MyMedR

Displaying all 5 publications

Abstract:

Sort:

An analysis of simple computational strategies to facilitate the design of functional molecular information processors

Lee Y, Roslan R, Azizan S, Firdaus-Raih M, Ramlan EI

BMC Bioinformatics, 2016 Oct 28;17(1):438.
PMID: 27793081

BACKGROUND: Biological macromolecules (DNA, RNA and proteins) are capable of processing physical or chemical inputs to generate outputs that parallel conventional Boolean logical operators. However, the design of functional modules that will enable these macromolecules to operate as synthetic molecular computing devices is challenging.
RESULTS: Using three simple heuristics, we designed RNA sensors that can mimic the function of a seven-segment display (SSD). Ten independent and orthogonal sensors representing the numerals 0 to 9 are designed and constructed. Each sensor has its own unique oligonucleotide binding site region that is activated uniquely by a specific input. Each operator was subjected to a stringent in silico filtering. Random sensors were selected and functionally validated via ribozyme self cleavage assays that were visualized via electrophoresis.
CONCLUSIONS: By utilising simple permutation and randomisation in the sequence design phase, we have developed functional RNA sensors thus demonstrating that even the simplest of computational methods can greatly aid the design phase for constructing functional molecular devices.
Exploring ethynyl-based chalcones as green semiconductor materials for optical limiting interests

Khairul WM, Hashim F, Rahamathullah R, Mohammed M, Aisyah Razali S, Ahmad Tajudin Tuan Johari S, et al.

Spectrochim Acta A Mol Biomol Spectrosc, 2024 Mar 05;308:123776.
PMID: 38134650 DOI: 10.1016/j.saa.2023.123776

The fabrication of molecular electronics from non-toxic functional materials which eventually would potentially able to degrade or being breaking down into safe by-products have attracted much interests in recent years. Hence, in this study, the introduction of mixed highly functional substructures of chalcone (-CO-CH=CH-) and ethynylated (C≡C) as building blocks has shown ideal performance as solution-processed thin film candidatures. Two types of derivatives, (MM-3a) and (MM-3b) repectively, showed a substantial Stokes shifts at 75 nm and 116 nm, in which such emission exhibits an intramolecular charge transfer (ICT) state and fluoresce characteristics. The density functional theory (DFT) simulation shows that MM-3a and MM-3b exhibit low energy gaps of 3.70 eV and 2.81 eV, respectively. TD-DFT computations for molecular electrostatic potential (MEP) and frontier molecular orbitals (FMO) were also used to emphasise the structure-property relationship. A solution-processed thin film with a single layer of ITO/PEDOT:PSS/MM-3a-MM-3b/Au exhibited electroluminescence behaviour with orange and purple emissions when supplied with direct current (DC) voltages. To promote the safer application of the derivatives formed, ethynylated chalcone materials underwent toxicity studies toward Acanthamoeba sp. to determine their suitability as non-toxic molecules prior to the determination as safer materials in optical limiting interests. From the preliminary test, no IC50 value was obtained for both compounds via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay analysis and molecular docking analysis between MM-3a and MM-3b, with profilin protein exhibited weak bond interactions and attaining huge interaction distances.
Fulltext Draft genome sequence of Vibrio sp. PBL-C16, isolated from Batu Laut Beach in Selangor, Malaysia

Kahar UM, Goh KM, Zakaria II, Radzlin N, Mohd Ruslan IH, Azizan S

Microbiol Resour Announc, 2024 Jul 18;13(7):e0016824.
PMID: 38847548 DOI: 10.1128/mra.00168-24

Vibrio sp. PBL-C16 is a bacterium that was isolated from Batu Laut Beach in Selangor, Malaysia. Here, we present a high-quality annotated draft genome of strain PBL-C16 and suggest its potential glycoside hydrolase enzymes for polysaccharide degradation.
Thermoluminescence properties of lithium magnesium borate glasses system doped with dysprosium oxide

Mhareb MH, Hashim S, Ghoshal SK, Alajerami YS, Saleh MA, Razak NA, et al.

Luminescence, 2015 Dec;30(8):1330-5.
PMID: 25828828 DOI: 10.1002/bio.2902

We report the impact of dysprosium (Dy(3+)) dopant and magnesium oxide (MgO) modifier on the thermoluminescent properties of lithium borate (LB) glass via two procedures. The thermoluminescence (TL) glow curves reveal a single prominent peak at 190 °C for 0.5 mol% of Dy(3+). An increase in MgO contents by 10 mol% enhances the TL intensity by a factor of 1.5 times without causing any shift in the maximum temperature. This enhancement is attributed to the occurrence of extra electron traps created via magnesium and the energy transfer to trivalent Dy(3+) ions. Good linearity in the range of 0.01-4 Gy with a linear correlation coefficient of 0.998, fading as low as 21% over a period of 3 months, excellent reproducibility without oven annealing and tissue equivalent effective atomic numbers ~8.71 are achieved. The trap parameters, including geometric factor (μg), activation energy (E) and frequency factor (s) associated with LMB:Dy are also determined. These favorable TL characteristics of prepared glasses may contribute towards the development of Li2O-MgO-B2O3 radiation dosimeters.
Insights into the molecular mechanisms and signalling pathways of epithelial to mesenchymal transition (EMT) in colorectal cancer: A systematic review and bioinformatic analysis of gene expression

Azizan S, Cheng KJ, Mejia Mohamed EH, Ibrahim K, Faruqu FN, Vellasamy KM, et al.

Gene, 2024 Feb 20;896:148057.
PMID: 38043836 DOI: 10.1016/j.gene.2023.148057

Colorectal cancer (CRC) is ranked as the second leading cause of mortality worldwide, mainly due to metastasis. Epithelial to mesenchymal transition (EMT) is a complex cellular process that drives CRC metastasis, regulated by changes in EMT-associated gene expression. However, while numerous genes have been identified as EMT regulators through various in vivo and in vitro studies, little is known about the genes that are differentially expressed in CRC tumour tissue and their signalling pathway in regulating EMT. Using an integration of systematic search and bioinformatic analysis, gene expression profiles of CRC tumour tissues were compared to non-tumour adjacent tissues to identify differentially expressed genes (DEGs), followed by performing systematic review on common identified DEGs. Fifty-eight common DEGs were identified from the analysis of 82 tumour tissue samples obtained from four gene expression datasets (NCBI GEO). These DEGS were then systematically searched for their roles in modulating EMT in CRC based on previously published studies. Following this, 10 common DEGs (CXCL1, CXCL8, MMP1, MMP3, MMP7, TACSTD2, VIP, HPGD, ABCG2, CLCA4) were included in this study and subsequently subjected to further bioinformatic analysis. Their roles and functions in modulating EMT in CRC were discussed in this review. This study enhances our understanding of the molecular mechanisms underlying EMT and uncovers potential candidate genes and pathways that could be targeted in CRC.