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Fulltext Development of swine-specific DNA markers for biosensor-based halal authentication

Ali ME, Hashim U, Kashif M, Mustafa S, Che Man YB, Abd Hamid SB

Genet. Mol. Res., 2012;11(2):1762-72.
PMID: 22843053 DOI: 10.4238/2012.June.29.9

The pig (Sus scrofa) mitochondrial genome was targeted to design short (15-30 nucleotides) DNA markers that would be suitable for biosensor-based hybridization detection of target DNA. Short DNA markers are reported to survive harsh conditions in which longer ones are degraded into smaller fragments. The whole swine mitochondrial-genome was in silico digested with AluI restriction enzyme. Among 66 AluI fragments, five were selected as potential markers because of their convenient lengths, high degree of interspecies polymorphism and intraspecies conservatism. These were confirmed by NCBI blast analysis and ClustalW alignment analysis with 11 different meat-providing animal and fish species. Finally, we integrated a tetramethyl rhodamine-labeled 18-nucleotide AluI fragment into a 3-nm diameter citrate-tannate coated gold nanoparticle to develop a swine-specific hybrid nanobioprobe for the determination of pork adulteration in 2.5-h autoclaved pork-beef binary mixtures. This hybrid probe detected as low as 1% pork in deliberately contaminated autoclaved pork-beef binary mixtures and no cross-species detection was recorded, demonstrating the feasibility of this type of probe for biosensor-based detection of pork adulteration of halal and kosher foods.

Matched MeSH terms: Base Sequence
Efficacy of an inactivated recombinant vaccine encoding a fimbrial protein of Pasteurella multocida B:2 against hemorrhagic septicemia in goats

Mohd Yasin IS, Mohd Yusoff S, Mohd ZS, Abd Wahid Mohd E

Trop Anim Health Prod, 2011 Jan;43(1):179-87.
PMID: 20697957 DOI: 10.1007/s11250-010-9672-5

This study was carried out to determine the antibody responses and protective capacity of an inactivated recombinant vaccine expressing the fimbrial protein of Pasteurella multocida B:2 following intranasal vaccination against hemorrhagic septicemia in goats. Goats were vaccinated intranasal with 10(6) CFU/mL of the recombinant vaccine (vaccinated group) and 10(6) CFU/mL of pET32/LIC vector without fimbrial protein (control group). All three groups were kept separated before all goats in the three groups were challenged with 10(9) CFU/mL of live pathogenic P. multocida B:2. During the course of study, both serum and lung lavage fluid were collected to evaluate the antibody levels via enzyme-linked immunosorbent assay. It was found that goats immunized with the inactivated recombinant vaccine developed a strong and significantly (p

Matched MeSH terms: Base Sequence
Fulltext Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTBR1/09 Isolated from a Sputum Sample in Malaysia

Issa R, Seradja VH, Abdullah MK, Abdul H

Genome Announc, 2016;4(3).
PMID: 27340053 DOI: 10.1128/genomeA.00513-16

This is a report of an annotated genome sequence of Mycobacterium tuberculosis MTBR1/09. The organism was isolated from a sputum sample from a male patient in Malaysia.

Matched MeSH terms: Base Sequence
Fulltext Annotated Sequence of Mycobacterium tuberculosis MTBR3/09 Isolated from a Sputum Sample in Malaysia

Issa R, Seradja VH, Abdullah MK, Abdul H

Genome Announc, 2016;4(3).
PMID: 27340055 DOI: 10.1128/genomeA.00517-16

This is a report of the annotated genome sequence of Mycobacterium tuberculosis MTBR3/09. The organism was isolated from a sputum sample in Malaysia.

Matched MeSH terms: Base Sequence
Fulltext Annotated Whole-Genome Shotgun Sequence of Mycobacterium tuberculosis MTBR2/09 Isolated from a Sputum Sample in Malaysia

Issa R, Seradja VH, Abdullah MK, Abdul H

Genome Announc, 2016;4(3).
PMID: 27340054 DOI: 10.1128/genomeA.00515-16

Mycobacterium tuberculosis MTBR2/09 was isolated from a sputum sample from a male patient in Malaysia. This is a report of an annotated genome sequence of M. tuberculosis MTBR2/09.

Matched MeSH terms: Base Sequence
Fulltext Preliminary prediction of lipase 3D protein structure and function in Rhodococcus sp. NAM81 using bioinformatics approach

Hasdianty Abdullah, Mohd Fadzli Ahmad, Farah Aula Mohd Fauzi, Nor Suhaila Yaacob, Abdul Latif Ibrahim

Bioremediation Science and Technology Research, 2015;3(1):11-15.
MyJurnal

Protein function depends greatly on its structure. Based on this principle, it is vital to study the
protein structure in order to understand its function. This study attempts to build the predicted
model of lipase gene in Rhodococcus sp. NAM81 using homology modelling method. The
predicted structure was then used to investigate the function of protein through several
bioinformatic tools. The DNA sequence of lipase gene was obtained from the Rhodococcus sp.
NAM81 genome scaffold. Blastx analysis showed 100% identity to the target enzyme andthe
appropriate template for homology modelling was determined using Blastp analysis. The 3D
protein structure was built using two homology modelling software, EsyPred3D and Swiss
Model Server. Both structures built obtained LGScore of greater than 4, which means they are
extremely good models according to ProQ validation criteria. Both structures also satisfied the
Ramachandran plot structure validation analysis. The predicted structures were 100% matched
with each other when superimposed with DaliLite pairwise. This shows that both structure
validation servers agreed on the same model. Structure analysis using ProFunc had found seven
motifs and active sites that indicate similar function of this protein with other known proteins.
Thus, this study has successfully produced a good 3D protein structure for the target enzyme.

Matched MeSH terms: Base Sequence
Fulltext Inactivation of the catalytic subunit of cAMP-dependent protein kinase A causes delayed appressorium formation and reduced pathogenicity of Colletotrichum gloeosporioides

Priyatno TP, Abu Bakar FD, Kamaruddin N, Mahadi NM, Abdul Murad AM

ScientificWorldJournal, 2012;2012:545784.
PMID: 22666136 DOI: 10.1100/2012/545784

The cyclic AMP- (cAMP-) dependent protein kinase A signaling pathway is one of the major signaling pathways responsible for regulation of the morphogenesis and pathogenesis of several pathogenic fungi. To evaluate the role of this pathway in the plant pathogenic fungus, Colletotrichum gloeosporioides, the gene encoding the catalytic subunit of cAMP-dependent protein kinase A, CgPKAC, was cloned, inactivated, and the mutant was analyzed. Analysis of the Cgpkac mutant generated via gene replacement showed that the mutants were able to form appressoria; however, their formation was delayed compared to the wild type. In addition, the mutant conidia underwent bipolar germination after appressoria formation, but no appressoria were generated from the second germ tube. The mutants also showed reduced ability to adhere to a hydrophobic surface and to degrade lipids localized in the appressoria. Based on the number of lesions produced during a pathogenicity test, the mutant's ability to cause disease in healthy mango fruits was reduced, which may be due to failure to penetrate into the fruit. These findings indicate that cAMP-dependent protein kinase A has an important role in regulating morphogenesis and is required for pathogenicity of C. gloeosporioides.

Matched MeSH terms: Base Sequence
Fulltext Molecular characterization of a recombinant manganese superoxide dismutase from Lactococcus lactis M4

Tan BH, Chor Leow T, Foo HL, Abdul Rahim R

Biomed Res Int, 2014;2014:469298.
PMID: 24592392 DOI: 10.1155/2014/469298

A superoxide dismutase (SOD) gene of Lactococcus lactis M4 was cloned and expressed in a prokaryotic system. Sequence analysis revealed an open reading frame of 621 bp which codes for 206 amino acid residues. Expression of sodA under T7 promoter exhibited a specific activity of 4967 U/mg when induced with 1 mM of isopropyl-β-D-thiogalactopyranoside. The recombinant SOD was purified to homogeneity by immobilised metal affinity chromatography and Superose 12 gel filtration chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blot analyses of the recombinant SOD detected a molecular mass of approximately 27 kDa. However, the SOD was in dimer form as revealed by gel filtration chromatography. The purified recombinant enzyme had a pI of 4.5 and exhibited maximal activity at 25°C and pH 7.2. It was stable up to 45°C. The insensitivity of this lactococcal SOD to cyanide and hydrogen peroxide established that it was a MnSOD. Although it has 98% homology to SOD of L. lactis IL1403, this is the first elucidated structure of lactococcal SOD revealing active sites containing the catalytic manganese coordinated by four ligands (H-27, H-82, D-168, and H-172).

Matched MeSH terms: Base Sequence
Fulltext In vitro chondrogenesis transformation study of mouse dental pulp stem cells

Zainal Ariffin SH, Kermani S, Megat Abdul Wahab R, Senafi S, Zainal Ariffin Z, Abdul Razak M

ScientificWorldJournal, 2012;2012:827149.
PMID: 22919354 DOI: 10.1100/2012/827149

A major challenge in the application of mesenchymal stem cells in cartilage reconstruction is that whether the cells are able to differentiate into fully mature chondrocytes before grafting. The aim of this study was to isolate mouse dental pulp stem cells (DPSC) and differentiate them into chondrocytes. For this investigation, morphological, molecular, and biochemical analyses for differentiated cells were used. To induce the chondrocyte differentiation, DPSC were cultured in chondrogenic medium (Zen-Bio, Inc.). Based on morphological analyses using toluidine blue staining, proteoglycan products appear in DPSC after 21 days of chondrocyte induction. Biochemical analyses in differentiated group showed that alkaline phosphatase activity was significantly increased at day 14 as compared to control (P < 0.05). Cell viability analyses during the differentiation to chondrocytes also showed that these cells were viable during differentiation. However, after the 14th day of differentiation, there was a significant decrease (P < 0.05) in the viability proportion among differentiated cells as compared to the control cells. In RT-PCR molecular analyses, mouse DPSC expressed Cd146 and Cd166 which indicated that these cells belong to mesenchymal stem cells. Coll I and Coll II markers showed high expression after 14 and 21 days, respectively. In conclusion, this study showed that DPSC successfully differentiated into chondrocytes.

Matched MeSH terms: Base Sequence
A tymovirus from Calopogonium mucunoides in Malaysia is not clitoria yellow vein tymovirus

Gibbs AJ, Mackenzie AM, Abdul-Samad N

Arch Virol, 1997;142(8):1697-702.
PMID: 9672629

A tymoyirus isolated from Malaysian crops of Calopogonium mucunoides has been shown to have virions that are serologically indistinguishable from those of clitoria yellow vein tymovirus. We have sequenced the virion protein (VP) gene of the virus and have found that although it is a member of the cluster that includes CYVV, it is the most distinct member of that cluster (< 62% sequence identity with all the others), and is clearly a separate species, which we propose should be named calopogonium yellow vein virus. Most of the serological specificity of the virions of tymoviruses seems to reside in the C-terminal hexapeptide of the virion protein.

Matched MeSH terms: Base Sequence
Fulltext mRNA expression of EgCHI1, EgCHI2, and EgCHI3 in oil palm leaves (Elaeis guineesis Jacq.) after treatment with Ganoderma boninense pat. and Trichoderma harzianum Rifai

Naher L, Tan SG, Ho CL, Yusuf UK, Ahmad SH, Abdullah F

ScientificWorldJournal, 2012;2012:647504.
PMID: 22919345 DOI: 10.1100/2012/647504

Basal stem rot (BSR) disease caused by the fungus Ganoderma boninense is the most serious disease affecting the oil palm; this is because the disease escapes the early disease detection. The biocontrol agent Trichoderma harzianum can protect the disease only at the early stage of the disease. In the present study, the expression levels of three oil palm (Elaeis guineensis Jacq.) chitinases encoding EgCHI1, EgCHI2, and EgCHI3 at 2, 5, and 8 weeks inoculation were measured in oil palm leaves from plants treated with G. boninense or T. harzianum alone or both.

Matched MeSH terms: Base Sequence
Fulltext Somatic mitochondrial DNA D-loop mutations in meningioma discovered: A preliminary data

Mohamed Yusoff AA, Mohd Khair SZN, Wan Abdullah WS, Abd Radzak SM, Abdullah JM

J Cancer Res Ther, 2020 12 22;16(6):1517-1521.
PMID: 33342822 DOI: 10.4103/jcrt.JCRT_1132_16

Background and Objective: Meningiomas are among the most common intracranial tumors of the central nervous system. It is widely accepted that the initiation and progression of meningiomas involve the accumulation of nucleus genetic alterations, but little is known about the implication of mitochondrial genomic alterations during development of these tumors. The human mitochondrial DNA (mtDNA) contains a short hypervariable, noncoding displacement loop control region known as the D-Loop. Alterations in the mtDNA D-loop have been reported to occur in most types of human cancers. The purpose of this study was to assess the mtDNA D-loop mutations in Malaysian meningioma patients.
Materials and Methods: Genomic DNA was extracted from 21 fresh-frozen tumor tissues and blood samples of the same meningioma patients. The entire mtDNA D-loop region (positions 16024-576) was polymerase chain reaction amplified using designed primers, and then amplification products were purified before the direct DNA sequencing proceeds.
Results: Overall, 10 (47.6%) patients were detected to harbor a total of 27 somatic mtDNA D-loop mutations. Most of these mtDNA mutations were identified in the hypervariable segment II (40.7%), with 33.3% being located mainly in the conserved sequence block II of the D310 sequence. Furthermore, 58 different germline variations were observed at 21 nucleotide positions.
Conclusion: Our results suggest that mtDNA alterations in the D-loop region may be an important and early event in developing meningioma. Further studies are needed, including validation in a larger patient cohort, to verify the clinicopathological outcomes of mtDNA mutation biomarkers in meningiomas.

Matched MeSH terms: Base Sequence/genetics
Fulltext Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTB221/11 Isolated from a Cerebrospinal Fluid Sample in Malaysia

Issa R, Seradja VH, Abdullah MK

Genome Announc, 2016;4(3).
PMID: 27365342 DOI: 10.1128/genomeA.00376-16

Here, we report of the annotated genome sequence of Mycobacterium tuberculosis MTB221/11. The organism was isolated from the cerebrospinal fluid of a patient in Malaysia.

Matched MeSH terms: Base Sequence
Characterization of promoter of EgPAL1, a novel PAL gene from the oil palm Elaeis guineensis Jacq

Yusuf CYL, Abdullah JO, Shaharuddin NA, Abu Seman I, Abdullah MP

Plant Cell Rep, 2018 Feb;37(2):265-278.
PMID: 29090330 DOI: 10.1007/s00299-017-2228-7

KEY MESSAGE: The oil palm EgPAL1 gene promoter and its regulatory region were functional as a promoter in the heterologous system of Arabidopsis according to the cis-acting elements present in that region. The promoter was developmentally regulated, vascular tissue specific and responsive to water stress agents. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the key enzyme of the phenylpropanoid pathway which plays important roles in plant development and adaptation. To date, there is no report on the study of PAL from oil palm (Elaeis guineensis), an economically important oil crop. In this study, the 5' regulatory sequence of a highly divergent oil palm PAL gene (EgPAL1) was isolated and fused with GUS in Arabidopsis to create two transgenic plants carrying the minimal promoter with (2302 bp) and without its regulatory elements (139 bp). The regulatory sequence contained cis-acting elements known to be important for plant development and stress response including the AC-II element for lignin biosynthesis and several stress responsive elements. The promoter and its regulatory region were fully functional in Arabidopsis. Its activities were characterised by two common fundamental features of PAL which are responsive to plant internal developmental programme and external factors. The promoter was developmentally regulated in certain organs; highly active in young organs but less active or inactive in mature organs. The presence of the AC elements and global activity of the EgPAL1 promoter in all organs resembled the property of lignin-related genes. The existence of the MBS element and enhancement of the promoter activity by PEG reflected the behaviour of drought-responsive genes. Our findings provide a platform for evaluating oil palm gene promoters in the heterologous system of Arabidopsis and give insights into the activities of EgPAL1 promoter in oil palm.

Matched MeSH terms: Base Sequence
Assessment of the association between three pfmdr1 point mutations and chloroquine resistance in vitro of Malaysian Plasmodium falciparum isolates

Cox-Singh J, Singh B, Alias A, Abdullah MS

Trans R Soc Trop Med Hyg, 1995 7 1;89(4):436-7.
PMID: 7570891
Matched MeSH terms: Base Sequence
Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region

Lee NK, Fong PK, Abdullah MT

Biomed Mater Eng, 2014;24(6):3807-14.
PMID: 25227097 DOI: 10.3233/BME-141210

Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that tree-based features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features.

Matched MeSH terms: Base Sequence
Fulltext Partial mtDNA sequencing data of vulnerable Cephalopachus bancanus from the Malaysian Borneo

Zahidin MA, Jalil NA, Naharuddin NM, Abd Rahman MR, Gani M, Abdullah MT

Data Brief, 2019 Aug;25:104133.
PMID: 31321260 DOI: 10.1016/j.dib.2019.104133

Tarsier is an endangered nocturnal primate in the family Tarsiidae and is an endemic to Sundaic islands of Philippine (Carlito syrichta), Sulawesi (Tarsius tarsier-complex) and Borneo (Cephalopachus bancanus). Recent records indicated that most molecular studies were done on the Eastern Tarsier and little information for the other group of tarsiers. Here, we present a partial cytochrome b data set of C. bancanus in Sarawak, Malaysian Borneo. Standard mist nets were deployed at strategic locations in various habitat types. A total of 18 individuals were caught, measured and weighed. Approximately, 2 × 2 mm of tissue samples were taken and preserved in molecular grade alcohol. Out of 18, only 11 samples were screened with partial mtDNA (cytochrome b) and the DNA sequences were registered in the GenBank (accession numbers: KY794797-KY794807). Phylogenetic trees were constructed with 20 additional mtDNA sequences downloaded from GenBank. The data are valuable for the management authorities to regulate the type of management units for the metapopulation to sustain population genetics integrity of tarsiers in the range countries across the Sunda Shelf.

Matched MeSH terms: Base Sequence
Fulltext Sequence polymorphism and haplogroup data of the hypervariable regions on mtDNA in Semoq Beri population

Zahidin MA, Omar WBW, Taib WRW, Japning JRR, Abdullah MT

Data Brief, 2018 Dec;21:2609-2615.
PMID: 30761343 DOI: 10.1016/j.dib.2018.10.158

Orang Asli is the aboriginal people in Peninsular Malaysia who have been recognized as indigenous to the country and still practicing traditional lifestyle. The molecular interest on the Orang Asli started when the earliest prehistoric migration occurred approximately 200 kya and entering Peninsular Malaysia 50 kya in stages. A total of three groups of Orang Asli present in Peninsular Malaysia, namely, Negrito also known as Semang, Senoi and Proto Malays. Through records, there is no research has been conducted on mtDNA variations in the Semoq Beri population, one of the tribes in Senoi group. In this report, variations of mtDNA were analysed in the population in Hulu Terengganu as an initial effort to establish the genetic characterisation and elucidating the history of Orang Asli expansion in Peninsular Malaysia. An array of mtDNA parameters was estimated and the observed polymorphisms with their respective haplogroups in comparison to rCRS were inferred respectively. The DNA sequences are registered in the NCBI with accession numbers KY853670-KY853753.

Matched MeSH terms: Base Sequence
Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure

Al-Khatib RM, Rashid NA, Abdullah R

J Biomol Struct Dyn, 2011 Aug;29(1):1-26.
PMID: 21696223

The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

Matched MeSH terms: Base Sequence
The stearoyl-acyl-carrier-protein desaturase promoter (Des) from oil palm confers fruit-specific GUS expression in transgenic tomato

Saed Taha R, Ismail I, Zainal Z, Abdullah SN

J Plant Physiol, 2012 Sep 01;169(13):1290-300.
PMID: 22658816 DOI: 10.1016/j.jplph.2012.05.001

The stearoyl-acyl-carrier-protein (ACP) desaturase is a plastid-localized enzyme that catalyzes the conversion of stearoyl-ACP to oleoyl-ACP and plays an important role in the determination of the properties of the majority of cellular glycerolipids. Functional characterization of the fatty acid desaturase genes and their specific promoters is a prerequisite for altering the composition of unsaturated fatty acids of palm oil by genetic engineering. In this paper, the specificity and strength of the oil palm stearoyl-ACP desaturase gene promoter (Des) was evaluated in transgenic tomato plants. Transcriptional fusions between 5' deletions of the Des promoter (Des1-4) and the β-glucuronidase (GUS) reporter gene were generated and their expression analyzed in different tissues of stably transformed tomato plants. Histochemical analysis of the Des promoter deletion series revealed that GUS gene expression was confined to the tomato fruits. No expression was detected in vegetative tissues of the transgenic plants. The highest levels of GUS activity was observed in different tissues of ripe red fruits (vascular tissue, septa, endocarp, mesocarp and columella) and in seeds, which harbored the promoter region located between -590 and +10. A comparison of the promoter-deletion constructs showed that the Des4 promoter deletion (314bp) produced a markedly low level of GUS expression in fruits and seeds. Fluorometric analysis of the GUS activity revealed a 4-fold increase in the activity of the full-length Des promoter compared to the CaMV35S promoter. RNA-hybridization analyses provided additional evidence of increased GUS expression in fruits driven by a Des fragment. Taken together, these results demonstrate the potential of the Des promoter as a tool for the genetic engineering of oil palms and other species, including dicots, in improving the quality and nutritional value of the fruits.

Matched MeSH terms: Base Sequence

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