Displaying publications 421 - 440 of 3507 in total

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  1. Fulltext Profil toksikologi ekstrak heksana alpinia conchigera (lengkuas kecil) secara in vitro
    Ahmad Rohi Ghazali, Fazrina Hamzah, Wan Marahaini Wan Razali, Norizah Awang
    Jurnal Sains Kesihatan Malaysia, 2015;13(1):69-76.
    MyJurnal
    Alpinia conchigera (lengkuas kecil) merupakan sejenis tumbuhan herba yang sering digunakan sebagai rawatan alternatif
    dalam bidang perubatan tradisional. Kajian ini dijalankan untuk menilai kesan sitotoksik, genotoksik serta mod kematian
    sel yang disebabkan oleh ekstrak heksana A. conchigera ke atas sel hepar Chang. Asai MTT selama 24 jam telah dijalankan
    untuk mengenal pasti peratus viabiliti sel hepar Chang setelah dirawat dengan ekstrak heksana A. conchigera. Keputusan
    menunjukkan terdapat penurunan viabiliti sel secara signifi kan (p < 0.05) dengan nilai IC50 (8.6 μg/ml) berbanding kawalan
    negatif. Berdasarkan nilai IC50 ini, pewarnaan AO/PI dilakukan untuk menentukan mod kematian sel hepar Chang iaitu sama
    ada secara apoptosis atau nekrosis. Didapati bahawa terdapat perbezaan secara signifi kan (p < 0.05) bagi mod kematian
    sel hepar Chang secara apoptosis berbanding kawalan negatif. Dalam kajian ini, penentuan tahap kerosakan DNA sel
    hepar Chang turut dilakukan dengan menggunakan asai komet beralkali dengan nilai IC10 dan IC25 yang diperoleh daripada
    asai MTT (4 μg/ml dan 6 μg/ml) masing-masing. Setelah sel hepar Chang dirawat dengan ekstrak heksana A. conchigera
    selama 2 jam, didapati terdapat perbezaan secara signifi kan (p < 0.05) bagi peratus kerosakan DNA bagi kumpulan rawatan
    berbanding kawalan negatif. Kesimpulannya, ekstrak heksana A. conchigera memberi kesan sitotoksik dan genotoksik
    terhadap sel hepar Chang serta menyebabkan kematian sel secara apoptosis.
    Matched MeSH terms: DNA
  2. Fulltext Pengimejan resonans magnet kefungsian: pemerolehan, analisis dan pentafsiran data
    Ahmad Nazlim Yusoff, Mohd Harith Hashim, Mohd Mahadir Ayob, Iskandar Kassim
    Jurnal Sains Kesihatan Malaysia, 2005;3(2):19-37.
    MyJurnal
    Kajian garis pangkal pengimejan resonans magnet kefungsian (fMRI) telah dijalankan di Jabatan Radiologi, Hospital Universiti Kebangsaan Malaysia ke atas seorang subjek lelaki sihat berumur 25 tahun menggunakan sistem pengimejan resonans magnet (MRI) 1.5 T. Kajian ini menggunakan gerakan jari tangan kanan dan kiri untuk merangsang aktiviti neuron di dalam korteks serebrum. Subjek diarahkan supaya menekan jari-jari pada ibu jari secara bergilir-gilir semasa imbasan kefungsian dilakukan. Paradigma 5 kitar aktifrehat digunakan dengan setiap kitar masing-masing mengandungi 20 siri pengukuran. Keputusan menunjukkan bahawa rantau otak yang aktif akibat gerakan jari adalah girus presentral merangkumi kawasan motor primer. Pengaktifan otak adalah secara kontralateral terhadap gerakan jari tangan kanan dan kiri. Keamatan isyarat keadaan aktif didapati lebih tinggi daripada keamatan isyarat keadaan rehat. Analisis yang dilakukan ke atas beberapa rantau pengaktifan yang diminati (ROI) pada beberapa hirisan menunjukkan perbezaan yang bererti (p < 0.05) antara keamatan keadaan aktif dan rehat untuk nilai ambang statistik (Z) = 1.0 dan 1.5. Perbezaan purata antara kedua-dua purata keamatan isyarat keadaan aktif dan rehat pada manamana hirisan untuk kedua-dua nilai Z menunjukkan magnitud pengaktifan yang lebih tinggi pada hemisfera kanan otak iaitu apabila subjek menggerakkan tangan kirinya. Bilangan voksel yang aktif juga didapati lebih tinggi pada hemisfera kanan berbanding pada hemisfera kiri otak. Keputusan ini menyokong fakta bahawa bagi subjek yang tidak kidal, kawasan pengaktifan motor pada hemisfera kanan otak semasa gerakan jari tangan kiri mengalami rangsangan hemodinamik yang lebih tinggi berbanding dengan hemisfera kiri otak semasa gerakan jari tangan kanan. Fenomena rangsangan hemodinamik yang diperhatikan dalam kajian ini dibincangkan berdasarkan kepada kebergantungan kontras isyarat kepada aras oksigen darah (BOLD).
    Matched MeSH terms: DNA Primers
  3. Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta)
    Carter BE, Larraín J, Manukjanová A, Shaw B, Shaw AJ, Heinrichs J, et al.
    Mol Phylogenet Evol, 2017 02;107:16-26.
    PMID: 27744015 DOI: 10.1016/j.ympev.2016.10.002
    Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.
    Matched MeSH terms: Sequence Analysis, DNA; DNA, Plant/isolation & purification; DNA, Plant/metabolism
  4. Fulltext Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences
    Bunawan H, Yen CC, Yaakop S, Noor NM
    BMC Res Notes, 2017 Jan 26;10(1):67.
    PMID: 28126013 DOI: 10.1186/s13104-017-2379-1
    The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus.
    Matched MeSH terms: DNA, Chloroplast/genetics*; DNA, Ribosomal Spacer/genetics*
  5. Fulltext Determinants of dna yield and quality from different non-invasive sampling methods
    Karen-Ng, L.P., Hassan, S., Marhazlinda, J., Zain, R.B., Choon, Y.F.
    Ann Dent, 2012;19(2):62-65.
    MyJurnal
    The purpose of this study was to determine the
    DNA yield and quality from different non-invasive
    sampling methods and to identify the method which
    gave the highest DNA yield. Method: Thirty-eight
    volunteers had been recruited in this study where
    blood, buccal cells and saliva were collected using
    various collection techniques. Buccal cells were
    collected by 1) cytobrush and 2) saline mouth rinsing
    or “swish”. Meanwhile saliva was collected by passive
    drooling method. Upon processing the white blood
    cell (WBC), buccal cells and saliva samples, DNA
    extraction was performed according to the
    manufacturer’s protocol. Quantification and quality
    (DNA ratio at A260/A280) of the extracted DNA were
    determined using NanoDropND-1000®. T-test was
    performed to compare means between DNA obtained
    from various collection methods. Results: DNA yields
    from buccal cells collected with cytobrush, “swish”,
    saliva and WBC (mean ± SD) were (8.2 ± 5.9)ng/μl,
    (28.2 ± 14.9)ng/μl, (5.9 ± 9.5)ng/μl and (105.3 ±
    75.0)ng/μl respectively. Meanwhile the mean DNA
    ratio at A260/A280 for cytobrush, “swish”, saliva and
    WBC were 2.3, 2.0, 1.7 and 1.8 respectively. Post hoc
    test with Bonferroni correction suggested that DNA
    yield from “swish” technique exhibited the least mean
    different as compared to the DNA extracted from WBC
    (p
    Matched MeSH terms: DNA
  6. DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines
    Casas PAS, Sing KW, Lee PS, Nuñeza OM, Villanueva RJT, Wilson JJ
    Mitochondrial DNA A DNA Mapp Seq Anal, 2018 03;29(2):206-211.
    PMID: 28155593 DOI: 10.1080/24701394.2016.1267157
    Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
    Matched MeSH terms: Sequence Analysis, DNA/methods*; DNA Barcoding, Taxonomic/methods*
  7. DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV)
    Sahtout AH, Hassan MD, Shariff M
    Dis Aquat Organ, 2001 Mar 9;44(2):155-9.
    PMID: 11324818
    Fifty black tiger shrimp Penaeus monodon from commercial cultivation ponds in Malaysia were examined by Tdt-mediated dUTP nick-end labeling (TUNEL) fluorescence assay and agarose gel electrophoresis of DNA extracts for evidence of DNA fragmentation as an indicator of apoptosis. From these specimens, 30 were grossly normal and 20 showed gross signs of white spot syndrome virus (WSSV) infection. Of the 30 grossly normal shrimp, 5 specimens were found to be positive for WSSV infection by normal histology and by nested polymerase chain reaction (PCR) analysis. All of the specimens showing gross signs of WSSV infection were positive for WSSV by normal histology, while 5 were positive by nested PCR only (indicating light infections) and 15 were positive by 1-step PCR (indicating heavy infections). Typical histological signs of WSSV infection included nuclear hypertrophy, chromatin condensation and margination. None of the 25 grossly normal shrimp negative for WSSV by 1-step PCR showed any signs of DNA fragmentation by TUNEL assay or agarose gel electrophoresis of DNA extracts. The 10 specimens that gave PCR-positive results for WSSV by nested PCR only (i.e., 5 grossly normal shrimp and 5 grossly positive for WSSV) gave mean counts of 16 +/- 8% TUNEL-positive cells, while the 25 specimens PCR positive by 1-step PCR gave mean counts of 40 +/- 7% TUNEL-positive cells. Thus, the number of TUNEL positive cells present in tissues increased with increasing severity of infection, as determined by gross signs of white spots on the cuticle, the number of intranuclear inclusions in histological sections, and results from single and nested PCR assays. DNA extracts of PCR-positive specimens tested by agarose gel electrophoresis showed indications of DNA fragmentation either as smears or as 200 bp ladders. Given that DNA fragmentation is generally considered to be a hallmark of apoptosis, the results suggested that apoptosis might be implicated in shrimp death caused by WSSV.
    Matched MeSH terms: DNA Viruses/physiology*; DNA Fragmentation*
  8. Revisiting the question of limited genetic variation within Schistosoma japonicum
    Le TH, Blair D, McManus DP
    Ann Trop Med Parasitol, 2002 Mar;96(2):155-64.
    PMID: 12080976
    Recent electrophoretic data have indicated that Schistosoma japonicum in mainland China may be a species complex, with the existence of a cryptic species being predicted from the analysis of schistosome populations from Sichuan province. To investigate the Sichuan form of S. japonicum, 4.9 kbp of mitochondrial DNA from each of three samples of the parasite from China (two from Sichuan and one from Hunan) and one from Sorsogon in the Philippines were amplified, sequenced and characterized. The sequence data were compared with those from the related South-east Asian species of S. mekongi (Khong Island, Laos) and S. mlayensis (Baling, Malaysia) and that from S. japonicm from Anhui (China). At both the nucleotide and amino-acid levels, the variation among the five S. japonicum samples was limited (< 1%). This was consistent with the conclusions drawn from previous molecular studies, in which minimal variation among S. japonicum populations was also detected. In contrast, S. mekongi and S. malayensis, species recognized as separate but closely related, differ from each other by about 10%, and each differs by 25%-26% from S. japonicum. Phylogenetic trees provided a graphic representation of these differences, showing all S. japonicum sequences to be very tightly clustered and distant from S. mekongi and S. malayensis, the last two being clearly distinct from each other. The results thus indicate no significant intra-specific genetic variation among S. japonicum samples collected from different geographical areas and do not support the idea of a distinct form in Sichuan.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Helminth/genetics
  9. SCAR markers and multiplex PCR-based identification of isomorphic species in the Anopheles dirus complex in Southeast Asia
    Manguin S, Kengne P, Sonnier L, Harbach RE, Baimai V, Trung HD, et al.
    Med Vet Entomol, 2002 Mar;16(1):46-54.
    PMID: 11963981
    The Anopheles dirus Peyton & Harrison complex of mosquitoes (Diptera: Culicidae) comprises seven known species, including important malaria vectors in Southeast Asia. Specific identification of each species of the complex, which cannot be distinguished using morphological characters, is crucial for understanding vector ecology and implementing effective control measures. Derived from individual random amplified polymorphic DNA (RAPD) markers, sequence characterized amplified regions (SCAR) were analysed for the design of specific paired-primers. Combination of six SCAR primers resulted in the development of a simple, robust, single multiplex PCR able to identify three important malaria vectors among the four most common species (A, B, C, D) of the complex: species A from several Southeast Asian countries, species B from Perlis, Malaysia, and species C and D from Thailand.
    Matched MeSH terms: DNA Primers; Random Amplified Polymorphic DNA Technique/methods; Random Amplified Polymorphic DNA Technique/veterinary*
  10. NMR characterization of guanine DNA site alkylated by kapurimycin A3, an antitumour antibiotic from Streptomyces sp
    Chan KL, Sugiyama H, Saito I, Hara M
    Phytochemistry, 1995 Nov;40(5):1373-4.
    PMID: 8534399
    The kapurimycin A3-guanine adduct was formed by alkylation of the antitumour antibiotic with d(CGCG)2. The site of alkylation of the guanine was confirmed by comparative NMR studies with N-7-methyl-guanine in DMSO-d6.
    Matched MeSH terms: DNA/drug effects*; DNA/metabolism*; DNA Damage
  11. Isothermal amplifications - a comprehensive review on current methods
    Glökler J, Lim TS, Ida J, Frohme M
    Crit Rev Biochem Mol Biol, 2021 12;56(6):543-586.
    PMID: 34263688 DOI: 10.1080/10409238.2021.1937927
    The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
    Matched MeSH terms: DNA
  12. Fulltext Complete mitochondrial genome of Dacus vijaysegarani and phylogenetic relationships with congeners and other tephritid fruit flies (Insecta: Diptera)
    Yong HS, Chua KO, Song SL, Liew YJ, Eamsobhana P, Chan KG
    Mol Biol Rep, 2021 Aug;48(8):6047-6056.
    PMID: 34357549 DOI: 10.1007/s11033-021-06608-2
    BACKGROUND: Tephritid fruit flies of the genus Dacus are members of the tribe Dacini, subfamily Dacinae. There are some 274 species worldwide, distributed in Africa and the Asia-Pacific. To date, only five complete mitochondrial genomes (mitogenomes) of Dacus fruit flies have been published and are available in the GenBank.

    METHODS AND RESULTS: In view of the lack of study on their mitogenome, we sequenced (by next generation sequencing) and annotated the complete mitogenome of D. vijaysegarani from Malaysia to determine its features and phylogenetic relationship. The whole mitogenome of D. vijaysegarani has identical gene order with the published mitogenomes of the genus Dacus, with 13 protein-coding genes, two rRNA genes, 22 tRNAs, a non-coding A + T rich control region, and intergenic spacer and overlap sequences. Phylogenetic analysis based on 15 mitochondrial genes (13 PCGs and two rRNA genes), reveals Dacus, Zeugodacus and Bactrocera forming a distinct clade. The genus Dacus forms a monophyletic group in the subclade containing also the Zeugodacus group; this Dacus-Zeugodacus subclade is distinct from the Bactrocera subclade. D. (Mellesis) vijaysegarani forms a lineage with D. (Mellesis) trimacula in the subcluster containing also the lineage of D. (Mellesis) conopsoides and D. (Callantra) longicornis. D. (Dacus) bivittatus and D. (Didacus) ciliatus form a distinct subcluster. Based on cox1 sequences, the Malaysia and Vietnam taxa of D. vijaysegarani may not be conspecific.

    CONCLUSIONS: Overall, the mitochondrial genome of D. vijaysegarani provided essential molecular data that could be useful for further studies for species diagnosis, evolution and phylogeny research of other tephritid fruit flies in the future.

    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA/methods
  13. Fulltext Characterization of bacterial communities associated with blood-fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis
    Lim L, Ab Majid AH
    Sci Rep, 2021 Apr 19;11(1):8465.
    PMID: 33875727 DOI: 10.1038/s41598-021-87946-w
    With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well-studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood-fed and starved tropical bed bugs were analysed and characterized by amplifying the v3-v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha-proteobacterium Wolbachia and gamma-proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood-fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood-fed bed bugs.
    Matched MeSH terms: DNA/analysis; DNA/genetics*; DNA Barcoding, Taxonomic
  14. Fulltext The Role of the Z-DNA Binding Domain in Innate Immunity and Stress Granules
    Chiang C, Li Y, Ng SK
    Front Immunol, 2020;11:625504.
    PMID: 33613567 DOI: 10.3389/fimmu.2020.625504
    Both DNA and RNA can maintain left-handed double helical Z-conformation under physiological condition, but only when stabilized by Z-DNA binding domain (ZDBD). After initial discovery in RNA editing enzyme ADAR1, ZDBD has also been described in pathogen-sensing proteins ZBP1 and PKZ in host, as well as virulence proteins E3L and ORF112 in viruses. The host-virus antagonism immediately highlights the importance of ZDBD in antiviral innate immunity. Furthermore, Z-RNA binding has been shown to be responsible for the localization of these ZDBD-containing proteins to cytoplasmic stress granules that play central role in coordinating cellular response to stresses. This review sought to consolidate current understanding of Z-RNA sensing in innate immunity and implore possible roles of Z-RNA binding within cytoplasmic stress granules.
    Matched MeSH terms: DNA-Binding Proteins/immunology*; DNA, Z-Form/immunology*
  15. Hebeloma in the Malay Peninsula: Masquerading within Psathyrella
    Eberhardt U, Schütz N, Beker HJ, Lee SS, Horak E
    MycoKeys, 2021;77:117-141.
    PMID: 33551660 DOI: 10.3897/mycokeys.77.57394
    In 1994 Corner published five new species within the genus Psathyrella, all having been collected on the Malay Peninsula between 1929 and 1930. Three of these species belong to the genus Hebeloma and with their vinaceous colored lamellae and spore print, when fresh, they belong to H. sect. Porphyrospora. Of these three species, only one, P. flavidifolia, was validly published and thus we herewith recombine it as H. flavidifolium. The other two species, P. splendens and P. verrucispora, are synonyms of H. parvisporum and H. lactariolens, respectively. We also describe a new Malayan species, H. radicans, which also belongs to H. sect. Porphyrospora. These findings confirm the western Pacific Rim as a diversity hotspot for H. sect. Porphyrospora. The records described within this paper, represent the first recognition that the genus Hebeloma, and indeed that members of the ectomycorrhizal Hymenogastraceae, are present on the Malay Peninsula.
    Matched MeSH terms: DNA, Ribosomal Spacer
  16. Fulltext DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia
    Zainal Abidin DH, Mohd Nor SA, Lavoué S, A Rahim M, Jamaludin NA, Mohammed Akib NA
    Sci Rep, 2021 Sep 07;11(1):17800.
    PMID: 34493747 DOI: 10.1038/s41598-021-97324-1
    The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.
    Matched MeSH terms: DNA/genetics; DNA Barcoding, Taxonomic*
  17. Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers
    Lim LWK, Chung HH, Lau MML, Aziz F, Gan HM
    Gene, 2021 Jul 30;791:145708.
    PMID: 33984441 DOI: 10.1016/j.gene.2021.145708
    The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.
    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA/methods
  18. Zinc oxide and gold textured Janus nanowire integration in an impedimetric sensor for leptospirosis DNA-biomarker recognition
    Haarindraprasad R, Gopinath SCB, Veeradassan P
    Biotechnol Appl Biochem, 2022 Dec;69(6):2698-2712.
    PMID: 34997977 DOI: 10.1002/bab.2316
    A "Janus particle" refers to the production of two materials in a single system and shows a difference in physical characteristics, and two surfaces participate in the formation with different chemistries. This research generated the Janus using a hybrid of zinc oxide (ZnO) and gold (Au) on the sensor surface toward making high-performance DNA sensors. The Janus ZnO/Au-textured film was synthesized via the one-step sol-gel method, which involves a suitable ratio of a mixture of ZnO sol seed solution. The synthesized Janus ZnO/Au-textured film undergoes a low-temperature aqueous hydrothermal route to synthesize quasi-one-dimensional nanowires. The average grain size in the Janus ZnO/Au nanotextured wire was 41.60 nm. The fabricated nanotextured wire was further optimized by tuning the thickness and characterized by XRD and high-resolution microscopy. Electrical characterization was conducted on the Janus ZnO/Au nanotextured wire coupled with an interdigitated electrode sensor to detect the specific leptospirosis DNA strand. The generated device is capable of detecting lower DNA concentration at 1 × 10-13 M with a sensitivity of 8.54 MΩ M-1 cm-2 . The high performance is attained on linear concentrations of 10-6 -10-13 M with the determination coefficient, "I = 135437.63C-3609.07" R2 = 0.9551. A potential strategy is proposed as a base for developing different high-performance sensors.
    Matched MeSH terms: DNA
  19. Fulltext Sequencing of Cladosporium sphaerospermum, a Dematiaceous fungus isolated from blood culture
    Ng KP, Yew SM, Chan CL, Soo-Hoo TS, Na SL, Hassan H, et al.
    Eukaryot Cell, 2012 May;11(5):705-6.
    PMID: 22544899 DOI: 10.1128/EC.00081-12
    Cladosporium sphaerospermum is one of the most widely distributed allergens causing serious problems in patients with respiratory tract disease. We report the 26,644,473-bp draft genome sequence and gene annotation of C. sphaerospermum UM843. Analysis of the genome sequence led to the finding of genes associated with C. sphaerospermum's melanin biosynthesis, allergens, and antifungal drug resistance.
    Matched MeSH terms: DNA, Fungal/analysis; DNA, Fungal/genetics; Sequence Analysis, DNA
  20. Molecular investigation of virulence determinants between a virulent clinical strain and an attenuated strain of Burkholderia pseudomallei
    Puthucheary SD, Puah SM, Chai HC, Thong KL, Chua KH
    J. Mol. Microbiol. Biotechnol., 2012;22(3):198-204.
    PMID: 22846664 DOI: 10.1159/000338985
    Burkholderia pseudomallei is the causative agent of melioidosis. We initiated this investigation with a virulent and an attenuated strain of B. pseudomallei. Pulsed-field gel electrophoresis was carried out initially for macrogenomic comparison of both strains of B. pseudomallei. However, the pulsotypes obtained were identical and therefore we applied a subtractive hybridization technique to distinguish and determine the possible differences between the two strains. Six virulence strain-specific DNA fragments were obtained and the encoding homolog proteins were identified as a xenobiotic-responsive element family of transcriptional regulator, a hypothetical protein, an unknown protein, a plasmid recombination enzyme, a regulatory protein and a putative hemolysin activator protein. A combination of at least three of these determinants was identified in 45 clinical isolates when screening was carried out with self-designed multiplex PCR targeting the six putative virulent determinants. Our data demonstrated that different combinations of the six putative virulence genes were present in the clinical isolates indicating their probable role in the pathogenesis of B. pseudomallei infections.
    Matched MeSH terms: DNA, Bacterial/genetics; Sequence Analysis, DNA; DNA Fragmentation
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