MyMedR

Displaying publications 21 - 30 of 30 in total

Abstract:

Sort:

Fulltext Anticancer effects and lysosomal acidification in A549 cells by Astaxanthin from Haematococcus lacustris

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.
Fulltext Cytotoxic potentials of silibinin assisted silver nanoparticles on human colorectal HT-29 cancer cells

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.
Fulltext A review on the nutritional, medicinal, molecular and genome attributes of Durian (Durio zibethinus L.), the King of fruits in Malaysia

Husin NA, Rahman S, Karunakaran R, Bhore SJ

Bioinformation, 2018;14(6):265-270.
PMID: 30237671 DOI: 10.6026/97320630014265

Durian (Durio zibethinus L.; Family Bombacaceae) is an iconic tropical fruit plant cultivated in Malaysia and the Southeast Asian countries. In Malaysia, durian is recognised as the King of fruits and well known as a rich source of volatile sulphur compounds that make it unique. Fruit pulp of this fruit is an excellent source of nutrients as it contains proteins, dietary fat, fibers, and carbohydrates. Durian leaf and root decoctions are known to have a febrifuge and anti-malarial properties. The understanding of this plant's molecular biology will help breeders to develop a strategy for its further improvements. Hence, there is a need to identify and understand the genes necessary for the quality improvement of the durian fruits. Its genome contains about 46,000 genes which is almost double that of humans (Homo sapiens). The understanding of durian genes will be useful not only in the molecular breeding but also in the microbial production of novel proteins and or enzymes. This review highlights nutritional and medicinal attributes of durian. The molecular studies including the importance of undertaking transcriptomics work and the insights from the most recently reported genome draft are also highlighted.
Fulltext Nipah: The looming post-covid pandemic

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.
An improved hybrid of SVM and SCAD for pathway analysis

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.
Insights from the GC content analysis of 76genome survey sequences (GSS) from Elaeisoleifera

Bhore SJ, Kassim A, Shah FH

Bioinformation, 2010 Sep 20;5(4):141-5.
PMID: 21364775

South American oil-palm (Elaeis oleifera) is not cultivated in tropical countries like Malaysia on large scale due to low yield of palm oil derived from its fruit mesocarp. However, its fruit mesocarp oil contains about 68.6 % oleic acid (C(18:1)) which is more than double in comparison to commercially cultivated oilpalm, E. guineensis Jacq Tenera (hybrid of Dura (♀) x Pisifera (♂)). It is also known that E. oleifera is a good source of tocotrienols and carotenoids. Therefore, it is of interest to know the genome sequence of E. oleifera. The objective of this study is to generate genome survey sequences (GSS) to get GC content insight in the E. oleifera genome. The nuclear genomic DNA isolated from young leaf-tissues was digested with EcoRI and NdeI/DraI restriction enzymes; and three genomic DNA libraries were constructed using Lambda ZAP-II, pGEM®-T Easy, and pDONR 222™ as cloning vectors. Generated 76 GSSs were analyzed by using Bioinformatics tools. The analysis result indicates that the adenine, cytosine, guanine and thymine content in generated GSSs are 30%, 20%, 20%, and 30% respectively. In conclusion, based on the precise GC content analysis of the randomly isolated 76 GSSs by using Bioinformatics tools we hypothesize that GC content in E. oleifera genome is 40%. The hypothesized 40% GC content in E. oleifera genome is expected to remain close to the GC content based on the whole genome analysis.(ψ)The nucleotide sequence data reported in this paper have been submitted to dbGSS division of the international DNA database (GenBank/DDBJ/EMBL) under accession numbers: DX575945- DX575972 and EI798032-EI798079.
ABBREVIATIONS: gDNA - Nuclear genomic DNA, GSSs - Genome survey sequences K12, SAOP - South American oil-palm Db1.
Screening of endophytic bacteria isolated from leaves of Sambung Nyawa [Gynura procumbens (Lour.) Merr.] for cytokinin-like compounds

Bhore SJ, Ravichantar N, Loh CY

Bioinformation, 2010 Nov 01;5(5):191-7.
PMID: 21364796

Endophytic bacteria are harmless in most plant species; and known to boost the growth and development of the host plants probably by secreting growth hormones. The isolation, identification and screening of endophytic bacteria for the plant growth regulators like cytokinin are needed to get the leads for their applications in agriculture sector. We describe the isolation and identification of the bacterial endophytes from the leaves of Sambung Nyawa [Gynura procumbens (Lour.) Merr.] and their screening for cytokinin-like compounds. We isolated three endophytic bacteria from the leaves of G. procumbens collected from the forest research institute of Malaysia (FRIM). They were further identified using amplified 16S rRNA gene sequence based method of bacterial identification. The ethyl acetate extracts of the isolates-broth were analyzed using cucumber cotyledon greening bioassay (CCGB) to determine the presence of cytokinin-like compounds. Consequently, the bacterial putative endophytes were identified as Psuedomonas resinovorans, Paenibacillus polymaxa, and Acenitobacter calcoaceticus. Broth-extracts from two (Psuedomonas resinovorans and Paenibacillus polymaxa) of the three putative bacterial endophytes show the positive results in their screening for cytokinin-like compounds using CCGB. Thus, we hypothesize that the bacterial putative endophytes of G. procumbens that produce cytokinin-like compounds might have a role in the growth and development of G. procumbens.
ABBREVIATIONS: CCGB - Cucumber cotyledon greening bioassay, rDNA - Ribosomal DNA, K12, BAP - 6-Benzylaminopurine, Db1, MSA - Multiple sequence alignment. 8081.
Fulltext Computational analysis of common bean (Phaseolus vulgaris L., genotype BAT93) lycopene β-cyclase and β-carotene hydroxylase gene's cDNA

Bhore SJ, Amelia K, Wang E, Priyadharsini S, Shah FH

Bioinformation, 2013;9(4):197-206.
PMID: 23519320 DOI: 10.6026/97320630009197

The identification of genes and understanding of genes' expression and regulation in common bean (Phaseolus vulgaris L.) is necessary in order to strategize its improvement using genetic engineering techniques. Generation of expressed sequence tags (ESTs) is useful in rapid isolation, identification and characterization of the genes. To study the gene expression in P. vulgaris pods tissue, ESTs generation work was initiated. Early stage and late stage bean-pod-tissues cDNA libraries were constructed using CloneMiner cDNA library construction kit. In total, 5972 EST clones were isolated using random method of gene isolation. While processing ESTs, we found lycopene β-cyclase (PvLCY-β) and β-carotene hydroxylase (PvCHY-β) gene's cDNA. In carotenoid biosynthesis pathway, PvLCY-β catalyzes the production of carotene; and PvCHY-β is known to function as a catalyst in the production of lutein and zeaxanthin. To understand more about PvLCY-β and PvCHY-β, both strands of both cDNA clones were sequenced using M13 forward and reverse primers. Nucleotide and deduced protein sequences were analyzed and annotated using online bioinformatics tools. Results showed that PvLCY-β and PvCHY-β cDNAs are 1639 and 1107 bp in length, respectively. Analysis results showed that PvLCY-β and PvCHY-β gene's cDNA contains an open reading frame (ORF) that encodes for 502 and 305 amino acid residues, respectively. The deduced protein sequence analysis results also showed the presence of conserved domains needed for PvLCY-β and PvCHY-β functions. The phylogenetic analysis of both PvLCY-β and PvCHY-β proteins showed it's closeness with the LCY-β and CHY-β proteins from Glycine max, respectively. The nucleotide sequence of PvLCY-β and PvCHY-β gene's cDNA and it's annotation is reported in this paper.
Bioinformatics in molecular immunology laboratories demonstrated: Modeling an anti-CMV scFv antibody

Heng CK, Othman RY

Bioinformation, 2006 Mar 27;1(4):118-20.
PMID: 17597869

A scFv (single chain variable fragment) antibody clone from anti-CMV (anti-cucumber mosaic virus) was successfully constructed from immunized mouse and the DNA sequence was submitted to GenBank (AY337618 and AY337619). The expression of a 32 kDa recombinant antibody in bacteria was verified using ELISA (enzyme-linked immunoassay) and western blot. However, elucidation of specific anti-CMV scFv function requires detailed and time consuming immuno-assays. Alternatively, useful functional information on anti-CMV scFV antibody can be obtained using available Bioinformatics tools and techniques without performing tedious assays. Here, we use the commonly used Bioinformatics tools and databases such as BLAST (basic local alignment search tool), GenBank, PDB (protein databank), KABAT numbering, SWISS-MODEL and Insight II to gain specific functional insights into anti-CMV scFv.
Iterative local Gaussian clustering for expressed genes identification linked to malignancy of human colorectal carcinoma

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.