Displaying publications 61 - 80 of 3426 in total

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  1. Fulltext Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family
    Wang H, Zheng K, Wang M, Ma K, Ren L, Guo R, et al.
    Microbiol Spectr, 2024 Feb 06;12(2):e0336723.
    PMID: 38214523 DOI: 10.1128/spectrum.03367-23
    Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.
    Matched MeSH terms: DNA, Viral/genetics; Sequence Analysis, DNA
  2. Fulltext Ancient proteins resolve controversy over the identity of Genyornis eggshell
    Demarchi B, Stiller J, Grealy A, Mackie M, Deng Y, Gilbert T, et al.
    Proc Natl Acad Sci U S A, 2022 Oct 25;119(43):e2109326119.
    PMID: 35609205 DOI: 10.1073/pnas.2109326119
    The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.
    Matched MeSH terms: DNA/genetics; DNA, Ancient
  3. Fulltext Design pattern mining using distributed learning automata and DNA sequence alignment
    Esmaeilpour M, Naderifar V, Shukur Z
    PLoS One, 2014;9(9):e106313.
    PMID: 25243670 DOI: 10.1371/journal.pone.0106313
    Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem.
    Matched MeSH terms: DNA*; Sequence Analysis, DNA/methods*
  4. A nucleotide signature for identification of Aglaia stellatopilosa Pannell
    Ng BL, Omarzuki M, Lau GS, Pannell CM, Yeo TC
    Mol Biotechnol, 2014 Jul;56(7):671-9.
    PMID: 24623047 DOI: 10.1007/s12033-014-9746-0
    Members of the genus Aglaia have been reported to contain bioactive phytochemicals. The genus, belonging to the Meliaceae family, is represented by at least 120 known species of woody trees or shrubs in the tropical rain forest. As some of these species are very similar in their morphology, taxonomic identification can be difficult. A reliable and definitive molecular method which can identify Aglaia to the level of the species will hence be useful in comparing the content of specific bioactive compounds between the species of this genus. Here, we report the analysis of DNA sequences in the internal transcribed spacer (ITS) of the nuclear ribosomal DNA and the observation of a unique nucleotide signature in the ITS that can be used for the identification of Aglaia stellatopilosa. The nucleotide signature consists of nine bases over the length of the ITS sequence (654 bp). This uniqueness was validated in 37 samples identified as Aglaia stellatopilosa by an expert taxonomist, whereas the nucleotide signature was lacking in a selection of other Aglaia species and non-Aglaia genera. This finding suggests that molecular typing could be utilized in the identification of Aglaia stellatopilosa.
    Matched MeSH terms: DNA, Ribosomal/genetics*; DNA, Ribosomal Spacer/genetics*
  5. The mitogenome of Pangasius sutchi (Teleostei, Siluriformes: Pangasiidae)
    Zhao H, Kong X, Zhou C
    Mitochondrial DNA, 2014 Oct;25(5):342-4.
    PMID: 23795847 DOI: 10.3109/19401736.2013.800492
    The Pangasius sutchi is an important ornamental and economic fish in Southeast Asia e.g. Thailand, Malaysia and China. The complete mitochondrial genome sequence of P. sutchi has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a non-coding control region with the total length of 16,522 bp. The gene order and composition are similar to most of other vertebrates. Just like most other vertebrates, the bias of G and C was found in different region/genes statistics results. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of P. sutchi would contribute to better understand population genetics, evolution of this lineage.
    Matched MeSH terms: DNA, Mitochondrial/analysis; Sequence Analysis, DNA/methods*
  6. Construction of cDNA library and preliminary analysis of expressed sequence tags from green microalga Ankistrodesmus convolutus Corda
    Thanh T, Chi VT, Abdullah MP, Omar H, Noroozi M, Ky H, et al.
    Mol Biol Rep, 2011 Jan;38(1):177-82.
    PMID: 20354903 DOI: 10.1007/s11033-010-0092-4
    Green microalga Ankistrodesmus convolutus Corda is a fast growing alga which produces appreciable amount of carotenoids and polyunsaturated fatty acids. To our knowledge, this is the first report on the construction of cDNA library and preliminary analysis of ESTs for this species. The titers of the primary and amplified cDNA libraries were 1.1×10(6) and 6.0×10(9) pfu/ml respectively. The percentage of recombinants was 97% in the primary library and a total of 337 out of 415 original cDNA clones selected randomly contained inserts ranging from 600 to 1,500 bps. A total of 201 individual ESTs with sizes ranging from 390 to 1,038 bps were then analyzed and the BLASTX score revealed that 35.8% of the sequences were classified as strong match, 38.3% as nominal and 25.9% as weak match. Among the ESTs with known putative function, 21.4% of them were found to be related to gene expression, 14.4% ESTs to photosynthesis, 10.9% ESTs to metabolism, 5.5% ESTs to miscellaneous, 2.0% to stress response, and the remaining 45.8% were classified as novel genes. Analysis of ESTs described in this paper can be an effective approach to isolate and characterize new genes from A. convolutus and thus the sequences obtained represented a significant contribution to the extensive database of sequences from green microalgae.
    Matched MeSH terms: Sequence Analysis, DNA/methods*; DNA, Complementary/genetics
  7. Durianella, a new gasteroid genus of boletes from Malaysia
    Desjardin DE, Wilson AW, Binder M
    Mycologia, 2009 2 11;100(6):956-61.
    PMID: 19202849
    Hydnangium echinulatum, described originally from a single specimen collected in Malaysia, has been recollected, and based on morphological and molecular characters is recognized as representing a new gasteroid genus of boletes with affinities to the Boletineae, herein named Durianella. Diagnostic features include an epigeous, ovoid, pyramidal-warted, durian fruit-like basidiome with gelatinized glebal locules and a columella that turns indigo blue upon exposure, and subglobose basidiospores with long, curved, thin-walled and collapsible spines. A redescription, phylogenetic analysis and comparison with allied taxa are presented.
    Matched MeSH terms: DNA, Fungal/genetics; DNA, Ribosomal/genetics
  8. Fulltext Molecular epidemiology and phylogenetic analysis of Dengue virus type-1 and 2 isolated in Malaysia
    Chew MH, Rahman MM, Hussin S
    Pak J Med Sci, 2015;31(3):615-20.
    PMID: 26150855 DOI: 10.12669/pjms.313.6340
    Detection of different serotypes of dengue virus and provide information on origin, distribution and genotype of the virus.
    Matched MeSH terms: DNA Viruses
  9. Fulltext Limitations of cytochrome oxidase I for the barcoding of Neritidae (Mollusca: Gastropoda) as revealed by Bayesian analysis
    Chee SY
    Genet. Mol. Res., 2015;14(2):5677-84.
    PMID: 26125766 DOI: 10.4238/2015.May.25.20
    The mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) gene has been universally and successfully utilized as a barcoding gene, mainly because it can be amplified easily, applied across a wide range of taxa, and results can be obtained cheaply and quickly. However, in rare cases, the gene can fail to distinguish between species, particularly when exposed to highly sensitive methods of data analysis, such as the Bayesian method, or when taxa have undergone introgressive hybridization, over-splitting, or incomplete lineage sorting. Such cases require the use of alternative markers, and nuclear DNA markers are commonly used. In this study, a dendrogram produced by Bayesian analysis of an mtDNA COI dataset was compared with that of a nuclear DNA ATPS-α dataset, in order to evaluate the efficiency of COI in barcoding Malaysian nerites (Neritidae). In the COI dendrogram, most of the species were in individual clusters, except for two species: Nerita chamaeleon and N. histrio. These two species were placed in the same subcluster, whereas in the ATPS-α dendrogram they were in their own subclusters. Analysis of the ATPS-α gene also placed the two genera of nerites (Nerita and Neritina) in separate clusters, whereas COI gene analysis placed both genera in the same cluster. Therefore, in the case of the Neritidae, the ATPS-α gene is a better barcoding gene than the COI gene.
    Matched MeSH terms: DNA, Mitochondrial/genetics*; DNA Barcoding, Taxonomic*
  10. Fulltext Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria
    Loong SK, Khor CS, Jafar FL, AbuBakar S
    J Clin Lab Anal, 2016 Nov;30(6):1056-1060.
    PMID: 27184222 DOI: 10.1002/jcla.21980
    BACKGROUND: Phenotypic identification systems are established methods for laboratory identification of bacteria causing human infections. Here, the utility of phenotypic identification systems was compared against 16S rDNA identification method on clinical isolates obtained during a 5-year study period, with special emphasis on isolates that gave unsatisfactory identification.

    METHODS: One hundred and eighty-seven clinical bacteria isolates were tested with commercial phenotypic identification systems and 16S rDNA sequencing. Isolate identities determined using phenotypic identification systems and 16S rDNA sequencing were compared for similarity at genus and species level, with 16S rDNA sequencing as the reference method.

    RESULTS: Phenotypic identification systems identified ~46% (86/187) of the isolates with identity similar to that identified using 16S rDNA sequencing. Approximately 39% (73/187) and ~15% (28/187) of the isolates showed different genus identity and could not be identified using the phenotypic identification systems, respectively. Both methods succeeded in determining the species identities of 55 isolates; however, only ~69% (38/55) of the isolates matched at species level. 16S rDNA sequencing could not determine the species of ~20% (37/187) of the isolates.

    CONCLUSION: The 16S rDNA sequencing is a useful method over the phenotypic identification systems for the identification of rare and difficult to identify bacteria species. The 16S rDNA sequencing method, however, does have limitation for species-level identification of some bacteria highlighting the need for better bacterial pathogen identification tools.

    Matched MeSH terms: DNA, Bacterial/genetics*; DNA, Ribosomal/genetics*
  11. Fulltext Escaping introns in COI through cDNA barcoding of mushrooms: Pleurotus as a test case
    Avin FA, Subha B, Tan YS, Braukmann TWA, Vikineswary S, Hebert PDN
    Ecol Evol, 2017 09;7(17):6972-6980.
    PMID: 28904776 DOI: 10.1002/ece3.3049
    DNA barcoding involves the use of one or more short, standardized DNA fragments for the rapid identification of species. A 648-bp segment near the 5' terminus of the mitochondrial cytochrome c oxidase subunit I (COI) gene has been adopted as the universal DNA barcode for members of the animal kingdom, but its utility in mushrooms is complicated by the frequent occurrence of large introns. As a consequence, ITS has been adopted as the standard DNA barcode marker for mushrooms despite several shortcomings. This study employed newly designed primers coupled with cDNA analysis to examine COI sequence diversity in six species of Pleurotus and compared these results with those for ITS. The ability of the COI gene to discriminate six species of Pleurotus, the commonly cultivated oyster mushroom, was examined by analysis of cDNA. The amplification success, sequence variation within and among species, and the ability to design effective primers was tested. We compared ITS sequences to their COI cDNA counterparts for all isolates. ITS discriminated between all six species, but some sequence results were uninterpretable, because of length variation among ITS copies. By comparison, a complete COI sequences were recovered from all but three individuals of Pleurotus giganteus where only the 5' region was obtained. The COI sequences permitted the resolution of all species when partial data was excluded for P. giganteus. Our results suggest that COI can be a useful barcode marker for mushrooms when cDNA analysis is adopted, permitting identifications in cases where ITS cannot be recovered or where it offers higher resolution when fresh tissue is. The suitability of this approach remains to be confirmed for other mushrooms.
    Matched MeSH terms: DNA; DNA Primers; DNA, Complementary; DNA Barcoding, Taxonomic
  12. Fulltext Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)
    Heckenhauer J, Abu Salim K, Chase MW, Dexter KG, Pennington RT, Tan S, et al.
    PLoS One, 2017;12(10):e0185861.
    PMID: 29049301 DOI: 10.1371/journal.pone.0185861
    DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.
    Matched MeSH terms: DNA, Plant/genetics*; DNA Barcoding, Taxonomic/methods*
  13. Molecular dynamics simulations suggest changes in electrostatic interactions as a potential mechanism through which serine phosphorylation inhibits DNA Polymerase β's activity
    Homouz D, Joyce-Tan KH, Shahir Shamsir M, Moustafa IM, Idriss H
    J Mol Graph Model, 2018 01;79:192.
    PMID: 29223917 DOI: 10.1016/j.jmgm.2017.11.002
    DNA polymerase β is a 39kDa enzyme that is a major component of Base Excision Repair in human cells. The enzyme comprises two major domains, a 31kDa domain responsible for the polymerase activity and an 8kDa domain, which bind ssDNA and has a deoxyribose phosphate (dRP) lyase activity. DNA polymerase β was shown to be phosphorylated in vitro with protein kinase C (PKC) at serines 44 and 55 (S44 and S55), resulting in loss of its polymerase enzymic activity, but not its ability to bind ssDNA. In this study, we investigate the potential phosphorylation-induced structural changes for DNA polymerase β using molecular dynamics. The simulations show drastic conformational changes of the polymerase structure as a result of S44 phosphorylation. Phosphorylation-induced conformational changes transform the closed (active) enzyme structure into an open one. Further analysis of the results points to a key hydrogen bond and newly formed salt bridges as potential drivers of these structural fluctuations. The changes observed with S44/55 and S55 phosphorylation were less dramatic than S44 and the integrity of the H-bond was not compromised. Thus the phosphorylation of S44 is likely the major contributor to structural fluctuations that lead to loss of enzymatic activity.
    Matched MeSH terms: DNA Repair; DNA Replication; DNA, Single-Stranded; DNA Polymerase beta
  14. Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration
    Lim LWK, Kamar CKA, Roja JS, Chung HH, Liao Y, Lam TT, et al.
    Comput Biol Chem, 2020 Dec;89:107403.
    PMID: 33120127 DOI: 10.1016/j.compbiolchem.2020.107403
    The Blueline Rasbora (Rasbora sarawakensis) is a small ray-finned fish categorized under the genus Rasbora in the Cyprinidae family. In this study, the complete mitogenome sequence of R. sarawakensis was sequenced using four primers targeting overlapping regions. The mitogenome is 16,709 bp in size, accommodating 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other genus counterparts. The heavy strand houses 28 genes while the light strand stores the other nine genes. Most protein-coding genes employ ATG as start codon, excluding COI gene, which utilizes GTG instead. The central conserved sequence blocks (CSB-F, CSB-E and CSB-D), variable sequence blocks (CSB-3, CSB-2 and CSB-1) as well as the terminal associated sequence (TAS) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of R. sarawakensis from the basal region of the Rasbora clade, where its evolutionary relationships with R. maculatus and R. pauciperforata are poorly resolved as indicated by the low bootstrap values. This work acts as steppingstone towards further molecular evolution and population genetics studies of Rasbora genus in future.
    Matched MeSH terms: DNA, Mitochondrial/analysis*; DNA, Mitochondrial/genetics; Sequence Analysis, DNA
  15. Complete genome sequence of Novosphingobium resinovorum SA1, a versatile xenobiotic-degrading bacterium capable of utilizing sulfanilic acid
    Hegedűs B, Kós PB, Bálint B, Maróti G, Gan HM, Perei K, et al.
    J Biotechnol, 2017 Jan 10;241:76-80.
    PMID: 27851894 DOI: 10.1016/j.jbiotec.2016.11.013
    Sulfanilic acid (4-aminobenzenesulfonic acid) is a sulfonated aromatic amine widely used in chemical industries for synthesis of various organic dyes and sulfa drugs. There are quite a few microbial co-cultures or single isolates capable of completely degrading this compound. Novosphingobium resinovorum SA1 was the first single bacterium which could utilize sulfanilic acid as its sole carbon, nitrogen and sulfur source. The strain has versatile catabolic routes for the bioconversion of numerous other aromatic compounds. Here, the complete genome sequence of the N. resinovorum SA1 strain is reported. The genome consists of a circular chromosome of 3.8 Mbp and four extrachromosomal elements between 67 and 1 759.8 kbp in size. Three alternative 3-ketoadipate pathways were identified on the plasmids. Sulfanilic acid is decomposed via a modified 3-ketoadipate pathway and the oxygenases involved form a phylogenetically separate branch on the tree. Sequence analysis of these elements might provide a genetic background for deeper insight into the versatile catabolic metabolism of various aromatic xenobiotics, including sulfanilic acid and its derivatives. Moreover, this is also a good model strain for understanding the role and evolution of multiple genetic elements within a single strain.
    Matched MeSH terms: DNA, Bacterial/analysis; DNA, Bacterial/genetics; Sequence Analysis, DNA
  16. Fulltext Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA
    Periasamy V, Rizan N, Al-Ta'ii HM, Tan YS, Tajuddin HA, Iwamoto M
    Sci Rep, 2016 07 20;6:29879.
    PMID: 27435636 DOI: 10.1038/srep29879
    The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology.
    Matched MeSH terms: DNA/genetics; DNA/isolation & purification; DNA/chemistry*
  17. Fulltext Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding
    Nurul Farhana S, Muchlisin ZA, Duong TY, Tanyaros S, Page LM, Zhao Y, et al.
    Sci Rep, 2018 Jul 17;8(1):10787.
    PMID: 30018357 DOI: 10.1038/s41598-018-29049-7
    Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.
    Matched MeSH terms: DNA, Mitochondrial/chemistry; Sequence Analysis, DNA; DNA Barcoding, Taxonomic
  18. DNA-templated silver nanoclusters: structural correlation and fluorescence modulation
    New SY, Lee ST, Su XD
    Nanoscale, 2016 Oct 20;8(41):17729-17746.
    PMID: 27722695
    12 years after the introduction of DNA-templated silver nanoclusters (DNA-AgNCs), exciting progress has been made and yet we are still in the midst of trying to fully understand this nanomaterial. The prominent excellence of DNA-AgNCs is undoubtedly its modulatable emission property, of which how variation in DNA templates causes emission tuning remains elusive. Based on the up-to-date DNA-AgNCs, we aim to establish the correlation between the structure/sequence of DNA templates and emission behaviour of AgNCs. Herein, we systematically present a wide-range of DNA-AgNCs based on the structural complexity of the DNA templates, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), triple-stranded DNA (tsDNA) and DNA nanostructures. For each DNA category, we discuss the emission property, quantum yield and synthesis condition of the respective AgNCs, before cross-comparing the impact of different DNA scaffolds on the properties of AgNCs. A future outlook for this area is given as a conclusion. By putting the information together, this review may shed new light on understanding DNA-AgNCs while we are expecting continuous breakthroughs in this field.
    Matched MeSH terms: DNA/chemistry*; DNA, Single-Stranded/chemistry*
  19. The Challenges of DNA Extraction in Different Assorted Food Matrices: A Review
    Sajali N, Wong SC, Hanapi UK, Abu Bakar Jamaluddin S, Tasrip NA, Mohd Desa MN
    J Food Sci, 2018 Oct;83(10):2409-2414.
    PMID: 30184265 DOI: 10.1111/1750-3841.14338
    High-quality DNA extracts are imperative for downstream applications in molecular identification. Most processed food products undergo heat treatments causing DNA degradation, which hampers application of DNA-based techniques for food authentication. Moreover, the presence of inhibitors in processed food products is also problematic, as inhibitors can impede the process of obtaining high qualities and quantities of DNA. Various approaches in DNA extraction and factors in structure and texture of various food matrices affecting DNA extraction are explained in this review.
    Matched MeSH terms: DNA/genetics; DNA/isolation & purification*; DNA/chemistry
  20. A robust test based on bootstrapping for the two-sample scale problem
    Padmanabhan A, Abdul Rahman Othman, Teh SY
    Sains Malaysiana, 2011;40:1123-1127.
    For testing the homogeneity of variances, modifications of well-known tests are known which combine rigorous theory with resampling (bootstrap). We propose versions of these tests, which are computationally simpler (although asymptotically equivalent). The earlier procedures used the smooth bootstrap with two thousand bootstrap replications per sample whereas our proposals use only the classical bootstrap (or percentile method) with just one thousand bootstrap replications per sample, and also required much less computing time. Our proposals cover the Ansari-Bradley-, Mood- and Klotz-tests. We explain their superiority over the existing methodologies available in textbooks and packages.
    Matched MeSH terms: DNA Replication
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