Ahmad Mukhlis Abdul Rahman
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Preferred name
Ahmad Mukhlis Abdul Rahman
Official Name
Ahmad Mukhlis, Abdul Rahman
Alternative Name
Abdul Rahman, Ahmad Mukhlis
Main Affiliation
Researcher ID
HGA-7390-2022

Research Output
Now showing 1 - 6 of 6
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Loop-mediated isothermal amplification of the toxR gene coupled with lateral flow dipstick (LAMP-LFD) for the novel, rapid and specific visual detection of Vibrio harveyi

2023 , Ahmad Mukhlis Abdul Rahman , Julian Ransangan , Vijay Kumar Subbiah

Vibrio harveyi is a serious pathogen for marine organisms particularly in hatcheries and grow-out ponds that attack their immune system. The rapid detection of V. harveyi is urgently needed to prevent bacterial spread. Here we described a rapid and specific visual detection method based on the Loop-Mediated Isothermal Amplification in combination with Lateral Flow Dipstick (LAMP-LFD). Methodology and results: A set of six novel primers were designed to target the toxR gene. These include the biotin-labelled inner primer that complements specifically to the target sequences. The resulting biotinylated LAMP amplicons were hybridised to the FAM-labelled probe resulting in lateral flow detection on the dipstick. The addition of loop primers improved the reaction time of LAMP by more than half and rapid detection was observed within 10-15 min. In comparison, the sensitivity of PCR-UV analysis was only at 104 copies while LAMP-LFD was able to detect lower amounts at 103 copies. The LFD provided higher specificity and selectivity since hybridization with specific probes to the LAMP amplicons was employed. In addition, detection of V. harveyi infected grouper was successful using the LAMP-LFD method described here. Conclusion, significance and impact of study: LAMP-LFD is specific to V. harveyi. Our method provides a useful tool to rapidly detect and monitor the outbreaks of the pathogen.

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DNA barcoding of common Malaysia spiders using the Cytochrome Oxidase I (COI) gene

2020 , Ahmad Mukhlis Abdul Rahman , Kek Chian Koay , Johan Ariff Mohtar , Anwardi Jamil , Mohd Mushahril Abdul Shukor , Nurul Ain Harmiza Abdullah

For the last twenty years, many newly described spiders were collected from Malaysia and in fact, more than 11,000 species were recorded in Peninsular Malaysia as well as in Sabah and Sarawak states. Scientists have put an immense effort on untangling the spider biology from its physical structure and behavior to silks and venoms. However, working with spiders is impeded by the difficulties in species identification via solely morphological methods. Thus, DNA barcoding is an alternative technique that employs standard fragment to facilitate species identification. Isolation of genomic DNA from three Malaysian spiders were performed using NucleoSpin® DNA insect extraction kit. Amplification of reference mitochondrial cytochrome oxidase I (COI) gene employing PCR with two set of primers followed by the DNA sequencing and validation through phylogenetic analysis were carried out. The commercial extraction kit was effective for the recovery of good quality of intact genomic DNA band as indicated by the integrity analysis. Both set of primers successfully amplified 100% of the samples with approximately 600 – 700 bp of PCR products. The obtained sequences (610 bp to 692 bp) were compared with the sequences available in Gene Bank. BLAST and phylogenetic analysis revealed that the analyzed individual samples belong to Nephila pilipes, Neoscona nautica and Crossopriza lyoni, respectively. Phylogenetic analysis provided unique insight into the evolutionary relationship of each analyzed sample. This study aids in an accurate identification of the selected local spider species at molecular level using the COI gene.

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Differential Display Reverse Transcription Polymerase Chain Reaction (DDRT-PCR) for Grey Oyster mushroom samples grown with acoustic sound treatment

2023 , Tham Khai Song , Norsahira Ezrin Mohd Zamri , Roshita Ibrahim , Johan Ariff Mohtar , Hartinee Abbas , Ahmad Mukhlis Abdul Rahman

Grey oyster mushroom is the most often farmed and marketed type of mushroom for household consumption in Malaysia. The mushroom cultivation takes a long time due to its complicated mycelium growth. Several treatments were introduced such as acoustic sound treatment to increase the growth rate and quality of the crop, but there is no in-depth study regarding the genetic expression of the genes affected. This study aims to evaluate the Differential Display Reverse Transcriptase-Polymerase Chain Reaction (DDRT-PCR) for grey oyster mushroom samples grown with acoustic sound treatment. The mushroom was subjected to the treatment and the RNA was extracted from the mushroom samples and converted into cDNA before undergoing DDRT-PCR. Ten Differential Expressed Transcripts (DETs) that were successfully identified based on the differences between the intensity and absence of amplicons were sent for gene sequencing and BLAST through the NCBI database to obtain relevant results regarding the possible gene annotation. Seven out of ten DETs hit potential genes encoding for housekeeping and structural and development functions. The results showed that acoustic sound treatment did affect the expression of certain genes differently as captured by DDRT-PCR analyses and offers new ideas for the development of ecological agriculture.

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Chloroplast DNA sequence of trnR-N and trnL-F regions in Harumanis mango from different orchards in Perlis, Malaysia

2020 , Ahmad Mukhlis Abdul Rahman , SFM Sabri , Yusuf, Arbai , Zarina Zakaria , SV Kumar

Harumanis is a premium mango cultivar widely known for its sweet taste, aroma and vibrant flesh colour. To date, the genetic identification of this mango based on multiple conserved DNA region using samples from different orchards has never been reported. The aim of this research is to identify the genetic signature of Harumanis mango at molecular level by analyzing chloroplast DNA sequences of the trnL-F and trnR-N regions. DNA samples were extracted from a total of 15 Harumanis samples collected from five selected orchards using Cetyl Trimethyl Ammonium Bromide (CTAB) extraction procedure. The extracted DNA and the PCR-amplified products were analyzed through gel electrophoresis and were then subjected to DNA Sequencing and in silico analysis. The obtained sequences were compared with the sequences available in the GeneBank. BLAST search for both the trnR-N and trnL-F regions confirmed that all the 15 samples belong to Mangifera indica with a 99% sequence identity. In addition, the trnL-F sequences were 99% identical to a number of specific mango cultivars such as, Tommy and Arunika. However, the trnR-N sequences were less informative as it gave hits to only two mango accessions (e.g. Mangifera indica voucher PDBK 2014-0249). It is postulated that the plastid trnR-N may be a potential candidate region for the development of the Harumanis genetic signature. The results may be used to complement other molecular data for the development of a genetic barcode for Harumanis.

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Morphological variability identification of Harumanis Mango (Mangifera indica L.) harvested from different location and tree age

2020-08 , Siti Nur Arina Yusuf , Ahmad Mukhlis Abdul Rahman , Zarina Zakaria , Vijay Kumar Subbiah , Maz Jamilah Masnan , Zakaria Wahab

Harumanis is one of the main signatures of Perlis with regards to its delightful taste, pleasant aroma and expensive price. Harumanis authenticity and productivity had become the remarks among the farmers, entrepreneurs, consumers and plant breeders due to the existence of morphological characteristics variation among the fruits and high production cost. Assessment of Harumanis morphological characteristics of natural population and different tree ages may represent a possible source of important characteristics for development and breeding purposes of Harumanis. The aim of this study is to evaluate the morphological variation of Harumanis collected from different location in Perlis and tree age. A total of 150 Harumanis fruits from 50 trees with three different stages of development (young, middle-aged and old) were characterised using 11 traits; 10 quantitative and one qualitative morphological trait. The ANOVA analyses in combination with Dunn’s pairwise and Kruskal-Wallis multiple comparison test able to point out the existence of environmental factor and age influence towards the significant different of identified morphological traits except for Total Soluble Solid (TSS) and pulp percentage. Five clusters of 50 Harumanis accessions reflect a grouping pattern which not according to neither geographical region nor age. The result of Principal Component Analysis (PCA) using the first two principal components (PCs) provided a good approximation of the data explaining 84.09% of the total variance which majorly contributed by parameters of weight, fruit dimensional characteristics, peel percentage and hue angle, h. Preliminary screening of important morphological characteristics which contribute to the phenotypic diversity of Harumanis is successfully achieved. The findings can be employed by the plant breeders and farmers for the establishment of standard grading of Harumanis and advancement of breeding crop of Harumanis in future.

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Isolation of cellulolytic microorganism from food waste-fertilized soil

2023 , Aliaa Rasyidina Idrus , Nor Hidayah Abd Aziz , Zarina Zakaria , Ahmad Mukhlis Abdul Rahman

Uncontrolled disposal of waste from cellulosic materials can add burden to the existing environmental crises. The aim of the study is to isolate microorganisms from food waste-fertilized soil and identification of the microorganism species by genotyping. Soil samples enriched with fruits, rice and vegetables wastes were collected, diluted and spread on agar supplemented with carboxymethylcellulose (CMC) for induction of growth and cellulase production. Following screening of cellulolytic activity, isolates with significant cellulolytic index (CI) were chosen for molecular identification by PCR, using the 16S rRNA as target sequence in combination with in silico analysis. Four out of eleven microorganisms isolated from fruits and vegetable-rich soils produced a CI ranging from 0.43 to 2.00. Of these, only two isolates produced clear bands on PCR with approximately 1500 bp in size. In silico analysis of the isolates suggested species of Ochrobactrum sp. and Bacillus sp. These microorganisms have the potential to be used for decomposition of the cellulosic wastes.

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