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  1. Fulltext Optical DNA Biosensor Based on Square-Planar Ethyl Piperidine Substituted Nickel(II) Salphen Complex for Dengue Virus Detection
    Ariffin EY, Tan LL, Abd Karim NH, Yook Heng L
    Sensors (Basel), 2018 Apr 12;18(4).
    PMID: 29649118 DOI: 10.3390/s18041173
    A sensitive and selective optical DNA biosensor was developed for dengue virus detection based on novel square-planar piperidine side chain-functionalized N,N'-bis-4-(hydroxysalicylidene)-phenylenediamine-nickel(II), which was able to intercalate via nucleobase stacking within DNA and be functionalized as an optical DNA hybridization marker. 3-Aminopropyltriethoxysilane (APTS)-modified porous silica nanospheres (PSiNs), was synthesized with a facile mini-emulsion method to act as a high capacity DNA carrier matrix. The Schiff base salphen complexes-labelled probe to target nucleic acid on the PSiNs renders a colour change of the DNA biosensor to a yellow background colour, which could be quantified via a reflectance transduction method. The reflectometric DNA biosensor demonstrated a wide linear response range to target DNA over the concentration range of 1.0 × 10-16-1.0 × 10-10 M (R² = 0.9879) with an ultralow limit of detection (LOD) at 0.2 aM. The optical DNA biosensor response was stable and maintainable at 92.8% of its initial response for up to seven days of storage duration with a response time of 90 min. The reflectance DNA biosensor obtained promising recovery values of close to 100% for the detection of spiked synthetic dengue virus serotypes 2 (DENV-2) DNA concentration in non-invasive human samples, indicating the high accuracy of the proposed DNA analytical method for early diagnosis of all potential infectious diseases or pathological genotypes.
    Matched MeSH terms: DNA
  2. Fulltext Epigenetic changes of DRD2 gene in Pathogenesis of Schizophrenia
    Nour El Huda Abd Rahim, Mohd Nabil Fikri Rahim, Norsidah Ku Zaifah, Hanisah Mohd Noor, Kartini Abdullah, Norlelawati A. Talib
    International Medical Journal Malaysia, 2017;16(11):3-3.
    MyJurnal
    The dopamine hypothesis has earlier dominated the theories for the
    development of schizophrenia based on the early pharmacologic evidence. The
    antipsychotic drugs, among others, is thought to interfere with the function of the
    dopamine D2 receptor (DRD2) resulting in clinical improvement. Accumulating evidence
    suggest the role of epigenetic mechanisms in the pathophysiology of schizophrenia.
    Despite this, specific evidence linking the DRD2 DNA methylation with schizophrenia is
    insufficient mainly due to the poor accessibility and limited brain samples. Of late, new
    data has suggested the global impact of DNA methylation in the development of
    schizophrenia, thus methylation in the peripheral blood could infer changes in the brain.
    The aim of this study was to assess the DRD2 DNA methylation in the peripheral blood of
    schizophrenia.
    Matched MeSH terms: DNA Methylation
  3. Fulltext Mitochondrial DNA copy number variation, leukocyte telomere length, and breast cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) study
    Campa D, Barrdahl M, Santoro A, Severi G, Baglietto L, Omichessan H, et al.
    Breast Cancer Res, 2018 04 17;20(1):29.
    PMID: 29665866 DOI: 10.1186/s13058-018-0955-5
    BACKGROUND: Leukocyte telomere length (LTL) and mitochondrial genome (mtDNA) copy number and deletions have been proposed as risk markers for various cancer types, including breast cancer (BC).

    METHODS: To gain a more comprehensive picture on how these markers can modulate BC risk, alone or in conjunction, we performed simultaneous measurements of LTL and mtDNA copy number in up to 570 BC cases and 538 controls from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. As a first step, we measured LTL and mtDNA copy number in 96 individuals for which a blood sample had been collected twice with an interval of 15 years.

    RESULTS: According to the intraclass correlation (ICC), we found very good stability over the time period for both measurements, with ICCs of 0.63 for LTL and 0.60 for mtDNA copy number. In the analysis of the entire study sample, we observed that longer LTL was strongly associated with increased risk of BC (OR 2.71, 95% CI 1.58-4.65, p = 3.07 × 10- 4 for highest vs. lowest quartile; OR 3.20, 95% CI 1.57-6.55, p = 1.41 × 10- 3 as a continuous variable). We did not find any association between mtDNA copy number and BC risk; however, when considering only the functional copies, we observed an increased risk of developing estrogen receptor-positive BC (OR 2.47, 95% CI 1.05-5.80, p = 0.04 for highest vs. lowest quartile).

    CONCLUSIONS: We observed a very good correlation between the markers over a period of 15 years. We confirm a role of LTL in BC carcinogenesis and suggest an effect of mtDNA copy number on BC risk.

    Matched MeSH terms: DNA, Mitochondrial/genetics*; DNA Copy Number Variations/genetics
  4. Fulltext Mutations inside rifampicin-resistance determining region of rpoB gene associated with rifampicin-resistance in Mycobacterium tuberculosis
    Zaw MT, Emran NA, Lin Z
    J Infect Public Health, 2018 04 26;11(5):605-610.
    PMID: 29706316 DOI: 10.1016/j.jiph.2018.04.005
    BACKGROUND: Rifampicin (RIF) plays a pivotal role in the treatment of tuberculosis due to its bactericidal effects. Because the action of RIF is on rpoB gene encoding RNA polymerase β subunit, 95% of RIF resistant mutations are present in rpoB gene. The majority of the mutations in rpoB gene are found within an 81bp RIF-resistance determining region (RRDR).

    METHODOLOGY: Literatures on RIF resistant mutations published between 2010 and 2016 were thoroughly reviewed.

    RESULTS: The most commonly mutated codons in RRDR of rpoB gene are 531, 526 and 516. The possibilities of absence of mutation in RRDR of rpoB gene in MDR-TB isolates in few studies was due to existence of other rare rpoB mutations outside RRDR or different mechanism of rifampicin resistance.

    CONCLUSION: Molecular methods which can identify extensive mutations associated with multiple anti-tuberculous drugs are in urgent need so that the research on drug resistant mutations should be extended.

    Matched MeSH terms: DNA-Directed RNA Polymerases
  5. Cell Proliferation and DNA Repair Ability of Ganoderma neo-japonicum (Agaricomycetes): An Indigenous Medicinal Mushroom from Malaysia
    Tan WC, Kuppusamy UR, Phan CW, Sabaratnam V
    Int J Med Mushrooms, 2018;20(2):155-163.
    PMID: 29773007 DOI: 10.1615/IntJMedMushrooms.2018025445
    Ganoderma neo-japonicum is an annual polypore that grows on decaying bamboo in the forests of Malaysia. The indigenous Temuan tribe uses this species as a medicinal mushroom to cure fever and epilepsy and to improve body strength. The potential use of G. neo-japonicum in genoprotection and DNA repair was established using a single-cell gel electrophoresis (comet) assay. The effects of the ethanol and hot aqueous extracts from wild and cultivated basidiocarps, solid substrate-fermented (SSF) wheat grains, and mycelia via submerged culture on H2O2-damaged murine RAW264.7 macrophages were investigated. An ethanol extract from wild basidiocarps showed the most significant protective effect on murine RAW264.7 macrophages, followed by ethanol and hot water extracts of cultivated basidiocarps, and this effect was dose dependent. However, only the ethanol extracts from SSF and submerged culture showed significant protective effects compared with the control. As for DNA repair ability, only the ethanol extract from wild and cultivated basidiocarps showed significant results when compared with the negative control. The findings suggest the potential therapeutic use of G. neo-japonicum in genome protection and as a DNA repair stimulator.
    Matched MeSH terms: DNA Damage/drug effects; DNA Repair/drug effects*
  6. Fulltext Molecular identification of a rare haemoglobin variant: Hb G coushatta in Malaysia
    Alifah Nadia Abu Hassan, Ezalia Esa, Nur Aisyah Aziz, Faidatul Syazlin Abd Hamid, Zubaidah Zakaria, Siti Aisyah Lazim
    Journal of Biomedical and Clinical Sciences, 2017;2(202):1-2.
    MyJurnal
    Thalassaemia screening programme was conducted to reduce the burden of the disease [1]. Here, we describe one unexpected discovery in a 33-year-old gentleman and also the importance of DNA analysis in detecting the globin gene mutation.
    Matched MeSH terms: DNA
  7. Mortality from scale drop disease in farmed Lates calcarifer in Southeast Asia
    Senapin S, Dong HT, Meemetta W, Gangnonngiw W, Sangsuriya P, Vanichviriyakit R, et al.
    J Fish Dis, 2019 Jan;42(1):119-127.
    PMID: 30397913 DOI: 10.1111/jfd.12915
    In Southeast Asia, a new disease called scale drop disease (SDD) caused by a novel Megalocytivirus (SDDV) has emerged in farmed Asian sea bass (Lates calcarifer) in Singapore, Malaysia and Indonesia. We received samples from an Eastern Thai province that also showed gross signs of SDD (loss of scales). Clinical samples of 0.2-1.1 kg L. calcarifer collected between 2016 and 2018 were examined for evidence of SDDV infection. Histopathology was similar to that in the first report of SDDV from Singapore including necrosis, inflammation and nuclear pyknosis and karyorrhexis in the multiple organs. Intracytoplasmic inclusion bodies were also observed in the muscle tissue. In a density-gradient fraction from muscle extracts, TEM revealed enveloped, hexagonal megalocytiviral-like particles (~100-180 nm). By PCR using primers derived from the Singaporean SDDV genome sequence, four different genes were amplified and sequenced from the Thai isolate revealing 98.7%-99.9% identity between the two isolates. Since viral inclusions were rarely observed, clinical signs and histopathology could not be used to easily distinguish between SDD caused by bacteria or SDDV. We therefore recommend that PCR screening be used to monitor broodstock, fry and grow-out fish to estimate the current impact of SDDV in Southeast Asia and to prevent its spread.
    Matched MeSH terms: DNA Virus Infections/mortality; DNA Virus Infections/pathology; DNA Virus Infections/veterinary*
  8. Fulltext Combating transnational organized crime by linking multiple large ivory seizures to the same dealer
    Wasser SK, Torkelson A, Winters M, Horeaux Y, Tucker S, Otiende MY, et al.
    Sci Adv, 2018 09;4(9):eaat0625.
    PMID: 30255141 DOI: 10.1126/sciadv.aat0625
    Rapid growth in world trade has enabled transnational criminal networks to conceal their contraband among the 1 billion containers shipped worldwide annually. Forensic methods are needed to identify the major cartels moving the contraband into transit. We combine DNA-based sample matching and geographic assignment of tusks to show that the two tusks from the same elephant are often shipped by the same trafficker in separate large consignments of ivory. The paired shipments occur close in time from the same initial place of export and have high overlap in the geographic origins of their tusks. Collectively, these paired shipments form a linked chain that reflects the sizes, interconnectedness, and places of operation of Africa's largest ivory smuggling cartels.
    Matched MeSH terms: DNA
  9. Penyaringan domain ADP-ribosilasi gen toksin daripada Burkholderia pseudomallei virulen
    Shahrul Hisham Zainal Ariffin, Rahmah Mohamed, Zulkeflie Zamrod, Mohammad Noor Embi
    Sains Malaysiana, 2008;37.
    Bahagian aktif bagi enzim toksin bakteria daripada Burkholderia pseudomallei, Pseudomonas aeruginosa dan difteria merupakan domain ADP-ribosilasi. Domain ini didapati terpelihara di antara ketiga-tiga mikroorganisme. Di dalam kajian ini, domain ADP-ribosilasi Burkholderia pseudomallei telah diamplifikasi daripada genom B. pseudomallei virulen dengan menggunakan pencetus-pencetus yang dibina berdasarkan kepada jujukan domain ADP ribosilasi Pseudomonas aeruginosa. Hasil DNA amplifikasi ditulenkan dan digunakan sebagai prob (HPCR2) untuk menyaring DNA selitan daripada B. pseudomallei yang diklonkan ke dalam vektor pengekspresan pSport-I. Objektif kajian ini adalah untuk menyaring lapan klon yang positif hasil daripada penyaringan awal melalui pendekatan immunoblot menggunakan antitoksin daripada arnab. Penyaringan ini juga melibatkan tiga klon yang tidak memberikan isyarat positif semasa penyaringan secara immunoblot. Keputusan menunjukkan hanya satu klon (L31) daripada lapan klon immunoblot positif mempunyai domain ADP-ribosilasi. Penjujukan DNA separa klon L31 secara manual melibatkan dua pencetus menghasilkan jujukan sepanjang 450pb. Analisis selanjutnya mendapati daripada enam kemungkinan translasi kepada polipeptida hanya satu polipeptida wujud yang tidak mempunyai sebarang kodon penamat pada jujukan kodonnya.
    Matched MeSH terms: DNA
  10. Pengklonan dan pencirian klon CUKMCS yang mengekodkan kapsaisin sintase (Cs)
    Nurulhikma Md. Isa, Ismanizan Ismail, Zamri Zainal
    Sains Malaysiana, 2010;39.
    Kapsaisinoid merupakan alkaloid yang memberikan ciri kepedasan pada cili serta khusus pada genus Capsicum. Sebatian kapsaisinoid terdiri daripada dua komponen utama iaitu kapsaisin dan dihidrokapsaisin. Dalam kajian ini, pengklonan cDNA Kapsaisin sintase (Cs) telah berjaya dilakukan menerusi kaedah transkripsi berbalik PCR (RT-PCR) dan klon cDNA tersebut dinamakan CUKMCS yang bersaiz 981 pb. Pencarian homologi menggunakan program blastx dan blastp yang terdapat pada pangkalan data NCBI mendapati CUKMCS mempunyai persamaan yang sangat tinggi terhadap Cs pada Capsicum frutescens, Capsicum annuum dan Capsicum chacoense. Saiz ramalan protein CUKMCS diangggarkan sekitar 36 kDa. Penentuan pengekspresan transkrip Cs pada 5 tisu yang berbeza mendapati transkrip dikesan pada tisu plasenta, mesokarp dan biji manakala tiada transkrip Cs dikesan pada daun dan akar
    Matched MeSH terms: DNA, Complementary
  11. Genetic characterization of two mahseer species (tor douronensis and tor tambroides) using microsatellite markers from other cyprinids
    Yuzine Esa, Khairul Adha A. Rahim, Siti Shapor Siraj, Muhammad Fadhil Syukri, Siti Khalijah Daud, Ho GC, et al.
    Sains Malaysiana, 2011;40:1087-1095.
    This study examined the genetic characteristics of twenty-six microsatellite primers developed from three cyprinid fishes (Cyprinus carpio Linnaeus, Barbus barbus Linnaeus and Barbonymus gonionotus Bleeker) in two indigenous mahseer. The Tor douronensis Valenciennes were randomly collected from two locations in Sarawak (N=52), while Tor tambroides Bleeker were obtained from Peninsular Malaysia (N=56). A total of ten and twelve primers were successfully amplified producing four and five polymorphic loci in T. douronensis and T. tambroides, respectively. The number of alleles per locus ranging from 2 to 5 in T. douronensis and 2 to 7 in T. tambroides. A significant deviation from Hardy-Weinberg equilibrium (HWE) was observed at three loci (Barb37, Barb59 and Barb62) in one or more populations in T. tambroides while two loci (Barb37 and Barb62) were deviated in T. douronensis population of Batang Ai. Population structure analysis showed low level of inter-population genetic differentiation in both mahseer. Overall, the identified microsatellite loci should be useful in analysing T. douronensis and T. tambroides natural populations.
    Matched MeSH terms: DNA Primers
  12. Fulltext Karyotypic and mtDNA based characterization of Malaysian water buffalo
    Shaari N'AL, Jaoi-Edward M, Loo SS, Salisi MS, Yusoff R, Ab Ghani NI, et al.
    BMC Genet, 2019 03 25;20(1):37.
    PMID: 30909863 DOI: 10.1186/s12863-019-0741-0
    BACKGROUND: In Malaysia, the domestic water buffaloes (Bubalus bubalis) are classified into the swamp and the murrah buffaloes. Identification of these buffaloes is usually made via their phenotypic appearances. This study characterizes the subspecies of water buffaloes using karyotype, molecular and phylogenetic analyses. Blood of 105 buffaloes, phenotypically identified as swamp, murrah and crossbred buffaloes were cultured, terminated and harvested using conventional karyotype protocol to determine the number of chromosomes. Then, the D-loop of mitochondrial DNA of 10 swamp, 6 crossbred and 4 murrah buffaloes which were identified earlier by karyotyping were used to construct a phylogenetic tree was constructed.

    RESULTS: Karyotypic analysis confirmed that all 93 animals phenotypically identified as swamp buffaloes with 48 chromosomes, all 7 as crossbreds with 49 chromosomes, and all 5 as murrah buffaloes with 50 chromosomes. The D-loop of mitochondrial DNA analysis showed that 10 haplotypes were observed with haplotype diversity of 0.8000 ± 0.089. Sequence characterization revealed 72 variables sites in which 67 were parsimony informative sites with sequence diversity of 0.01906. The swamp and murrah buffaloes clearly formed 2 different clades in the phylogenetic tree, indicating clear maternal divergence from each other. The crossbreds were grouped within the swamp buffalo clade, indicating the dominant maternal swamp buffalo gene in the crossbreds.

    CONCLUSION: Thus, the karyotyping could be used to differentiate the water buffaloes while genotypic analysis could be used to characterize the water buffaloes and their crossbreds.

    Matched MeSH terms: DNA, Mitochondrial
  13. Fulltext Polymer Pen Lithography-Fabricated DNA Arrays for Highly Sensitive and Selective Detection of Unamplified Ganoderma Boninense DNA
    Rani E, Mohshim SA, Ahmad MZ, Goodacre R, Alang Ahmad SA, Wong LS
    Polymers (Basel), 2019 Mar 25;11(3).
    PMID: 30960545 DOI: 10.3390/polym11030561
    There is an increasing demand for lithography methods to enable the fabrication of diagnostic devices for the biomedical and agri-food sectors. In this regard, scanning probe lithography methods have emerged as a possible approach for this purpose, as they are not only convenient, robust and accessible, but also enable the deposition of "soft" materials such as complex organic molecules and biomolecules. In this report, the use of polymer pen lithography for the fabrication of DNA oligonucleotide arrays is described, together with the application of the arrays for the sensitive and selective detection of Ganoderma boninense, a fungal pathogen of the oil palm. When used in a sandwich assay format with DNA-conjugated gold nanoparticles, this system is able to generate a visually observable result in the presence of the target DNA. This assay is able to detect as little as 30 ng of Ganoderma-derived DNA without any pre-amplification and without the need for specialist laboratory equipment or training.
    Matched MeSH terms: DNA
  14. Development of the compact UV illuminator with single UV lamp
    Lee DJ, Kim SY, Kim JD, Kim YS, Song HJ, Park CY
    Sains Malaysiana, 2015;44:1693-1699.
    This paper presents a low-cost method of constructing the compact UV illuminator, which is considered as an important
    component of a gel documentation system. The procedure involves using a smallest-possible UV lamp and a motor which
    moves the UV lamp in the UV illuminator instead of conventional 4 UV lamps. A comparative analysis of images produced
    by using the commercial gel documentation system and our prototype was carried out. These comparisons were done
    in real DNA gel as well as a reference plate made of quantum dot. The plate was composed of the chambers filled with
    various densities of the quantum dot instead of the Agarose gel containing the ETBR in order to increase the accuracy of
    comparison and the convenience of experiments. Despite the use of only 1 UV lamp, the proposed system demonstrated
    a similar imaging performance compared with the conventional gel documentation system equipped with 4 UV lamps,
    resulting in the great reduction of the system cost.
    Matched MeSH terms: DNA
  15. Kesan psikostres terhadap kerosakan dna dan ketaknormalan titisan sitoplasma sperma manusia
    Norhamizan Hashim, Khairul Osman, Siti Fatimah Ibrahim, Rosliah Harun, Rafeah Pakri Mohamed
    Sains Malaysiana, 2016;45:1931-1938.
    Ketidaksuburan idiopati dalam kalangan lelaki telah dikaitkan dengan kesan psikostres. Walaupun begitu, hubungan langsung antara psikostres dan ketaknormalan kualiti semen masih samar. Maka, kajian ini dijalankan untuk menentukan kesan psikostres terhadap kualiti semen terutama kesan berdasarkan residu sitoplasma dan kerosakan DNA sperma. Dalam kajian ini, responden lelaki berumur antara 25-45 tahun dipilih secara rawak dalam kalangan pesakit yang mendapatkan rawatan di Pusat Kesuburan Lembaga Penduduk dan Pembangunan Keluarga Negara (LPPKN). Seramai 331 responden akhirnya telah dipilih daripada 628 responden selepas mengambil kira faktor penolakan. Setiap responden perlu menjawab borang keizinan dan soal selidik GHQ-12 bagi penentuan tahap stres sebelum pengambilan sampel semen mengikut piawaian WHO (2010). Tahap stres diukur berdasarkan keadaan semasa responden dalam tempoh 3-4 minggu sebelum kajian. Analisis semen, pewarnaan papanicolau dan asai komet neutral digunakan untuk penentuan kualiti semen dan kerosakan DNA sperma. Keputusan menunjukkan tidak terdapat hubungan yang signifikan antara psikostres dan ketaknormalan residu sitoplasma (U=895.50, p=0.08). Namun begitu, psikostres memberi kesan kepada peratus morfologi normal (U=6317.50, p<0.05) dan kerosakan DNA sperma (U=1047.00, p<0.01). Kesimpulannya, psikostres kronik boleh menjejaskan kualiti semen dan kerosakan DNA sperma serta mempengaruhi kesuburan.
    Matched MeSH terms: DNA
  16. Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from pome metagenome
    Farah Fadwa Benbelgacem, Oualid Abdelkader Bellag, Adibah Parman, Ibrahim Ali Noorbatcha, Mohd Noor Mat Isa, Muhammad Alfatih Muddathir Abdelrahim, et al.
    Sains Malaysiana, 2018;47:2951-2960.
    Metagenomic DNA library from palm oil mill effluent (POME) was constructed and subjected to high-throughput screening
    to find genes encoding cellulose- and xylan-degrading enzymes. DNA of 30 positive fosmid clones were sequenced with next
    generation sequencing technology and the raw data (short insert-paired) was analyzed with bioinformatic tools. First,
    the quality of 64,821,599 reverse and forward sequences of 101 bp length raw data was tested using Fastqc and SOLEXA.
    Then, raw data filtering was carried out by trimming low quality values and short reads and the vector sequences were
    removed and again the output was checked and the trimming was repeated until a high quality read sets was obtained.
    The second step was the de novo assembly of sequences to reconstruct 2900 contigs following de Bruijn graph algorithm.
    Pre-assembled contigs were arranged in order, the distances between contigs were identified and oriented with SSPACE,
    where 2139 scaffolds have been reconstructed. 16,386 genes have been identified after gene prediction using Prodigal
    and putative ID assignment with Blastp vs NR protein. The acceptable strategy to handle metagenomic NGS-data in order
    to detect known and potentially unknown genes is presented and we showed the computational efficiency of de Bruijn
    graph algorithm of de novo assembly to 21 bioprospect genes encoding cellulose-degrading enzymes and 6 genes
    encoding xylan-degrading enzymes of 30.3% to 100% identity percentage.
    Matched MeSH terms: DNA
  17. Fulltext Infectious hematopoietic necrosis virus: advances in diagnosis and vaccine development
    Yong CY, Ong HK, Tang HC, Yeap SK, Omar AR, Ho KL, et al.
    PeerJ, 2019;7:e7151.
    PMID: 31341728 DOI: 10.7717/peerj.7151
    The aquaculture of salmonid fishes is a multi-billion dollar industry with production over 3 million tons annually. However, infectious hematopoietic necrosis virus (IHNV), which infects and kills salmon and trout, significantly reduces the revenue of the salmon farming industry. Currently, there is no effective treatment for IHNV infected fishes; therefore, early detection and depopulation of the infected fishes remain the most common practices to contain the spread of IHNV. Apart from hygiene practices in aquaculture and isolation of infected fishes, loss of fishes due to IHNV infection can also be significantly reduced through vaccination programs. In the current review, some of the diagnostic methods for IHNV, spanning from clinical diagnosis to cell culture, serological and molecular methods are discussed in detail. In addition, some of the most significant candidate vaccines for IHNV are also extensively discussed, particularly the DNA vaccines.
    Matched MeSH terms: Vaccines, DNA
  18. Fulltext An Electrochemical DNA Biosensor for Carcinogenicity of Anticancer Compounds Based on Competition between Methylene Blue and Oligonucleotides
    Md Sani ND, Ariffin EY, Sheryn W, Shamsuddin MA, Heng LY, Latip J, et al.
    Sensors (Basel), 2019 Nov 22;19(23).
    PMID: 31766637 DOI: 10.3390/s19235111
    A toxicity electrochemical DNA biosensor has been constructed for the detection of carcinogens using 24 base guanine DNA rich single stranded DNA, and methylene blue (MB) as the electroactive indicator. This amine terminated ssDNA was immobilized onto silica nanospheres and deposited on gold nanoparticle modified carbon-paste screen printed electrodes (SPEs). The modified SPE was initially exposed to a carcinogen, followed by immersion in methylene blue for an optimized duration. The biosensor response was measured using differential pulse voltammetry. The performance of the biosensor was identified on several anti-cancer compounds. The toxicity DNA biosensor demonstrated a linear response range to the cadmium chloride from 0.0005 ppm to 0.01 ppm (R2 = 0.928) with a limit of detection at 0.0004 ppm. The biosensor also exhibited its versatility to screen the carcinogenicity of potential anti-cancer compounds.
    Matched MeSH terms: DNA/chemistry*; DNA, Single-Stranded/chemistry
  19. Fulltext Expediting the sampling, decalcification, and forensic DNA analysis of large elephant ivory seizures to aid investigations and prosecutions
    Ewart KM, Lightson AL, Sitam FT, Rovie-Ryan JJ, Mather N, McEwing R
    Forensic Sci Int Genet, 2020 01;44:102187.
    PMID: 31670244 DOI: 10.1016/j.fsigen.2019.102187
    The illegal ivory trade continues to drive elephant poaching. Large ivory seizures in Africa and Asia are still commonplace. Wildlife forensics is recognised as a key enforcement tool to combat this trade. However, the time and resources required to effectively test large ivory seizures is often prohibitive. This limits or delays testing, which may impede investigations and/or prosecutions. Typically, DNA analysis of an ivory seizure involves pairing and sorting the tusks, sampling the tusks, powdering the sample, decalcification, then DNA extraction. Here, we optimize the most time-consuming components of this process: sampling and decalcification. Firstly, using simulations, we demonstrate that tusks do not need to be paired to ensure an adequate number of unique elephants are sampled in a large seizure. Secondly, we determined that directly powdering the ivory using a Dremel drill with a high-speed cutter bit, instead of cutting the ivory with a circular saw and subsequently powdering the sample in liquid nitrogen with a freezer mill, produces comparable results. Finally, we optimized a rapid 2 -h decalcification protocol that produces comparable results to a standard 3-day protocol. We tested/optimised the protocols on 33 raw and worked ivory samples, and demonstrated their utility on a case study, successfully identifying 94% of samples taken from 123 tusks. Using these new rapid protocols, the entire sampling and DNA extraction process takes less than one day and requires less-expensive equipment. We expect that the implementation of these rapid protocols will promote more consistent and timely testing of ivory seizures suitable for enforcement action.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA Fingerprinting*
  20. Rapid detection of porcine DNA in processed food samples using a streamlined DNA extraction method combined with the SYBR Green real-time PCR assay
    Tan LL, Ahmed SA, Ng SK, Citartan M, Raabe CA, Rozhdestvensky TS, et al.
    Food Chem, 2020 Mar 30;309:125654.
    PMID: 31678669 DOI: 10.1016/j.foodchem.2019.125654
    A specialized DNA extraction method and a SYBR Green quantitative polymerase chain reaction (SyG-qPCR) assay were combined to generate a ready-to-use kit for rapid detection of porcine admixtures in processed meat products. Our qPCR assay utilized repetitive LINE-1 elements specific to the genome of Sus scrofa domesticus (pig) as a target and incorporated internal controls. We improved the genomic DNA extraction method, and reduced extraction times to the minimum. The method was validated for specificity, sensitivity (0.001% w/w) and robustness, and values were compared with those of a commercially available kit. We also tested our method using 121 processed food products and consistently detected amplification only in samples containing pork. Due to its efficiency and cost-effectiveness, our method represents a valuable new method for detecting food adulteration with pork that is superior to existing quality control approaches.
    Matched MeSH terms: DNA/analysis*; DNA/isolation & purification; DNA/standards
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