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Fulltext Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation

Nwawuba Stanley U, Mohammed Khadija A, Bukola AT, Omusi Precious I, Ayevbuomwan Davidson E

Malays J Med Sci, 2020 Jul;27(4):22-35.
PMID: 32863743 DOI: 10.21315/mjms2020.27.4.3

Short tandem repeat (STR) typing continues to be the primary workhorse in forensic DNA profiling. Therefore, the present review discusses the prominent role of STR marker in criminal justice system. All over the world, deoxyribonucleic acid (DNA) profiling provides evidence that may be used to convict criminals, as an irrefutable proof of wrongful convictions, invaluable links to the actual perpetrators of crimes, and could also deter some offenders from committing more serious offences. Clearly, DNA profiling tools have also aided forensic scientists to re-evaluate old cases that were considered closed as a result of inadequate evidence. In carrying out this review, a comprehensive electronic literature search using PubMed, ScienceDirect, Google Scholar and Google Search were used, and all works meeting the subject matter were considered, including reviews, retrospective studies, observational studies and original articles. Case reports presented here, further demonstrates the crucial role of forensic DNA profiling in mitigating and providing compelling evidence for the resolution of crimes. For case report 1, there was a 100% match between the DNA recovered from the items found in the crime scene, and the suspect's DNA sample collected via buccal swab following 15 STR loci examination. Case report 2 further highlights the indispensable contribution of DNA database in solving crime. Therefore, it has become very necessary for developing countries like Nigeria to develop a national DNA database and make policies and legislatures that will further expand and enable the practice of forensic genetics, particularly DNA profiling.

Matched MeSH terms: DNA; DNA Fingerprinting
Fulltext Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats

Drinkwater R, Jucker T, Potter JHT, Swinfield T, Coomes DA, Slade EM, et al.

Mol Ecol, 2021 07;30(13):3299-3312.
PMID: 33171014 DOI: 10.1111/mec.15724

The application of metabarcoding to environmental and invertebrate-derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land-use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood-feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human-modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments.

Matched MeSH terms: DNA/genetics
Box-Behnken design optimisation of a green novel nanobio-based reagent for rapid visualisation of latent fingerprints on wet, non-porous substrates

Azman AR, Mahat NA, Wahab RA, Ahmad WA, Puspanadan JK, Huri MAM, et al.

Biotechnol Lett, 2021 Apr;43(4):881-898.
PMID: 33389272 DOI: 10.1007/s10529-020-03052-3

OBJECTIVE: Optimisation of the green novel nanobio-based reagent (NBR) for rapid visualisation of groomed fingerprints on wet non-porous substrates using response surface methodology and assessment of its stability and sensitivity were attempted for forensic applications.
RESULTS: Scanning electron microscopy images demonstrated successful attachments of NBR onto the constituents of fingerprints on the substrates. The highest average quality of visualised fingerprints was attained at the optimum condition (100 mg of CRL; 75 mg of acid-functionalised multi-walled carbon nanotubes; 5 h of immobilisation). The NBR produced comparable average quality of fingerprints with the commercially available small particle reagent, even after 4 weeks of storage (without any preservatives) in both chilled and sultry conditions. The NBR was sensitive enough to visualise the increasingly weaker fingerprints, particularly on glass slides.
CONCLUSION: The optimised novel NBR could be the relatively greener option for visualising latent fingerprints on wet, non-porous substrates for forensic applications.

Matched MeSH terms: DNA Fingerprinting/methods*
Allele frequency distribution for 10 STR loci in the Malay population of Malaysia

Panneerchelvam S, Haslindawaty N, Ravichandran M, Norazmi MN, Zainuddin ZF

J Forensic Sci, 2003 Mar;48(2):451-2.
PMID: 12665016
Matched MeSH terms: DNA Fingerprinting/methods
Genetic variation estimated in three Shorea species by the RAPD analysis

Harada K, Kinoshita A, Shukor NA, Tachida H, Yamazaki T

Jpn. J. Genet., 1994 Dec;69(6):713-8.
PMID: 7857675

Three species of Shorea (S. leprosula, S. acuminata and S. cursitii) were collected from a natural forest reserve of Malaysia and analyzed for genetic variation using the technique of random amplification of polymorphic DNA (RAPD) by the polymerase chain reaction (PCR). The average number of nucleotide substitutions was estimated. The nucleotide diversities within species were very similar and larger than those found in Drosophila melanogaster. The nucleotide divergences between these species are about 1.5 times the nucleotide diversities within the species, indicating that these species diverged from a common ancestor relatively recently.

Matched MeSH terms: DNA, Plant/genetics*
Hybridisation analysis for serum hepatitis B virus DNA

Yap SF, Wong PW, Kenneth-Raj

Br J Biomed Sci, 1994 Dec;51(4):336-40.
PMID: 7756940

A study was carried out to determine optimal assay conditions for an in-house hybridisation assay for detection of hepatitis B virus (HBV) genome in serum samples. Pre-treatment of samples, blot treatment and hybridisation conditions were found to affect assay performance. The indirect serum blot procedure was more robust and reliable than direct serum blotting. In the former, viral particles were isolated from the sample, lysed and then extracted. In comparison, no approaches to the direct serum spot method performed adequately. Sensitivity studies showed that labelling of the nucleic acid probe with dCTP was more efficient than with dATP. Using probes labelled to a specific activity of > 1 x 10(8) and an autoradiography period of about 48 h we could achieve a detection limit of < 1 pg. Specificity was achieved by use of a highly purified probe and moderately stringent hybridisation and wash conditions. Background binding was minimal and there was no non-specific binding of probe to negative control samples. Factors affecting speed of the assay were studied to identify steps that could be modified to shorten assay time without sacrificing performance. A shorter centrifugation step and the use of a high specific-activity probe permitted completion of an assay within four days.

Matched MeSH terms: DNA, Viral/blood*
Fulltext Future impact of molecular biology and biotechnology on bacterial and viral diseases

Pang T

Med J Malaysia, 1993 Jun;48(2):101-6.
PMID: 8350782

The advent of recombinant DNA technology has already made a significant impact on various aspects related to the basic understanding of pathogenic mechanisms in infectious diseases, as well as practical applications related to diagnostics and prevention. The present paper discusses recent technological innovations and increased analytical capabilities which promise to have an even more significant impact on the control of viral and bacterial diseases.

Matched MeSH terms: DNA, Recombinant/genetics
Fulltext First trimester prenatal diagnosis of beta-thalassaemia following chorionic villus sampling

Chandran R, Ainoon O, Anson I, Anne J, Cheong SK

Med J Malaysia, 1993 Sep;48(3):341-4.
PMID: 8183149

DNA analysis for the diagnosis of beta-thalassaemia is a relatively new technique in Malaysia. This, combined with chorionic villus sampling, has enabled us to offer prenatal diagnosis in the first trimester for this common condition. To the best of our knowledge, this has not hitherto been reported in Malaysia.

Matched MeSH terms: DNA/analysis
Molecular characterization of Pasteurella multocida isolates from rabbits

Al-Haddawi MH, Jasni S, Son R, Mutalib AR, Bahaman AR, Zamri-Saad M, et al.

J Gen Appl Microbiol, 1999 Dec;45(6):269-275.
PMID: 12501355

Forty isolates of Pasteurella multocida from healthy (17 isolates) and diseased (23 isolates) rabbits were assayed for the presence of plasmids in seeking to determine whether any correlation exists between the presence of plasmids and health status, sensitivity to antimicrobial agents, capsular and somatic type, and the anatomic site of isolation. Six isolates were found harboring plasmids. A similar ladder pattern ranging from 18 to 3 megadalton (Mda) were found in three isolates recovered from diseased rabbits. One band of molecular weight 6.6 Mda was shared by four of five (4/5) isolates from the diseased rabbits. No correlation was found between the presence of the common plasmids and serotype, resistance to antimicrobial agents, and anatomic sites from which the bacteria were cultured. Random amplification polymorphic DNA was applied to subtype all the isolates of P. multocida. Two single primers were tested for their abilities to generate individual fingerprints by using PCR. Primer 1 grouped the isolates into 7 profiles, and primer 2 grouped them into 15. Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) results show the presence of a wide heterogeneity within P. multocida isolates. Therefore RAPD-PCR is an efficient technique to detect the DNA polymorphism and could be used to discriminate P. multocida of rabbit isolates together with serologic typing.

Matched MeSH terms: DNA; Random Amplified Polymorphic DNA Technique
Phylogeographic analysis of pigtail macaque populations (Macaca nemestrina) inferred from mitochondrial DNA

Rosenblum LL, Supriatna J, Melnick DJ

Am J Phys Anthropol, 1997 Sep;104(1):35-45.
PMID: 9331452

Mitochondrial DNA variation was surveyed in nine populations of the pigtail macaque (Macaca nemestrina), covering all three recognized subspecies in Southeast Asia. To do this, a 2,300 base pair fragment spanning the mitochondrial NAD 3 and NAD 4 genes and flanking tRNA subunits leucine and glycine was targeted for amplification and digested with a battery of 16 restriction endonucleases. Out of a total of 107 individuals, 32 unique haplotypes could be distinguished. Parsimony and neighbor-joining analyses grouped the haplotypes into five strongly supported assemblages representing China/Thailand, Malaysia, Sumatra, Borneo, and Siberut. These results indicate that the mainland and island mtDNA haplotypes are strictly and uniquely limited to the geographic ranges of the recognized morphological subspecies. Cladistic and neighbor-joining analyses indicate that inferred phylogenies of mtDNA haplotypes are congruent with subspecies designations. Furthermore, in support of morphological studies, results indicate that the Mentawai macaque is most likely not a distinct species but a subspecies of M. nemestrina.

Matched MeSH terms: DNA, Mitochondrial/genetics*
Molecular and ecological investigations on the wild populations of Glycyrrhiza L. taxa distributed in the East Mediterranean Area of Turkey

Altay V, Karahan F, Öztürk M, Hakeem KR, Ilhan E, Erayman M

J Plant Res, 2016 Nov;129(6):1021-1032.
PMID: 27655558

This paper covers studies on the molecular and ecological aspects of G. glabra var. glandulifera, G. flavescens ssp. flavescens and G. echinata collected from Hatay (Turkey); with the aim to better understand their genetic variation and ecological requirements for possible conservation programs. The material including total genomic DNA was extracted by the CTAB, and for PCR reaction, a total of 14 SSR primers developed for Medicago truncatula were used. PCR amplifications were performed in a Multigen(®) Thermal Cycler. Soil samples were analysed for their texture, pH, total soluble salts, calcium carbonate, total N content, total phosphorus and organic matter content. In order to see the association between genetic, ecological and geographical data, a similarity matrix was generated. Genetic similarity distances between genotypes were correlated with those of Eucledian distances obtained from ecological and geographical data. Analysis of molecular variance (AMOVA) was performed using GenAlEx 6.5 software to determine variation among and within genetic variations. The genetic analysis showed that the highest expected heterozygosity values were obtained from G. glabra while the lowest were obtained from G. echinata. In general heterozygosity values were low, especially for G. echinata. Therefore, variation appears to be lower within each species than among three species. The physical and chemical analysis of soil and plant samples indicates that mineral accumulation in plants is substantially affected by the soil characteristics. There is a need for identification of better strategies for the improvement of varieties, especially for small farmers managing marginal soils. More studies should be conducted in order to safeguard these taxa, especially G. glabra var. glandulifera which is collected intensively due to its economic value, the same is true for endemic taxon G. flavescens ssp. flavescens.

Matched MeSH terms: DNA; DNA Primers
Comparison of the fine-scale genetic structure of three dipterocarp species

Takeuchi Y, Ichikawa S, Konuma A, Tomaru N, Niiyama K, Lee SL, et al.

Heredity (Edinb), 2004 Apr;92(4):323-8.
PMID: 14735142

We investigated the fine-scale genetic structure of three tropical-rainforest trees, Hopea dryobalanoides, Shorea parvifolia and S. acuminata (Dipterocarpaceae), in Peninsular Malaysia, all of which cooccurred within a 6-ha plot in Pasoh Forest Reserve. A significant genetic structure was found in H. dryobalanoides, weaker (but still significant) genetic structure in S. parvifolia and nonsignificant structure in S. acuminata. Seeds of all three species are wind dispersed, and their flowers are thought to be insect pollinated. The most obvious difference among these species is their height: S. parvifolia and S. acuminata are canopy species, whereas H. dryobalanoides is a subcanopy species. Clear differences were also found among these species in their range of seed dispersal, which depends on the height of the release point; so taller trees disperse their seed more extensively. The estimates of seed dispersal area were consistent with the degree of genetic structure found in the three species. Therefore, tree height probably had a strong influence on the fine-scale genetic structure of the three species.

Matched MeSH terms: DNA, Plant/chemistry*
Allele frequencies for the PowerPlex 16 STR loci in Javanese population in Malaysia

Othman MI, Seah LH, Panneerchelvam S, Nor NM

J Forensic Sci, 2004 Jan;49(1):190-1.
PMID: 14979376
Matched MeSH terms: DNA Fingerprinting/methods
Fulltext Halal analysis of raw materials, ingredients and finished bakery products using PCR and gene chip southern-hybridization for detection of porcine DNA

Norrakiah, A.S., Shahrul Azim, M. G., Sahilah, A.M., Abdul Salam, B.

International Food Research Journal, 2015;22(5):1883-1887.
MyJurnal

This study was conducted to investigate the sensitivity and detection of porcine DNA in raw materials, ingredients and finished bakery products by polymerase chain reaction (PCR) - southern hybridization on chip analysis. A total of 20 samples (n=20* 3) with three replicates for each samples were obtained from a bakery factory located in Bangi, Selangor from January to December 2012. The sensitivity level of PCR-southern hybridization on chip was 0.001 ng. The species-specific oligonucleotide primers used in PCR-southern hybridization were targeted on the mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence, namely cty b biotin-labeled oligonucleotide primers. The amplicon from PCR amplification was 276 bp in size. None of the raw materials, ingredients and finished bakery product samples was positive towards porcine DNA, except for the positive control. The results in the present study demonstrated that the PCR- southern-hybridization technique on the gene chip (OliproTM Porcine gene chip) is a sensitive tool for monitoring the porcine component in highly processed ingredients and finished bakery products.

Matched MeSH terms: DNA, Mitochondrial; DNA Primers
Fulltext Pre-enrichment effect on PCR Detection of Salmonella Enteritidis in artificially-contaminated raw chicken meat

Mohd Afendy, A.T., Son, R.

International Food Research Journal, 2015;22(6):2571-2575.
MyJurnal

Salmonella remains to be a major foodborne pathogen for animals and humans and is the
leading cause of foodborne infections and outbreaks in various countries. Salmonella Enteritidis
is one of the most frequently isolated serotypes in poultry and poultry products from human
food poisoning cases. It can cause mild to acute gastroenterititis as well as other common
food poisoning symptoms when infection takes place in human. Nucleic acid amplification
technologies such as Polymerase Chain Reaction (PCR) is a tool that is rapid and sensitive
for detection of bacterial pathogen. We report the successful detection of S. Enteritidis by
PCR in raw chicken meat artificially-contaminated with serial concentration of S. Enteritidis
using crude DNA extracts as DNA template. PCR primers, ENT-F and ENT-R targeted on sdfI
gene were used to amplify DNA region unique to S. Enteritidis with crude DNA extract of the
samples, yielded product with the size of 303 bp. These primers were specific to S. Enteritidis
when tested by in-silico simulation against genome database of targeted bacterial species and
confirmed in PCR as amplification bands were observed with S. Typhimurium, S. Polarum and
S. Gallinarum. The established PCR can detect as few as 9.4 X 101
CFU/ml of inoculated S.
Enteritidis concentration and proved that pre-enrichment effect have significant effect on PCR
detection by increasing 1000-fold of the sensitivity limit compared to the non pre-enriched
samples. The PCR technique indicated that it can be successfully coupled with pre-enrichment
step to offer advantage in routine screening and surveillance of bacterial contamination in food
samples.

Matched MeSH terms: DNA; DNA Primers
Fulltext Molecular characterisation of Vibrio parahaemolyticus carrying tdh and trh genes using ERIC-, RAPD- and BOX-PCR on local Malaysia bloody clam and Lala

Yoke-Kqueen, C., Teck-Ee, K., Son, R, Yoshitsugu, N., Mitsuaki, N.

International Food Research Journal, 2013;20(6):3299-3305.
MyJurnal

Molecular typing methods have been widely applied for many purposes. In this study, such methods were adopted as DNA fingerprinting tools to determine the origin and divergence of virulent Vibrio parahaemolyticus strains found in local seafood. Although not all strain carry virulent tdh and trh gene, increasing prevalence demands an effective fingerprinting scheme which can constantly monitor and trace the sources of such emerging food pathogens. By using ERIC-, RAPD-, and BOX-PCR methods, 33 Vibrio parahaemolyticus isolates from local Malaysia bloody clam (Anadara granosa) and Lala (Orbicularia orbiculata) with confirmed presence of tdh and trh gene were characterised, followed by determination of clonal relatedness among virulent strains using cluster analysis and discriminatory index. This study also involved application of Immunomagnetic Separation (IMS) Method which significantly improved the specificity of strain isolation. Cluster analysis using Unweighted Pair Group Mathematical Averaging (UPGMA) and Dice Coefficient shown clustering according to isolation food source, IMS level and haemolysin gene possessed. Nevertheless, different DNA fingerprinting methods generated different clustering at different similarity cut-off percentage, regardless as individual or as composite dendrograms. ERIC- and RAPD-PCR composite fingerprinting relatively shown the highest discriminatory index at following similarity cutoff percentage: 0.68 at 50%; 0.83 at 65%; and 0.93 at 75%. Discriminatory power increased with similarity cut-off percentage. However, result also suggested that BOX-PCR might be an effective fingerprinting tool, as it generated three clusters with no single-colony isolate at 70% similarity cut-off. This study not only achieved its objective to determine clonal relatedness among virulent strains from local seafood via characterisation, but also speculated the best possible combination of molecular typing methods to effectively do so.

Matched MeSH terms: DNA Fingerprinting; Random Amplified Polymorphic DNA Technique
A comparative study of two methods for the isolation of human leucocytes for DNA extraction

Lim LH, Ton SH, Cheong SK

Malays J Pathol, 1990 Jun;12(1):39-41.
PMID: 2090888

The 'Dextran' and the 'Buffy-coat' methods for isolation of human leucocytes for DNA extraction were compared on the basis of DNA yield from the same amounts (10 ml) of blood. Human leucocytes from a total of 11 samples were isolated using both methods for each sample after which DNA was extracted. Extracted DNA samples were treated with ribonucleases and proteinase K after which the yields were quantitated by measuring absorbance at 260 nm. The 'Buffy-coat' method yielded a mean concentration of DNA of 476.7 micrograms/ml (range: 212 to 700 micrograms/ml) while the 'Dextran' method yielded 188.4 micrograms/ml (range: 64 to 340 micrograms/ml). The difference was confirmed by subjecting the extracted DNA samples to agarose gel electrophoresis.

Matched MeSH terms: DNA/analysis*
Fulltext Sequencing crop genomes: a gateway to improve tropical agriculture

Thottathil, Gincy Paily, Jayasekaran, Kandakumar, Ahmad Sofiman Othman

Trop Life Sci Res, 2016;27(1):93-114.
MyJurnal

Agricultural development in the tropics lags behind development in the
temperate latitudes due to the lack of advanced technology, and various biotic and abiotic
factors. To cope with the increasing demand for food and other plant-based products,
improved crop varieties have to be developed. To breed improved varieties, a better
understanding of crop genetics is necessary. With the advent of next-generation DNA
sequencing technologies, many important crop genomes have been sequenced. Primary
importance has been given to food crops, including cereals, tuber crops, vegetables, and
fruits. The DNA sequence information is extremely valuable for identifying key genes
controlling important agronomic traits and for identifying genetic variability among the
cultivars. However, massive DNA re-sequencing and gene expression studies have to be
performed to substantially improve our understanding of crop genetics. Application of the
knowledge obtained from the genomes, transcriptomes, expression studies, and
epigenetic studies would enable the development of improved varieties and may lead to a
second green revolution. The applications of next generation DNA sequencing
technologies in crop improvement, its limitations, future prospects, and the features of
important crop genome projects are reviewed herein.

Matched MeSH terms: DNA; Sequence Analysis, DNA
Fulltext Absence of nucleotide alteration in region of exon 34 of NOTCH1 and NOTCH2 receptor genes analysed in oral cancer samples: a preliminary observation

Nor Nasyitah Ismail, Khairani Idah Mokhtar

Archives of Orofacial Sciences, 2010;5(1):17-23.
MyJurnal

Oral cancer is one of the common cancer cases identified in the developing countries. Genetic mutation and overexpression of certain genes and proteins have been associated in the development of this cancer. Notch signalling pathway is normally involved in controlling the development process of vertebrates and invertebrates; however, deregulation of this pathway was found to be responsible in the formation of certain cancers including oral cancers. Activation of this pathway requires binding of the ligands to its receptors. Four NOTCH receptors (NOTCH 1, 2, 3 and 4) have been identified in mammals. Disruptions within these molecules might interfere with the normal functions of Notch signalling pathway. Hence, this study was conducted to detect mutations of NOTCH1 and NOTCH2 receptor genes which might be occurring in the oral cancer cases obtained from the local population. DNA extracted from fresh-frozen tissue biopsy of the tongue and buccal mucosa from 10 confirmed cases of oral cancer were subjected for polymerase chain reaction (PCR) amplification using the specific sets of primers. The PCR products were sent for sequencing before final results were analysed.
Due to time and cost limitation, only two out of four NOTCH receptor genes; NOTCH1 and NOTCH2, were used in this analysis. The results revealed absence of nucleotide changes for both NOTCH receptor genes amplified from these oral cancer samples. More samples and further analysis looking into other regions in these genes are required to conclude the involvement of NOTCH receptor genes mutation in causing oral cancer.

Matched MeSH terms: DNA; DNA Primers
Molecular genetic approach in the forensic science of animal species identification

Chong, Lee Kim

Buletin Persatuan Genetik Malaysia, 2005;11(1):0-0.
MyJurnal

Animal species identification is one of the important fields in forensic science. Unlike human forensics which makes use of DNA fingerprinting techniques to identify individuals of the same species - humans, animal forensic species identification is much more complicated as it involves the ability to identify and distinguish between hundreds to thousands of species when the material evidence is only a trace of animal tissue without the presence of any visual physical morphology. It is even more difficult when the specimen is an unknown and no reference material is available. Animal species identification is not only important for the prevention of wildlife crimes for the purpose of wildlife protection and conservation but it is also becoming more and more significant in food safety issues especially for the meat industry. Owing to the demand and the necessity of providing such services for regulation and enforcement in the context of environmental protection, food safety and biosafety, the Department of Chemistry (DOC)
Malaysia has initiated the use of DNA techniques employing the most widely used genetic markers as part of its scientific solution for animal species identification.

Matched MeSH terms: DNA; DNA Fingerprinting

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