with small ligand molecules like flavones and anthocyanidins and analyzed through insilico docking studies. The binding energy evaluation shows the importance of hydroxyl groups at various positions on the flavone and anthocyanidin nucleus. Over all binding interaction shows these ligands occupied the potential sites of cysteine rich C1 domain of scaffold protein KSR.
  16. Jackson K, Devaraj E, Lakshmi T, Rajeshkumar S, Dua K, Chellappan DK, et al.
    Bioinformation, 2020;16(11):817-827.
    PMID: 34803254 DOI: 10.6026/97320630016817
    It is of interest to study the cytotoxicity of silibinin assisted silver nanoparticles in human colorectal (HT-29) cancer cells. Silver nanoparticles were synthesized using silibinin as a reducing agent. The synthesized silibinin assisted silver nanoparticles ( SSNPs) were characterized and analyzed using a transmission electron microscope and spectrophotometer. The SSNPs synthesized in this study are spherical and their size ranges from 10 to 80 nm. HT-29 cells were treated with different concentrations (2, 4, 6, 8 and 10 ng/mL) of SSNPs and cytotoxicity was evaluated. The apoptosis was using flow cytometry. p53 protein expression using western blot. SSNPs are induced a decrease in viability and increased concentration-dependent cytotoxicity in HT-29 cells. SSNPs treatment also caused apoptosis-related morphological changes. SSNPs treatments at 8 and 16 ng/ml showed a prominent apoptotic change i.e., 70.3% and 83.6% respectively, and decreased viability of HT-29 cells 20% and 11.2% respectively as compared to control cells. SSNPs treatments induced p53 expression in HT-29 cells. Data shows that SSNPs have the potential to induce apoptosis in colorectal cancer cells. This provides insights for the further evaluation of SSNPs in fighting colon cancer.
  17. Iyappan P, Bala MD, Sureshkumar M, Veeraraghavan VP, Palanisamy A
    Bioinformation, 2021;17(1):181-191.
    PMID: 34393435 DOI: 10.6026/97320630017181
    Fucoxanthin (Fx) is an active compound commonly found in the many types of seaweed with numerous biological activities. The main goal of this investigation is to explore the effect of Fx against the cell proliferation, apoptotic induction and oxidative stress in the oral squamous (KB) cell line. Cytotoxicity of Fx was determined by MTT assay. The intracellular ROS production, mitochondrial membrane potential (MMP) and apoptosis induction in KB cells were examined through DCFH-DA, Rhodamine-123 and DAPI, and dual staining techniques. Effect of Fx on the antioxidant enzymes and lipid peroxidation in the KB cells was studied through the standard procedures. Fx treated KB cells showed morphological changes and reduced cell survival, which is exhibited by the cytotoxic activity of 50 µM/ml (IC50) Fx against the KB cells. The Fx treatment considerably induced the apoptotosis cells (EB/AO) and decreased the MMP (Rh-123) in KB cells. Further, it was pointed out that there was an increased lipid peroxidation (LPO) with decreased antioxidants (CAT, SOD and GSH). These results concluded that Fx has the cytotoxic effect against KB cells and has the potential to induce the apoptosis via increased oxidative stress. Hence, the Fx can be a promising agent for the treatment of oral cancer and it may lead to the development of cancer therapeutics.
  18. Iyappan P, Bala MD, Sureshkumar M, Veeraraghavan VP, Palanisamy A
    Bioinformation, 2021;17(1):171-180.
    PMID: 34393434 DOI: 10.6026/97320630017171
    The immature lymphoid cells with chromosomal structural and numerical abnormalities cause the acute lymphoblastic leukemia (ALL). This hematologic disorder constitutes about 25% of cancer prognosis among children and adolescents. D-Carvone, a monocyclic monoterpene obtained from the essential oils extracted from plants is reported to possess the various biological activities. The present study was aimed to investigate the anticancer potential of D-Carvone against the human leukemic Molt-4 cells. The cytotoxicity of DCarvone was analyzed by MTT assay. The level of lipid peroxidation and antioxidants were determined. The intracellular ROS, MMP and apoptosis were demonstrated by fluorescent staining techniques. The MTT assay revealed that the D-Carvone treatment suppressed the viability of Molt-4 cells and the IC50 was determined at 20 µM/ml. The D-Carvone treatment was increased the oxidative stress and reduced the level of antioxidants in the Molt-4 cell lines. The increased intracellular ROS, apoptotic cell death, and diminished MMP was noted in the D-Carvone treatment. In the Molt-4 cells, D-carvone induced the apoptosis in a time and dose dependent manner by the activation of caspases-8, -9 and -3. Thus, data provide insights for the clinical application of D-Carvone in the treatment of blood cancer Molt-4 cells. Our study suggests the therapeutic potential D-Carvone for the treatment of leukemia in future.
  19. Islam MM, Aktaruzzaman M, Mohamed Z
    Bioinformation, 2015;11(2):67-72.
    PMID: 25848166 DOI: 10.6026/97320630011067
    Normal blood glucose level depends on the availability of insulin and its ability to bind insulin receptor (IR) that regulates the downstream signaling pathway. Insulin sequence and blood glucose level usually vary among animals due to species specificity. The study of genetic variation of insulin, blood glucose level and diabetics symptoms development in Aves is interesting because of its optimal high blood glucose level than mammals. Therefore, it is of interest to study its evolutionary relationship with other mammals using sequence data. Hence, we compiled 32 Aves insulin from GenBank to compare its sequence-structure features with phylogeny for evolutionary inference. The analysis shows long conserved motifs (about 14 residues) for functional inference. These sequences show high leucine content (20%) with high instability index (>40). Amino acid position 11, 14, 16 and 20 are variable that may have contribution to binding to IR. We identified functionally critical variable residues in the dataset for possible genetic implication. Structural models of these sequences were developed for surface analysis towards functional representation. These data find application in the understanding of insulin function across species.
  20. Hussein ZA, Loke KK, Abidin RA, Othman R
    Bioinformation, 2011;7(4):157-62.
    PMID: 22102771
    Functional genomics has proven to be an efficient tool in identifying genes involved in various biological functions. However the availability of commercially important seaweed Eucheuma denticulatum functional resources is still limited. EuDBase is the first seaweed online repository that provides integrated access to ESTs of Eucheuma denticulatum generated from samples collected from Kudat and Semporna in Sabah, Malaysia. The database stored 10,031 ESTs that are clustered and assembled into 2,275 unique transcripts (UT) and 955 singletons. Raw data were automatically processed using ESTFrontier, an in-house automated EST analysis pipeline. Data was collected in MySQL database. Web interface is implemented using PHP and it allows browsing and querying EuDBase through search engine. Data is searchable via BLAST hit, domain search, Gene Ontology or KEGG Pathway. A user-friendly interface allows the identification of sequences either using a simple text query or similarity search. The development of EuDBase is initiated to store, manage and analyze the E. denticulatum ESTs and to provide accumulative digital resources for the use of global scientific community. EuDBase is freely available from http://www.inbiosis.ukm.my/eudbase/.
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