Displaying publications 641 - 660 of 3445 in total

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  1. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
    Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM
    Mol Ecol, 2020 10;29(20):3970-3987.
    PMID: 32808335 DOI: 10.1111/mec.15603
    Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  2. Comparison of several lizard Leishmania species and strains in terms of kinetoplast minicircle and maxicircle DNA sequences, nuclear chromosomes, and membrane lipids
    Gomez-Eichelmann MC, Holz G, Beach D, Simpson AM, Simpson L
    Mol Biochem Parasitol, 1988 Jan 15;27(2-3):143-58.
    PMID: 3344003
    Eight strains of a lizard Leishmania species, L. tarentolae, were compared with four other saurian species [L. hoogstrali, L. adleri, L. agamae and Leishmania sp. LizS], with L. major from man and with Trypanosoma platydactyli, a putative lizard trypanosome, in terms of kinetoplast DNA minicircle and maxicircle sequences and in terms of nuclear chromosome patterns on orthogonal gel electrophoresis. The L. tarentolae strains fell into two major groups, one (group A) consisting of the L. tarentolae strains, UC, Krassner and Trager, derived from an Algerian gecko isolate and the other (group B) consisting of five L. tarentolae LEM strains isolated from geckos in southern France. T. platydactyli TPCL2, which was postulated by Wallbanks et al. to represent the lizard form of a French L. tarentolae strain, was closely related to the UC strain and not to the LEM strains, in all respects analyzed. Leishmania sp. LizS from a Mongolian gecko and L. hoogstrali from a Sudanese gecko showed some sequence similarities to the L. tarentolae strains, but the leishmanias said to be L. adleri from a Kenyan lacertid and L. agamae from an Israeli agamid showed no minicircle sequence similarities with lizard Leishmania and in fact were probably the same species. The maxicircle divergent region was larger in the group B strains than in the group A strains, but there were sequences in common with both groups, and not with L. hoogstrali and L. major. Four strains of L. tarentolae, the four other supposed saurian Leishmania species, three mammalian leishmanias, T. platydactyli and four other trypanosomes, T. cyclops (Malaysian macaque), T. conorrhini (Hawaiian reduviid bug), T. cruzi (man) and T. lewisi (feral rat) were analyzed for their contents of sterols and phosphoglyceride fatty acyl groups. T. platydactyli TPCL2 contained a sterol (5-dehydroepisterol), a phosphatidylcholine fatty acyl group (alpha-linolenic acid) and a phosphatidylethanolamine fatty acyl group (dihydrosterculic acid) characteristic of members of the genus Leishmania and not the genus Trypanosoma. The proportions of those lipids in the free sterol and phosphoglyceride fractions of T. platydactyli TPCL2 most closely resembled those seen in the Leishmania strains from Algerian, French, Mongolian and Sudanese geckos.
    Matched MeSH terms: DNA, Circular/analysis
  3. Fulltext Sequencing and Annotated of Goat's Milk using Bioinformatics Tool: ClustalX
    Muhammad Najmi Mohammad Fauzi, Aisyah Aqilah Abu Bakar, Liyana Amalina Adnan, Tg Ainul Farha Tg Abdul Rahman, A’wani Aziz Nurdalila
    Malaysian Journal of Science, Health & Technology, 2021;7(1):28-33.
    MyJurnal
    Bioinformatics tool is a software program made to extract meaningful information from the mass of molecular biology or biological databases and carry out sequence or structural analysis. The method of determining the order of nucleotides within a deoxyribonucleic acid (DNA) molecule is known as DNA sequencing. This analysis is meant to be run to the commercialized or factorymade goat's milk (pasteurised) from various states in Malaysia to identify the milk's authenticity, either it is pure or mixed with other foreign substances from other animals. The main objective is to compare DNA sequences of commercialized and raw goat's milk (handmilking and non-pasteurised). To achieve this, we used ClustalX to align and compare the obtained DNA from both milk samples. The sequences will be aligned using ClustalX software. ClustalX is a provider of an automated system for performing multiple alignments of sequences and profiles and evaluating the outcomes. The usage of ClustalX is helpful as it is cost-effective, user-friendly, and showing a high accuracy of the analysis.

    Matched MeSH terms: DNA; Sequence Analysis, DNA
  4. Ant-termite interactions: an important but under-explored ecological linkage
    Tuma J, Eggleton P, Fayle TM
    Biol Rev Camb Philos Soc, 2020 06;95(3):555-572.
    PMID: 31876057 DOI: 10.1111/brv.12577
    Animal interactions play an important role in understanding ecological processes. The nature and intensity of these interactions can shape the impacts of organisms on their environment. Because ants and termites, with their high biomass and range of ecological functions, have considerable effects on their environment, the interaction between them is important for ecosystem processes. Although the manner in which ants and termites interact is becoming increasingly well studied, there has been no synthesis to date of the available literature. Here we review and synthesise all existing literature on ant-termite interactions. We infer that ant predation on termites is the most important, most widespread, and most studied type of interaction. Predatory ant species can regulate termite populations and subsequently slow down the decomposition of wood, litter and soil organic matter. As a consequence they also affect plant growth and distribution, nutrient cycling and nutrient availability. Although some ant species are specialised termite predators, there is probably a high level of opportunistic predation by generalist ant species, and hence their impact on ecosystem processes that termites are known to provide varies at the species level. The most fruitful future research direction will be to evaluate the impact of ant-termite predation on broader ecosystem processes. To do this it will be necessary to quantify the efficacy both of particular ant species and of ant communities as a whole in regulating termite populations in different biomes. We envisage that this work will require a combination of methods, including DNA barcoding of ant gut contents along with field observations and exclusion experiments. Such a combined approach is necessary for assessing how this interaction influences entire ecosystems.
    Matched MeSH terms: DNA/analysis
  5. Fulltext Sex Chromosome Turnover in Bent-Toed Geckos (Cyrtodactylus)
    Keating SE, Blumer M, Grismer LL, Lin A, Nielsen SV, Thura MK, et al.
    Genes (Basel), 2021 01 19;12(1).
    PMID: 33477871 DOI: 10.3390/genes12010116
    Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed geckos. We uncovered XX/XY sex chromosomes in Cyrtodactylus chaunghanakwaensis and ZZ/ZW sex chromosomes in Cyrtodactylus pharbaungensis. This is the third instance of intrageneric turnover of sex chromosomes in geckos. Additionally, Cyrtodactylus are closely related to another genus with intrageneric turnover, Hemidactylus. Together, these data suggest that sex chromosome turnover may be common in this clade, setting them apart as exceptionally diverse in a group already known for diverse sex determination systems.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  6. Fulltext Mitochondrial Respiration Is Reduced in Atherosclerosis, Promoting Necrotic Core Formation and Reducing Relative Fibrous Cap Thickness
    Yu EPK, Reinhold J, Yu H, Starks L, Uryga AK, Foote K, et al.
    Arterioscler Thromb Vasc Biol, 2017 12;37(12):2322-2332.
    PMID: 28970293 DOI: 10.1161/ATVBAHA.117.310042
    OBJECTIVE: Mitochondrial DNA (mtDNA) damage is present in murine and human atherosclerotic plaques. However, whether endogenous levels of mtDNA damage are sufficient to cause mitochondrial dysfunction and whether decreasing mtDNA damage and improving mitochondrial respiration affects plaque burden or composition are unclear. We examined mitochondrial respiration in human atherosclerotic plaques and whether augmenting mitochondrial respiration affects atherogenesis.

    APPROACH AND RESULTS: Human atherosclerotic plaques showed marked mitochondrial dysfunction, manifested as reduced mtDNA copy number and oxygen consumption rate in fibrous cap and core regions. Vascular smooth muscle cells derived from plaques showed impaired mitochondrial respiration, reduced complex I expression, and increased mitophagy, which was induced by oxidized low-density lipoprotein. Apolipoprotein E-deficient (ApoE-/-) mice showed decreased mtDNA integrity and mitochondrial respiration, associated with increased mitochondrial reactive oxygen species. To determine whether alleviating mtDNA damage and increasing mitochondrial respiration affects atherogenesis, we studied ApoE-/- mice overexpressing the mitochondrial helicase Twinkle (Tw+/ApoE-/-). Tw+/ApoE-/- mice showed increased mtDNA integrity, copy number, respiratory complex abundance, and respiration. Tw+/ApoE-/- mice had decreased necrotic core and increased fibrous cap areas, and Tw+/ApoE-/- bone marrow transplantation also reduced core areas. Twinkle increased vascular smooth muscle cell mtDNA integrity and respiration. Twinkle also promoted vascular smooth muscle cell proliferation and protected both vascular smooth muscle cells and macrophages from oxidative stress-induced apoptosis.

    CONCLUSIONS: Endogenous mtDNA damage in mouse and human atherosclerosis is associated with significantly reduced mitochondrial respiration. Reducing mtDNA damage and increasing mitochondrial respiration decrease necrotic core and increase fibrous cap areas independently of changes in reactive oxygen species and may be a promising therapeutic strategy in atherosclerosis.

    Matched MeSH terms: DNA Damage*; DNA Helicases/genetics; DNA Helicases/metabolism; DNA, Mitochondrial/genetics; DNA, Mitochondrial/metabolism*
  7. Molecular differentiation and antifungal susceptibilities of Candida parapsilosis isolated from patients with bloodstream infections
    Tay ST, Na SL, Chong J
    J Med Microbiol, 2009 Feb;58(Pt 2):185-191.
    PMID: 19141735 DOI: 10.1099/jmm.0.004242-0
    The genetic heterogeneity and antifungal susceptibility patterns of Candida parapsilosis isolated from blood cultures of patients were investigated in this study. Randomly amplified polymorphic DNA (RAPD) analysis generated 5 unique profiles from 42 isolates. Based on the major DNA fragments of the RAPD profiles, the isolates were identified as RAPD type P1 (29 isolates), P2 (6 isolates), P3 (4 isolates), P4 (2 isolates) and P5 (1 isolate). Sequence analysis of the internal transcribed spacer (ITS) gene of the isolates identified RAPD type P1 as C. parapsilosis, P2 and P3 as Candida orthopsilosis, P4 as Candida metapsilosis, and P5 as Lodderomyces elongisporus. Nucleotide variations in ITS gene sequences of C. orthopsilosis and C. metapsilosis were detected. Antifungal susceptibility testing using Etests showed that all isolates tested in this study were susceptible to amphotericin B, fluconazole, ketoconazole, itraconazole and voriconazole. C. parapsilosis isolates exhibited higher MIC(50) values than those of C. orthopsilosis for all of the drugs tested in this study; however, no significant difference in the MICs for these two Candida species was observed. The fact that C. orthopsilosis and C. metapsilosis were responsible for 23.8 and 4.8 % of the cases attributed to C. parapsilosis bloodstream infections, respectively, indicates the clinical relevance of these newly described yeasts. Further investigations of the ecological niche, mode of transmission and virulence of these species are thus essential.
    Matched MeSH terms: DNA, Fungal/genetics; DNA Fingerprinting; Sequence Analysis, DNA; Random Amplified Polymorphic DNA Technique; DNA, Intergenic/genetics; DNA, Intergenic/chemistry
  8. Developing critical thinking in STEM education through inquiry-based writing in the laboratory classroom
    Jeon AJ, Kellogg D, Khan MA, Tucker-Kellogg G
    Biochem Mol Biol Educ, 2021 01;49(1):140-150.
    PMID: 32746505 DOI: 10.1002/bmb.21414
    Laboratory pedagogy is moving away from step-by-step instructions and toward inquiry-based learning, but only now developing methods for integrating inquiry-based writing (IBW) practices into the laboratory course. Based on an earlier proposal (Science 2011;332:919), we designed and implemented an IBW sequence in a university bioinformatics course. We automatically generated unique, double-blinded, biologically plausible DNA sequences for each student. After guided instruction, students investigated sequences independently and responded through IBW writing assignments. IBW assignments were structured as condensed versions of a scientific research article, and because the sequences were double blinded, they were also assessed as authentic science and evaluated on clarity and persuasiveness. We piloted the approach in a seven-day workshop (35 students) at Perdana University in Malaysia. We observed dramatically improved student engagement and indirect evidence of improved learning outcomes over a similar workshop without IBW. Based on student feedback, initial discomfort with the writing component abated in favor of an overall positive response and increasing comfort with the high demands of student writing. Similarly, encouraging results were found in a semester length undergraduate module at the National University of Singapore (155 students).
    Matched MeSH terms: DNA/genetics
  9. Fulltext A new record of Iranihindia martellata (Senior-White,1924) (Diptera: Sarcophagidae) from peninsular Malaysia and female identification using both morphology and DNA-based approaches
    Tan SH, Mohd Aris E, Kurahashi H, Mohamed Z
    Trop Biomed, 2010 Aug;27(2):287-93.
    PMID: 20962727
    Iranihindia martellata (Senior-White, 1924) is recorded from peninsular Malaysia for the first time. Male and female specimens in the recent collections of forensically important sarcophagid flies were examined and identified based on morphology and DNA sequencing analysis. Male genitalia offer unambiguous species identification characteristics in the traditional taxonomy of flesh flies but the female flies are very similar to one another in general morphology. Female of I. martellata was determined by DNA sequencing (COI and COII) and PCR-RFLP (COI) analysis. Identified females were carefully examined and compared with the morphologically similar species, Liopygia ruficornis (Fabricius, 1794). Female genitalia are re-described and illustrated in this paper.
    Matched MeSH terms: DNA/genetics*
  10. Fulltext DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells
    Mohamed Sa'dom SAF, Raikundalia S, Shamsuddin S, See Too WC, Few LL
    Genes (Basel), 2021 06 01;12(6).
    PMID: 34205960 DOI: 10.3390/genes12060853
    Choline kinase (CK) is the enzyme catalyzing the first reaction in CDP-choline pathway for the biosynthesis of phosphatidylcholine. Higher expression of the α isozyme of CK has been implicated in carcinogenesis, and inhibition or downregulation of CKα (CHKA) is a promising anticancer approach. This study aimed to investigate the regulation of CKα expression by DNA methylation of the CpG islands found on the promoter of this gene in MCF-7 cells. Four CpG islands have been predicted in the 2000 bp promoter region of ckα (chka) gene. Six CpG island deletion mutants were constructed using PCR site-directed mutagenesis method and cloned into pGL4.10 vectors for promoter activity assays. Deletion of CpG4C region located between -225 and -56 significantly increased the promoter activity by 4-fold, indicating the presence of important repressive transcription factor binding site. The promoter activity of methylated full-length promoter was significantly lower than the methylated CpG4C deletion mutant by 16-fold. The results show that DNA methylation of CpG4C promotes the binding of the transcription factor that suppresses the promoter activity. Electrophoretic mobility shift assay analysis showed that cytosine methylation at MZF1 binding site in CpG4C increased the binding of putative MZF1 in nuclear extract. In conclusion, the results suggest that DNA methylation decreased the promoter activity by promoting the binding of putative MZF1 transcription factor at CpG4C region of the ckα gene promoter.
    Matched MeSH terms: DNA Methylation*
  11. Therapeutic applications of transdermal microneedles
    Kumar Singla S, Muthuraman A, Sahai D, Mangal N, Dhamodharan J
    Front Biosci (Elite Ed), 2021 01 01;13:158-184.
    PMID: 33048780
    Transdermal drug-delivery systems (TDDS) offer an attractive alternative to the oral route for delivery of biotherapeutics. Technological advancements in the past few decades have revolutionized the fabrication of micro-structured devices including creation of microneedles (MC). These devices are used for delivering peptides, macromolecules such as proteins and DNA, and other therapeutics through the skin. Here, we review the current use of MCs as a cost effective method for the self-administration of therapeutics. We will then review the current and common use of MCs as an effective treatment strategy for a broad range of diseases and their utility in the generation of effective vaccination delivery platforms. Finally, we will summarize the currently FDA approved MCs and their applications, along with the ongoing clinical trials that use such devices.
    Matched MeSH terms: DNA/administration & dosage
  12. 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
  13. Fulltext Assessment of DNA strand breakage in streptozotocin-induced diabetic rats
    Siti Balkis Budin, Norfadilah Rejab, Abdul Gapor Mohd Top, Wan Nazaimoon Wan Mohamud, Mokhtar Abu Bakar, Khairul Osman, et al.
    Jurnal Sains Kesihatan Malaysia, 2005;3(1):2-12.
    MyJurnal
    This study was conducted to evaluate the oxidative damage in diabetic mellitus induced rats. The evaluation of DNA damage was carried out by the Alkaline Comet Assay using peripheral lymphocyte cells taken from streptozotocin-induced diabetic rats (50 mg/kg) and control rats. The levels of malondealdehyde (MDA), 4-hydroxynonenal (4-HNE), fasting blood glucose (FBG) and HbA1c were also measured. All the induced diabetic rats were hyperglycemic until the end of the study with significantly higher levels of FBG and HbA1c as compared to the control rats. The results showed the percentage of tail DNA and tail moment values were also significantly higher in the diabetic induced rats. The same observations were made on the levels of plasma MDA and 4-HNE. In conclusion, this study indicated that hyperglycemic condition in diabetic induced rats could generate oxidative DNA damage.
    Matched MeSH terms: DNA; DNA Damage
  14. Fulltext Development of a SYBR green based real-time polymerase chain reaction assay for specific detection and quantification of Vibrio parahaemolyticus from food and environmental samples
    Micky, V., Nur Quraitu’ Aini, T., Velnetti, L., Patricia Rowena, M.B., Christy, C., Lesley Maurice, B.
    International Food Research Journal, 2014;21(3):921-927.
    MyJurnal
    Vibrio parahaemolyticus is a foodborne pathogen and their human infection is regularly associated with the consumption of raw or undercooked seafood and contaminated water supplies. Many conventional biochemical identification and confirmation procedures are performed to detect the presence of this pathogen, both from seafood or environmental samples. However, these procedures not only require two or more days to complete, they do not have the capabilities to determine the number of V. parahaemolyticus cells in any given samples. Thus, in this study we describe the development of a rapid SYBR green based real-time PCR assay, targeting the thermo labile (tl) gene of V. parahaemolyticus for the detection and enumeration of this bacterium from seafood and environmental samples. We report that the real-time PCR assay and the primers designed are highly specific, and only generated the desired amplicons with V. parahaemolyticus DNA samples against other bacteria and fungi species. Our assay is also highly sensitive, and, is able to detect V. parahaemolyticus with high coefficient values in concentrations as low as 1.0 pg/μl DNA for pure genomic DNA solutions and 10 cells/ml in serially diluted cell suspension and spiked samples. This assay can be completed in less than 3 hours and may be used as a tool for rapid determination of V. parahaemolyticus densities in the food industries, environmental risk assessment and for clinical diagnostics purposes.
    Matched MeSH terms: DNA; DNA Primers
  15. Fulltext Biosafety of Vibrio parahaemolyticus from vegetables based on antimicrobial sensitivity and RAPD profiling
    Tunung, R., Jeyaletchumi, P., Noorlis, A., Tang, Y.H., Sandra, A., Ghazali, F.M., et al.
    International Food Research Journal, 2012;19(2):467-474.
    MyJurnal
    This study was undertaken to characterize the antibiotic resistance and randomly amplified polymorphic DNA (RAPD) profiles of Vibrio parahaemolyticus isolates from raw vegetable samples. A total of 46 isolates of V. parahaemolyticus recovered from raw vegetables samples and were confirmed by PCR were analyzed in this study. Most of the isolates were resistant to nalidixic acid (93.48%) and were the least resistant towards imipinem (4.35%). The MAR index results also demonstrated high individual and multiple resistances to antibiotics among the isolates. From the RAPD analysis, the size for RAPD fragments generated ranged from 250 bp to 1,500 bp, with most of the strains contained three major gene fragments of 350, 1,000 and 1,350 bp. The RAPD profiles revealed a high level of DNA sequence diversity within the isolates. Antibiotic resistance and RAPD proved to be effective tools in characterizing and differentiating the V. parahaemolyticus strains.
    Matched MeSH terms: DNA; Random Amplified Polymorphic DNA Technique
  16. 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
  17. 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
  18. Fulltext Technical aspects in understanding effects of gamma irradiation on flower colour changes in Dendrobium Sonia
    Sakinah Ariffin, Azhar Mohamad, Ratnam, Wickneswari
    Jurnal Sains Nuklear Malaysia, 2012;24(1):91-101.
    MyJurnal
    Colour is one of the most important traits in orchids and has created great interest in breeding programmes. Gamma irradiation is an alternative way for generation of somaclonal variation for new flower colours. Phenotypic changes are usually observed during screening and selection of mutants. Understanding of targeted gene expression level and evaluation of the changes facilitate in the development of functional markers for selection of desired flower colour mutants. Four Dendrobium orchid sequences (NCBI accessions: AM490639, AY41319, FM209429 and DQ462460) were selected to design gene specific primers based on information for chalcone synthase (CHS) from NCBI database. Quantitative real-time PCR (qPCR) was used to understand flower colour expression quantitatively derived from the CHS gene activities in different flower tissues (petal and sepal) from control Dendrobium Sonia (red purple), mutant DS 35-1/M (purple pink) and mutant DS 35-WhiteA. It was found that expression of CHS gene was highest in sepals of white flowers and lowest in both sepals and petals of purple pink flowers. Genomic DNA was amplified and PCR products were sequenced, aligned and compared. Sequence variations of CHS partial gene in Dendrobium Sonia mutants with different flower colour showed that two protein positions have been changed as compared to the control. These non-synonymous mutations may have contributed to the colour alterations in the white and purple pink mutants. This paper describes important procedures to quantify gene expression such as RNA isolation (quantity and quality), cDNA synthesis and primer design steps for CHS genes.
    Matched MeSH terms: DNA Primers; DNA, Complementary
  19. 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
  20. Fulltext Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing
    Aziz SA, Clements GR, Peng LY, Campos-Arceiz A, McConkey KR, Forget PM, et al.
    PeerJ, 2017;5:e3176.
    PMID: 28413729 DOI: 10.7717/peerj.3176
    There is an urgent need to identify and understand the ecosystem services of pollination and seed dispersal provided by threatened mammals such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of bats presents a particularly challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through DNA metabarcoding of plants in flying fox droppings, using primers targeting the rbcL gene, we identified at least 29 Operationally Taxonomic Units (OTUs) comprising the diet of this giant pteropodid. OTU sequences matched at least four genera and 14 plant families from online reference databases based on a conservative Least Common Ancestor approach, and eight species from our site-specific plant reference collection. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox's diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. At this point in time, more accurate genus- and species-level identification of OTUs not only requires support from databases with more representative sequences of relevant plant DNA, but probably necessitates in situ collection of plant specimens to create a reference collection. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa and spatio-temporal patterns in flying fox diets.
    Matched MeSH terms: DNA Primers; DNA, Plant
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