Displaying publications 121 - 140 of 3504 in total

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  1. Fulltext Chemical reaction of soybean flavonoids with DNA: a computational study using the implicit solvent model
    Abdallah HH, Mavri J, Repič M, Lee VS, Wahab HA
    Int J Mol Sci, 2012;13(2):1269-83.
    PMID: 22408390 DOI: 10.3390/ijms13021269
    Genistein, daidzein, glycitein and quercetin are flavonoids present in soybean and other vegetables in high amounts. These flavonoids can be metabolically converted to more active forms, which may react with guanine in the DNA to form complexes and can lead to DNA depurination. We assumed two ultimate carcinogen forms of each of these flavonoids, diol epoxide form and diketone form. Density functional theory (DFT) and Hartree-Fock (HF) methods were used to study the reaction thermodynamics between active forms of flavonoids and DNA guanine. Solvent reaction field method of Tomasi and co-workers and the Langevin dipoles method of Florian and Warshel were used to calculate the hydration free energies. Activation free energy for each reaction was estimated using the linear free energy relation. Our calculations show that diol epoxide forms of flavonoids are more reactive than the corresponding diketone forms and are hence more likely flavonoid ultimate carcinogens. Genistein, daidzein and glycitein show comparable reactivity while quercetin is less reactive toward DNA.
    Matched MeSH terms: DNA/chemistry*
  2. Fulltext Complete genome and proteome of Acholeplasma laidlawii
    Lazarev VN, Levitskii SA, Basovskii YI, Chukin MM, Akopian TA, Vereshchagin VV, et al.
    J Bacteriol, 2011 Sep;193(18):4943-53.
    PMID: 21784942 DOI: 10.1128/JB.05059-11
    We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.
    Matched MeSH terms: DNA, Bacterial/genetics*; DNA, Bacterial/chemistry*; DNA, Circular/genetics; DNA, Circular/chemistry; Sequence Analysis, DNA*
  3. Long-Range Polymerase Chain Reaction
    Kee PS, Karunanathie H, Maggo SDS, Kennedy MA, Chua EW
    Methods Mol Biol, 2023;2967:181-192.
    PMID: 37608112 DOI: 10.1007/978-1-0716-3358-8_15
    Polymerase chain reaction (PCR) is a laboratory technique used to amplify a targeted region of DNA, demarcated by a set of oligonucleotide primers. Long-range PCR is a form of PCR optimized to facilitate the amplification of large fragments. Using the adapted long-range PCR protocol described in this chapter, we were able to generate PCR products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples. For some of the long PCRs, successful amplification was not possible without the use of PCR enhancers. Thus, we also evaluated the impact of some enhancers on long-range PCR and included the findings as part of this updated chapter.
    Matched MeSH terms: DNA Primers/genetics
  4. Fulltext Electronic Properties of DNA-Based Schottky Barrier Diodes in Response to Alpha Particles
    Al-Ta'ii HM, Periasamy V, Amin YM
    Sensors (Basel), 2015;15(5):11836-53.
    PMID: 26007733 DOI: 10.3390/s150511836
    Detection of nuclear radiation such as alpha particles has become an important field of research in recent history due to nuclear threats and accidents. In this context; deoxyribonucleic acid (DNA) acting as an organic semiconducting material could be utilized in a metal/semiconductor Schottky junction for detecting alpha particles. In this work we demonstrate for the first time the effect of alpha irradiation on an Al/DNA/p-Si/Al Schottky diode by investigating its current-voltage characteristics. The diodes were exposed for different periods (0-20 min) of irradiation. Various diode parameters such as ideality factor, barrier height, series resistance, Richardson constant and saturation current were then determined using conventional, Cheung and Cheung's and Norde methods. Generally, ideality factor or n values were observed to be greater than unity, which indicates the influence of some other current transport mechanism besides thermionic processes. Results indicated ideality factor variation between 9.97 and 9.57 for irradiation times between the ranges 0 to 20 min. Increase in the series resistance with increase in irradiation time was also observed when calculated using conventional and Cheung and Cheung's methods. These responses demonstrate that changes in the electrical characteristics of the metal-semiconductor-metal diode could be further utilized as sensing elements to detect alpha particles.
    Matched MeSH terms: DNA/chemistry*
  5. Three novel species in the Pseudo-nitzschia pseudodelicatissima complex: P. batesiana sp. nov., P. lundholmiae sp. nov., and P. fukuyoi sp. nov. (Bacillariophyceae) from the Strait of Malacca, Malaysia
    Lim HC, Teng ST, Leaw CP, Lim PT
    J Phycol, 2013 Oct;49(5):902-16.
    PMID: 27007315 DOI: 10.1111/jpy.12101
    A study on the morphology and phylogeny of 18 strains of Pseudo-nitzschia established from the Strait of Malacca, Peninsular Malaysia, was undertaken. Morphological data combined with molecular evidence show that they constitute three new species, for which the names, P. batesiana sp. nov., P. lundholmiae sp. nov., and P. fukuyoi sp. nov., are proposed. The three new species closely resemble species in the P. pseudodelicatissima complex sensu lato. Morphologically, P. batesiana differs from other species in the complex by having a smaller part of cell overlapping in the chain, whereas P. lundholmiae differs by having fewer poroid sectors and P. fukuyoi by having a distinct type of poroid sectors. Nucleotide sequences of the LSU rDNA (D1-D3) of the three new species reveal significant nucleotide sequence divergence (0.1%-9.3%) from each other and from other species in the P. pseudodelicatissima complex s.l. The three species are phylogenetically closely related to species in the P. pseudodelicatissima complex, with P. batesiana appearing as a sister taxon to P. circumpora, P. caciantha, and P. subpacifica; whereas P. lundholmiae and P. fukuyoi are more closely related to P. pseudodelicatissima and P. cuspidata. The three species show 2-3 compensatory base changes (CBCs) in their ITS2 transcripts when compared to the closely related species. The ITS2 with its structural information has proven its robustness in constructing a better resolved phylogenetic framework for Pseudo-nitzschia.
    Matched MeSH terms: DNA, Ribosomal; DNA, Ribosomal Spacer
  6. Fulltext Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy
    Chikira M, Ng CH, Palaniandavar M
    Int J Mol Sci, 2015;16(9):22754-80.
    PMID: 26402668 DOI: 10.3390/ijms160922754
    The interaction of simple and ternary Cu(II) complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II) complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR) spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements.
    Matched MeSH terms: DNA; DNA Cleavage
  7. Fulltext Mitochondrial Cardiomyopathy: Molecular Epidemiology, Diagnosis, Models, and Therapeutic Management
    Yang J, Chen S, Duan F, Wang X, Zhang X, Lian B, et al.
    Cells, 2022 Nov 06;11(21).
    PMID: 36359908 DOI: 10.3390/cells11213511
    Mitochondrial cardiomyopathy (MCM) is characterized by abnormal heart-muscle structure and function, caused by mutations in the nuclear genome or mitochondrial DNA. The heterogeneity of gene mutations and various clinical presentations in patients with cardiomyopathy make its diagnosis, molecular mechanism, and therapeutics great challenges. This review describes the molecular epidemiology of MCM and its clinical features, reviews the promising diagnostic tests applied for mitochondrial diseases and cardiomyopathies, and details the animal and cellular models used for modeling cardiomyopathy and to investigate disease pathogenesis in a controlled in vitro environment. It also discusses the emerging therapeutics tested in pre-clinical and clinical studies of cardiac regeneration.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  8. Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
    Tajuddin S, Khan AM, Chong LC, Wong CL, Tan JS, Ina-Salwany MY, et al.
    Appl Microbiol Biotechnol, 2023 Feb;107(2-3):749-768.
    PMID: 36520169 DOI: 10.1007/s00253-022-12312-3
    Vibrio alginolyticus is a Gram-negative bacterium commonly associated with mackerel poisoning. A bacteriophage that specifically targets and lyses this bacterium could be employed as a biocontrol agent for treating the bacterial infection or improving the shelf-life of mackerel products. However, only a few well-characterized V. alginolyticus phages have been reported in the literature. In this study, a novel lytic phage, named ΦImVa-1, specifically infecting V. alginolyticus strain ATCC 17749, was isolated from Indian mackerel. The phage has a short latent period of 15 min and a burst size of approximately 66 particles per infected bacterium. ΦImVa-1 remained stable for 2 h at a wide temperature (27-75 °C) and within a pH range of 5 to 10. Transmission electron microscopy revealed that ΦImVa-1 has an icosahedral head of approximately 60 nm in diameter with a short tail, resembling those in the Schitoviridae family. High throughput sequencing and bioinformatics analysis elucidated that ΦImVa-1 has a linear dsDNA genome of 77,479 base pairs (bp), with a G + C content of ~ 38.72% and 110 predicted gene coding regions (106 open reading frames and four tRNAs). The genome contains an extremely large virion-associated RNA polymerase gene and two smaller non-virion-associated RNA polymerase genes, which are hallmarks of schitoviruses. No antibiotic genes were found in the ΦImVa-1 genome. This is the first paper describing the biological properties, morphology, and the complete genome of a V. alginolyticus-infecting schitovirus. When raw mackerel fish flesh slices were treated with ΦImVa-1, the pathogen loads reduced significantly, demonstrating the potential of the phage as a biocontrol agent for V. alginolyticus strain ATCC 17749 in the food. KEY POINTS: • A novel schitovirus infecting Vibrio alginolyticus ATCC 17749 was isolated from Indian mackerel. • The complete genome of the phage was determined, analyzed, and compared with other phages. • The phage is heat stable making it a potential biocontrol agent in extreme environments.
    Matched MeSH terms: DNA-Directed RNA Polymerases/genetics
  9. Fulltext Changes in Mitochondrial Epigenome in Type 2 Diabetes Mellitus
    Low HC, Chilian WM, Ratnam W, Karupaiah T, Md Noh MF, Mansor F, et al.
    Br J Biomed Sci, 2023;80:10884.
    PMID: 36866104 DOI: 10.3389/bjbs.2023.10884
    Type 2 Diabetes Mellitus is a major chronic metabolic disorder in public health. Due to mitochondria's indispensable role in the body, its dysfunction has been implicated in the development and progression of multiple diseases, including Type 2 Diabetes mellitus. Thus, factors that can regulate mitochondrial function, like mtDNA methylation, are of significant interest in managing T2DM. In this paper, the overview of epigenetics and the mechanism of nuclear and mitochondrial DNA methylation were briefly discussed, followed by other mitochondrial epigenetics. Subsequently, the association between mtDNA methylation with T2DM and the challenges of mtDNA methylation studies were also reviewed. This review will aid in understanding the impact of mtDNA methylation on T2DM and future advancements in T2DM treatment.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  10. Fulltext Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy
    Kuan SW, Chua KH, Tan EW, Tan LK, Loch A, Kee BP
    PeerJ, 2022;10:e13265.
    PMID: 35441061 DOI: 10.7717/peerj.13265
    Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  11. Fulltext Insights into subspecies classification and conservation priorities of Central Asian lynx populations revealed by morphometric and genetic analyses
    Bizhanova N, Nanova O, Fadakar D, Grachev A, Hong Z, Mohd Sah SA, et al.
    Sci Rep, 2024 Mar 02;14(1):5186.
    PMID: 38431728 DOI: 10.1038/s41598-024-55807-x
    The Eurasian lynx (Lynx lynx) exhibits geographic variability and phylogenetic intraspecific relationships. Previous morphological studies have suggested the existence of multiple lynx subspecies, but recent genetic research has questioned this classification, particularly in Central Asia. In this study, we aimed to analyse the geographic and genetic variation in Central Asian lynx populations, particularly the Turkestan lynx and Altai lynx populations, using morphometric data and mtDNA sequences to contribute to their taxonomic classification. The comparative analysis of morphometric data revealed limited clinal variability between lynx samples from the Altai and Tien Shan regions. By examining mtDNA fragments (control region and cytochrome b) obtained from Kazakhstani lynx populations, two subspecies were identified: L. l. isabellinus (represented by a unique haplotype of the South clade, H46) and L. l. wrangeli (represented by haplotypes H36, H45, and H47 of the East clade). L. l. isabellinus was recognized only in Tien Shan Mountain, while Altai lynx was likely identical to L. l. wrangeli and found in northern Kazakhstan, Altai Mountain, Saur and Tarbagatai Mountains, and Tien Shan Mountain. The morphological and mtDNA evidence presented in this study, although limited in sample size and number of genetic markers, renders the differentiation of the two subspecies challenging. Further sampling and compilation of whole-genome sequencing data are necessary to confirm whether the proposed subspecies warrant taxonomic standing.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  12. Exosome-mediated viral nucleic acid presentation in a crustacean expounds innate immunity from a novel perspective
    Gong Y, Hu H, Zhao X, Wei W, Zhang M, Tran NT, et al.
    J Virol, 2024 Dec 17;98(12):e0151924.
    PMID: 39545727 DOI: 10.1128/jvi.01519-24
    As an enduring hot topic in the field of innate immunity, apoptosis is widely considered an effective approach to eliminate pathogenic microbes and plays a crucial role during host-pathogen interactions. Recently, researchers have found that the virus-containing host cells could transmit apoptotic signals to the surrounding uninfected cells during infection, but the mechanism remains unclear. Here, we found that exosomes secreted by WSSV-infected mud crab hemocytes contain viral nucleic acid wsv277, which could be transported to the recipient cells and further expressed viral protein with phosphokinase activity. Besides, by using transcriptome, proteome, ChIP-seq, and coIP techniques, the results revealed that wsv277 could activate the transcription and translation of apoptotic genes via interacting with CBF and EF-1α so as to suppress the spread of virus infection by inducing apoptosis of the surrounding cells. Therefore, for the first time, our study proved that the components of DNA virus could be encapsulated into exosomes and elucidated the mechanism of apoptotic signal transduction between cells from the perspective of exosomes.

    IMPORTANCE: Our study revealed that the components of DNA virus could be packaged and transmitted through the exosomes of lower invertebrates, which strongly demonstrated the diversity of exosome-mediated viral immunity and its universality in animals. Furthermore, we elucidated the mechanism of apoptotic signal transduction between cells from the perspective of exosomes and revealed a novel strategy for the host to cope with viral infection.

    Matched MeSH terms: DNA, Viral/genetics
  13. Scoping review on the genotoxicity of silver nanoparticles in endodontics: therapeutic saviors or genetic saboteurs?
    Lin GSS, Lestari W, Muhamad Halil MH, Abd Aziz MS
    Odontology, 2025 Apr;113(2):457-465.
    PMID: 39367937 DOI: 10.1007/s10266-024-01012-1
    Silver nanoparticles (AgNPs) have gained prominence in endodontics due to their exceptional antimicrobial properties. However, concerns regarding their genotoxic potential have prompted investigations into their safety profiles. This scoping review aims to consolidate current knowledge on the genotoxic effects of AgNPs in the field of endodontics. A thorough literature search across seven electronic databases was conducted using specific keywords. Inclusion criteria included experimental studies published in English from January 1960 to March 2024, addressing the genotoxicity of AgNPs in endodontic applications. Study selection and data extraction were conducted independently. The Quality Assessment Tool For In Vitro Studies (QUIN) tool was employed to evaluate the risk of bias in each study. 5 articles were selected, of which 3 were in vitro experimental designs, while the remaining were ex vivo studies. All were published between 2009 and 2021. AgNPs have been used as root canal irrigating solutions, pulp-capping materials, and root canal sealers. Most studies employed the comet assay for genotoxic evaluation. One study was found to have a low risk of bias, while others were categorized as having a medium risk. Mixed findings were noted on the genotoxic effects of AgNPs using various assays. The genotoxic potential of AgNPs somewhat poses concerns for endodontic practices. This review highlights the need for further research to develop safer alternatives and optimize their concentrations and exposure durations.
    Matched MeSH terms: DNA Damage/drug effects
  14. Fulltext Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions
    Conte-Grand C, Britz R, Dahanukar N, Raghavan R, Pethiyagoda R, Tan HH, et al.
    PLoS One, 2017;12(9):e0184017.
    PMID: 28931084 DOI: 10.1371/journal.pone.0184017
    Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.
    Matched MeSH terms: DNA/metabolism*; DNA/chemistry; Sequence Analysis, DNA; DNA Barcoding, Taxonomic*
  15. Pentaplacodinium saltonense gen. et sp. nov. (Dinophyceae) and its relationship to the cyst-defined genus Operculodinium and yessotoxin-producing Protoceratium reticulatum
    Mertens KN, Carbonell-Moore MC, Pospelova V, Head MJ, Highfield A, Schroeder D, et al.
    Harmful Algae, 2018 01;71:57-77.
    PMID: 29306397 DOI: 10.1016/j.hal.2017.12.003
    Strains of a dinoflagellate from the Salton Sea, previously identified as Protoceratium reticulatum and yessotoxin producing, have been reexamined morphologically and genetically and Pentaplacodinium saltonense n. gen. et sp. is erected to accommodate this species. Pentaplacodinium saltonense differs from Protoceratium reticulatum (Claparède et Lachmann 1859) Bütschli 1885 in the number of precingular plates (five vs. six), cingular displacement (two widths vs. one), and distinct cyst morphology. Incubation experiments (excystment and encystment) show that the resting cyst of Pentaplacodinium saltonense is morphologically most similar to the cyst-defined species Operculodinium israelianum (Rossignol, 1962) Wall (1967) and O. psilatum Wall (1967). Collections of comparative material from around the globe (including Protoceratium reticulatum and the genus Ceratocorys) and single cell PCR were used to clarify molecular phylogenies. Variable regions in the LSU (three new sequences), SSU (12 new sequences) and intergenic ITS 1-2 (14 new sequences) were obtained. These show that Pentaplacodinium saltonense and Protoceratium reticulatum form two distinct clades. Pentaplacodinium saltonense forms a monophyletic clade with several unidentified strains from Malaysia. LSU and SSU rDNA sequences of three species of Ceratocorys (C. armata, C. gourreti, C. horrida) from the Mediterranean and several other unidentified strains from Malaysia form a well-supported sister clade. The unique phylogenetic position of an unidentified strain from Hawaii is also documented and requires further examination. In addition, based on the V9 SSU topology (bootstrap values >80%), specimens from Elands Bay (South Africa), originally described as Gonyaulax grindleyi by Reinecke (1967), cluster with Protoceratium reticulatum. The known range of Pentaplacodinium saltonense is tropical to subtropical, and its cyst is recorded as a fossil in upper Cenozoic sediments. Protoceratium reticulatum and Pentaplacodinium saltonense seem to inhabit different niches: motile stages of these dinoflagellates have not been found in the same plankton sample.
    Matched MeSH terms: DNA, Ribosomal; DNA, Protozoan/analysis; Sequence Analysis, DNA; DNA, Algal/analysis
  16. Morphology, ultrastructure, and molecular phylogeny of Wangodinium sinense gen. et sp. nov. (Gymnodiniales, Dinophyceae) and revisiting of Gymnodinium dorsalisulcum and Gymnodinium impudicum
    Luo Z, Hu Z, Tang Y, Mertens KN, Leaw CP, Lim PT, et al.
    J Phycol, 2018 10;54(5):744-761.
    PMID: 30144373 DOI: 10.1111/jpy.12780
    The genus Gymnodinium includes many morphologically similar species, but molecular phylogenies show that it is polyphyletic. Eight strains of Gymnodinium impudicum, Gymnodinium dorsalisulcum and a novel Gymnodinium-like species from Chinese and Malaysian waters and the Mediterranean Sea were established. All of these strains were examined with light microscopy, scanning electron microscopy and transmission electron microscopy. SSU, LSU and internal transcribed spacers rDNA sequences were obtained. A new genus, Wangodinium, was erected to incorporate strains with a loop-shaped apical structure complex (ASC) comprising two rows of amphiesmal vesicles, here referred to as a new type of ASC. The chloroplasts of Wangodinium sinense are enveloped by two membranes. Pigment analysis shows that peridinin is the main accessory pigment in W. sinense. Wangodinium differs from other genera mainly in its unique ASC, and additionally differs from Gymnodinium in the absence of nuclear chambers, and from Lepidodinium in the absence of Chl b and nuclear chambers. New morphological information was provided for G. dorsalisulcum and G. impudicum, e.g., a short sulcal intrusion in G. dorsalisulcum; nuclear chambers in G. impudicum and G. dorsalisulcum; and a chloroplast enveloped by two membranes in G. impudicum. Molecular phylogeny was inferred using maximum likelihood and Bayesian inference with independent SSU and LSU rDNA sequences. Our results support the classification of Wangodinium within the Gymnodiniales sensu stricto clade and it is close to Lepidodinium. Our results also support the close relationship among G. dorsalisulcum, G. impudicum, and Barrufeta. Further research is needed to assign these Gymnodinium species to Barrufeta or to erect new genera.
    Matched MeSH terms: DNA, Ribosomal/analysis; DNA, Protozoan/analysis; DNA, Algal/analysis
  17. Cytosine methylation of rice mitochondrial DNA from grain and leaf tissues
    Muniandy K, Tan MH, Shehnaz S, Song BK, Ayub Q, Rahman S
    Planta, 2020 Feb 01;251(2):57.
    PMID: 32008119 DOI: 10.1007/s00425-020-03349-7
    MAIN CONCLUSION: The rice leaf mitochondrial DNA is  more methylated compared to the rice grain mitochondrial DNA. The old rice leaf mitochondrial DNA has also a higher methylation level than the young rice leaf mitochondrial DNA. The presence of DNA methylation in rice organelles has not been well characterized. We have previously shown that cytosine methylation of chloroplast DNA is different between leaf and grain, and varies between young and old leaves in rice. However, the variation in cytosine methylation of mitochondrial DNA is still poorly characterized. In this study, we have investigated cytosine methylation of mitochondrial DNA in the rice grain and leaf. Based on CpG, CHG, and CHH methylation analyses, the leaf mitochondrial DNA was found to be  more methylated compared to the grain mitochondrial DNA. The methylation of the leaf mitochondrial DNA was also higher in old compared to young leaves. Differences in methylation were observed at different cytosine positions of the mitochondrial DNA between grain and leaf, although there were also positions with a similar level of high methylation in all the tissues examined. The differentially methylated cytosine positions in rice mitochondrial DNA were observed mostly in the intergenic region and in some mitochondrial-specific genes involved in ATP production, transcription, and translation. The functional importance of cytosine methylation in the life cycle of rice mitochondria is still to be determined.
    Matched MeSH terms: DNA, Mitochondrial/genetics*; DNA, Chloroplast/genetics; DNA Methylation/genetics*
  18. Molecular phylogeographic studies on Paragonimus westermani in Asia
    Iwagami M, Ho LY, Su K, Lai PF, Fukushima M, Nakano M, et al.
    J Helminthol, 2000 Dec;74(4):315-22.
    PMID: 11138020
    The lung fluke, Paragonimus westermani (Kerbert, 1878), is widely distributed in Asia, and exhibits much variation in its biological properties. Previous phylogenetic studies using DNA sequences have demonstrated that samples from north-east Asia form a tight group distinct from samples from south Asia (Philippines, Thailand, Malaysia). Among countries from the latter region, considerable molecular diversity was observed. This was investigated further using additional DNA sequences (partial mitochondrial cytochrome c oxidase subunit 1 (COI) and the second internal transcribed spacer of the nuclear ribosomal gene repeat (ITS2)) from additional samples of P. westermani. Phylogenies inferred from these again found three or four groups within P. westermani, depending on the method of analysis. Populations of P. westermani from north-east Asia use snail hosts of the family Pleuroceridae and differ in other biological properties from populations in south Asia (that use snail hosts of the family Thiaridae). It is considered that the populations we sampled can be divided into two species, one in north-east Asia and the other in south Asia.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Helminth/genetics; DNA, Ribosomal Spacer/genetics
  19. Mitochondrial DNA and nuclear DNA indicate that the Japanese Fasciola species is F. gigantica
    Hashimoto K, Watanobe T, Liu CX, Init I, Blair D, Ohnishi S, et al.
    Parasitol Res, 1997;83(3):220-5.
    PMID: 9089716
    For elucidation of the taxonomic status of the Japanese Fasciola species, whole mitochondrial DNA of Fasciola hepatica from Australia, F. gigantica from Malaysia, and Fasciola sp. from Japan was digested with three four-base-cutting endonucleases: HinfI, MspI, and RsaI. The resulting digestion patterns showed that for each enzyme there were some bands specific for each geographical isolate and that the Japanese Fasciola sp. shared more bands with F. gigantica than with F. hepatica. Nucleotide sequences of two regions, the second internal transcribed spacer (ITS2) of the nuclear ribosomal RNA cluster and mitochondrial cytochrome c oxidase subunit I (COI), were also compared among them. The ITS2 sequence was highly conserved among the three isolates. F. gigantica and the Japanese Fasciola sp. were identical, but they differed from the Australian F. hepatica at six sites, one of which was a deletion. The COI sequence was less conserved but implied a similar relationship between the isolates. There seems no reason to regard the Japanese Fasciola sp. as anything other than a strain of F. gigantica.
    Matched MeSH terms: DNA, Mitochondrial*; DNA, Ribosomal*; DNA, Helminth*
  20. Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping
    Nair S, Schreiber E, Thong KL, Pang T, Altwegg M
    J Microbiol Methods, 2000 Jun;41(1):35-43.
    PMID: 10856775
    Amplified fragment length polymorphism (AFLP) is a recently developed, PCR-based high resolution fingerprinting method that is able to generate complex banding patterns which can be used to delineate intraspecific genetic relationships among bacteria. In the present study, AFLP was evaluated for its usefulness in the molecular typing of Salmonella typhi in comparison to ribotyping and pulsed-field gel electrophoresis (PFGE). Six S. typhi isolates from diverse geographic areas (Malaysia, Indonesia, India, Chile, Papua New Guinea and Switzerland) gave unique, heterogeneous profiles when typed by AFLP, a result which was consistent with ribotyping and PFGE analysis. In a further study of selected S. typhi isolates from Papua New Guinea which caused fatal and non-fatal disease previously shown to be clonally related by PFGE, AFLP discriminated between these isolates but did not indicate a linkage between genotype with virulence. We conclude that AFLP (discriminatory index=0.88) has a higher discriminatory power for strain differentiation among S. typhi than ribotyping (DI=0.63) and PFGE (DI=0.74).
    Matched MeSH terms: DNA, Bacterial/analysis; DNA, Ribosomal/analysis; DNA Fingerprinting/methods*
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