Displaying publications 901 - 920 of 3507 in total

Abstract:
Sort:
  1. The complete mitochondrial genome of Bactrocera diaphora (Diptera: Tephtitidae)
    Zhang KJ, Liu L, Rong X, Zhang GH, Liu H, Liu YH
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4314-4315.
    PMID: 26462416
    We sequenced and annotated the complete mitochondrial genome (mitogenome) of Bactrocera diaphora (Diptera: Tephtitidae), which is an economically important pest in the southwest area of China, India, Sri Lanka, Vietnam and Malaysia. This mitogenome is 15 890 bp in length with an A + T content of 74.103%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the inferred ancestral insects. All protein-coding genes (PCGs) start with a typical ATN codon, except cox1 that begins with TCG. Ten PCGs stop with termination codon TAA or TAG, whereas cox1, nad1 and nad5 have single T-- as the incomplete stop codon. All of the transfer RNA genes present the typical clover leaf secondary structure except trnS1 (AGN) with a looping D-arm. The A + T-rich region is located between rrnS and trnI with a length of 946 bp, and contains a 20 bp poly-T stretch and 22 bp poly-A stretch. Except the control region, the longest intergenic spacer is located between trnR and trnN that is 94 bp long with an excessive high A + T content (95.74%) and a microsatellite-like region (TA)13.
    Matched MeSH terms: DNA, Mitochondrial/genetics*; Sequence Analysis, DNA/methods
  2. Modification of gelatin-DNA interaction for optimised DNA extraction from gelatin and gelatin capsule
    Mohamad NA, Mustafa S, El Sheikha AF, Khairil Mokhtar NF, Ismail A, Ali ME
    J Sci Food Agric, 2016 May;96(7):2344-51.
    PMID: 26441285 DOI: 10.1002/jsfa.7482
    Poor quality and quantity of DNA extracted from gelatin and gelatin capsules often causes failure in the determination of animal species using PCR. Gelatin, which is mainly derived from porcine and bovine, has been a matter of concern among customers in order to fulfill religious obligation and safety precaution against several transmissible infectious diseases associated with bovine species. Thus, optimised DNA extraction from gelatin is very important for successful real-time PCR detection of gelatin species. In this work, the DNA extraction method was optimised in terms of lysis incubation period and inclusion of pre-treatment pH modification of samples.
    Matched MeSH terms: DNA
  3. Achieving crop stress tolerance and improvement--an overview of genomic techniques
    Rasool S, Ahmad P, Rehman MU, Arif A, Anjum NA
    Appl Biochem Biotechnol, 2015 Dec;177(7):1395-408.
    PMID: 26440315 DOI: 10.1007/s12010-015-1830-9
    The inexorable exposure of plants to the combinations of abiotic stresses has affected the worldwide food supply. The crop improvement against these abiotic stresses has been captivating approach to increase the yield and enhance the stress tolerance. By using traditional and modern breeding methods, the characters that confer tolerance to these stresses were accomplished. No doubt genetic engineering and molecular breeding have helped in comprehending the intricate nature of stress response. Understanding of abiotic stress-involved cellular pathways provides vital information on such responses. On the other hand, genomic research for crop improvement has raised new assessments in breeding new varieties against abiotic stresses. Interpretation of responses of the crop plants under stress is of great significance by studying the main role of crops in food and biofuel production. This review presents genomic-based approaches revealing the complex networks controlling the mechanisms of abiotic stress tolerance, and the possible modes of assimilating information attained by genomic-based approaches due to the advancement in isolation and functional analysis of genes controlling the yield and abiotic stress tolerance are discussed.
    Matched MeSH terms: DNA Shuffling
  4. Fulltext Mathematical Modelling and Prediction of the Effect of Chemotherapy on Cancer Cells
    Namazi H, Kulish VV, Wong A
    Sci Rep, 2015;5:13583.
    PMID: 26316014 DOI: 10.1038/srep13583
    Cancer is a class of diseases characterized by out-of-control cells' growth which affect DNAs and make them damaged. Many treatment options for cancer exist, with the primary ones including surgery, chemotherapy, radiation therapy, hormonal therapy, targeted therapy and palliative care. Which treatments are used depends on the type, location, and grade of the cancer as well as the person's health and wishes. Chemotherapy is the use of medication (chemicals) to treat disease. More specifically, chemotherapy typically refers to the destruction of cancer cells. Considering the diffusion of drugs in cancer cells and fractality of DNA walks, in this research we worked on modelling and prediction of the effect of chemotherapy on cancer cells using Fractional Diffusion Equation (FDE). The employed methodology is useful not only for analysis of the effect of special drug and cancer considered in this research but can be expanded in case of different drugs and cancers.
    Matched MeSH terms: DNA
  5. Fulltext Visual inspection reveals a novel pathogenic mutation in PKD1 missed by the variant caller in whole‑exome sequencing
    Koay BT, Chiow MY, Ismail J, Fahmy NK, Yee SY, Mustafa N, et al.
    Mol Med Rep, 2022 Dec;26(6).
    PMID: 36281931 DOI: 10.3892/mmr.2022.12882
    Autosomal dominant polycystic kidney disease (ADPKD) is the most common type of inherited cystic kidney disease. The feasibility of whole‑exome sequencing (WES) to obtain molecular diagnosis of ADPKD is still in question as previous studies showed conflicting results. Utilizing WES on a patient with ADPKD, standard bioinformatics pipeline demonstrated no pathogenic variant in the genes of interest. By visualizing read alignments using the Integrative Genomics Viewer, a region with atypical alignment of numerous soft‑clipped reads at exon 45 of polycystin 1, transient receptor potential channel interacting (PKD1) gene was demonstrated. A total of four visual inspection steps were outlined to assess the origin of these soft‑clipped reads as strand bias during capture, poor mapping, sequencing error or DNA template contamination. Following assessment, the atypical alignment at PKD1 was hypothesized to be caused by an insertion/deletion mutation. Sanger sequencing confirmed the presence of a novel 20‑bp insertion in PKD1 (NM_001009944.3; c.12143_12144insTCC​CCG​CAG​TCT​TCC​CCG​CA; p.Val4048LeufsTer157), which introduced a premature stop codon and was predicted to be pathogenic. The present study demonstrated that WES could be utilized as a molecular diagnostic tool for ADPKD. Furthermore, visual inspection of read alignments was key in identifying the pathogenic variant. The proposed visual inspection steps may be incorporated into a typical WES data analysis workflow to improve the diagnostic yield.
    Matched MeSH terms: DNA
  6. Adoption of analytical technologies for verification of authenticity of halal foods - a review
    Kua JM, Azizi MMF, Abdul Talib MA, Lau HY
    Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2022 Dec;39(12):1906-1932.
    PMID: 36252206 DOI: 10.1080/19440049.2022.2134591
    Halal authentication has become essential in the food industry to ensure food is free from any prohibited ingredients according to Islamic law. Diversification of food origin and adulteration issues have raised concerns among Muslim consumers. Therefore, verification of food constituents and their quality is paramount. From conventional methods based on physical and chemical properties, various diagnostic methods have emerged relying on protein or DNA measurements. Protein-based methods that have been used in halal detection including electrophoresis, chromatographic-based methods, molecular spectroscopy and immunoassays. Polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) are DNA-based techniques that possess better accuracy and sensitivity. Biosensors are miniatured devices that operate by converting biochemical signals into a measurable quantity. CRISPR-Cas is one of the latest novel emerging nucleic acid detection tools in halal food analysis as well as quantification of stable isotopes method for identification of animal species. Within this context, this review provides an overview of the various techniques in halal detection along with their advantages and limitations. The future trend and growth of detection technologies are also discussed in this review.
    Matched MeSH terms: DNA
  7. Genotoxicity and apoptotic effect of silver(I) complexes with mixed-ligands of thiosemicarbazones and diphenyl(p-tolyl)phosphine on malignant melanoma cells, SK-MEL-28
    Ooi TC, Nordin FJ, Rahmat NS, Abdul Halim SN', Sarip R, Chan KM, et al.
    Mutat Res Genet Toxicol Environ Mutagen, 2023;886:503581.
    PMID: 36868695 DOI: 10.1016/j.mrgentox.2022.503581
    Complexes of coinage metals can potentially be used as alternatives to platinum-based chemotherapeutic drugs. Silver is a coinage metal that can potentially improve the spectrum of efficacy in various cancers treatment, such as malignant melanoma. Melanoma is the most aggressive form of skin cancer that is often diagnosed in young and middle-aged adults. Silver has high reactivity with skin proteins and can be developed as a malignant melanoma treatment modality. Therefore, this study aims to identify the anti-proliferative and genotoxic effects of silver(I) complexes with mixed-ligands of thiosemicarbazones and diphenyl(p-tolyl)phosphine ligands in the human melanoma SK-MEL-28 cell line. The anti-proliferative effects of a series of silver(I) complex compounds labelled as OHBT, DOHBT, BrOHBT, OHMBT, and BrOHMBT were evaluated on SK-MEL-28 cells by using the Sulforhodamine B assay. Then, DNA damage analysis was performed in a time-dependent manner (30 min, 1 h and 4 h) by using alkaline comet assay to investigate the genotoxicity of OHBT and BrOHMBT at their respective IC50 values. The mode of cell death was studied using Annexin V-FITC/PI flow cytometry assay. Our current findings demonstrated that all silver(I) complex compounds showed good anti-proliferative activity. The IC50 values of OHBT, DOHBT, BrOHBT, OHMBT, and BrOHMBT were 2.38 ± 0.3 μM, 2.70 ± 0.17 μM, 1.34 ± 0.22 μM, 2.82 ± 0.45 μM, and 0.64 ± 0.04 μM respectively. Then, DNA damage analysis showed that OHBT and BrOHMBT could induce DNA strand breaks in a time-dependent manner, with OHBT being more prominent than BrOHMBT. This effect was accompanied by apoptosis induction in SK-MEL-28, as evaluated using Annexin V-FITC/PI assay. In conclusion, silver(I) complexes with mixed-ligands of thiosemicarbazones and diphenyl(p-tolyl)phosphine exerted anti-proliferative activities by inhibiting cancer cell growth, inducing significant DNA damage and ultimately resulting in apoptosis.
    Matched MeSH terms: DNA Damage
  8. Fulltext Using 157Gd doped carbon and 157GdF4 nanoparticles in proton-targeted therapy for effectiveness enhancement and thermal neutron reduction: a simulation study
    Tabbakh F, Hosmane NS, Tajudin SM, Ghorashi AH, Morshedian N
    Sci Rep, 2022 Oct 18;12(1):17404.
    PMID: 36258012 DOI: 10.1038/s41598-022-22429-0
    There are two major problems in proton therapy. (1) In comparison with the gamma-ray therapy, proton therapy has only ~ 10% greater biological effectiveness, and (2) the risk of the secondary neutrons in proton therapy is another unsolved problem. In this report, the increase of biological effectiveness in proton therapy has been evaluated with better performance than 11B in the presence of two proposed nanomaterials of 157GdF4 and 157Gd doped carbon with the thermal neutron reduction due to the presence of 157Gd isotope. The present study is based on the microanalysis calculations using GEANT4 Monte Carlo tool and GEANT4-DNA package for the strand breaks measurement. It was found that the proposed method will increase the effectiveness corresponding to the alpha particles by more than 100% and also, potentially will decrease the thermal neutrons fluence, significantly. Also, in this work, a discussion is presented on a significant contribution of the secondary alpha particles in total effectiveness in proton therapy.
    Matched MeSH terms: DNA
  9. Fulltext Chromosome-level genome assembly of the silver pomfret Pampus argenteus
    Wei J, Xiao Y, Liu J, Herrera-Ulloa A, Loh KH, Xu K
    Sci Data, 2024 Feb 23;11(1):234.
    PMID: 38395996 DOI: 10.1038/s41597-024-03070-0
    Pampus argenteus (Euphrasen, 1788) is one of the major fishery species in coastal China. Pampus argenteus has a highly specialized morphology, and its declining fishery resources have encouraged massive research efforts on its aquacultural biology. In this study, we reported the first high-quality chromosome-level genome of P. argenteus obtained by integrating Illumina, PacBio HiFi, and Hi-C sequencing techniques. The final size of the genome was 518.06 Mb, with contig and scaffold N50 values of 20.47 and 22.86 Mb, respectively. The sequences were anchored and oriented onto 24 pseudochromosomes based on Hi-C data corresponding to the 24-chromatid karyotype of P. argenteus. A colinear relationship was observed between the P. argenteus genome and that of a closely related species (Scomber japonicus). A total of 24,696 protein-coding genes were identified from the genome, 98.9% of which were complete BUSCOs. This report represents the first case of high-quality chromosome-level genome assembly for P. argenteus and can provide valuable information for future evolutionary, conservation, and aquacultural research.
    Matched MeSH terms: Sequence Analysis, DNA
  10. Revisiting the gene mutations and protein profile of WT 9-12: An autosomal dominant polycystic kidney disease cell line
    Chai HC, Mahendran R, Ong KC, Chua KH
    Genes Cells, 2024 Jul;29(7):599-607.
    PMID: 38782708 DOI: 10.1111/gtc.13129
    WT 9-12 is one of the cell lines commonly used for autosomal dominant polycystic kidney disease (ADPKD) studies. Previous studies had described the PKD gene mutations and polycystin expression in WT 9-12. Nonetheless, the mutations occurring in other ADPKD-associated genes have not been investigated. This study aims to revisit these mutations and protein profile of WT 9-12. Whole genome sequencing verified the presence of truncation mutation at amino acid 2556 (Q2556X) in PKD1 gene of WT 9-12. Besides, those variations with high impacts included single nucleotide polymorphisms (rs8054182, rs117006360, and rs12925771) and insertions and deletions (InDels) (rs145602984 and rs55980345) in PKD1L2; InDel (rs1296698195) in PKD1L3; and copy number variations in GANAB. Protein profiles generated from the total proteins of WT 9-12 and HK-2 cells were compared using isobaric tags for relative and absolute quantitation (iTRAQ) analysis. Polycystin-1 was absent in WT 9-12. The gene ontology enrichment and reactome pathway analyses revealed that the upregulated and downregulated proteins of WT 9-12 relative to HK-2 cell line leaded to signaling pathways related to immune response and amino acid metabolism, respectively. The ADPKD-related mutations and signaling pathways associated with differentially expressed proteins in WT 9-12 may help researchers in cell line selection for their studies.
    Matched MeSH terms: DNA Copy Number Variations
  11. A systematic review on current approaches in bat virus discovered between 2018 and 2022
    Mo Y, Lim LS, Ng SK
    J Virol Methods, 2024 Sep;329:115005.
    PMID: 39128772 DOI: 10.1016/j.jviromet.2024.115005
    Zoonotic viruses are widely seen as the primary threat for future pandemics. Bats are the most diverse group of mammals, with more than 1400 species distributed across most habitats on Earth. So far, 31 known virus families were associated with bats, although the understanding of most viruses were insufficient. Continuous efforts to discover, understand and monitor these bats viruses, is thereby an area of public health interest. This systematic review was designed to catalogue publications reporting novel bat virus discoveries within PubMed, SCOPUS, and Web of Science databases, within a 5-year period from 2018 to 2022. Various experimental parameters, including sampling locations, methodology, bat species diversity, similarity to known viruses, species demarcation of new viruses, and genomic sequencing strategies, were extracted from 41 publications and analyzed. In total, 72 novel viruses from 19 virus families were identified between 2018 and 2022, particularly from Genomoviridae (DNA viruses) and Coronaviridae (RNA viruses). That said, only a limited number of bat families featured extensively despite noticeable shift towards next generation sequencing methods and metagenomics pipeline for virus identification across different sampling methods. This review aims to provide a comprehensive analysis of the global efforts made over the past five years to identify and characterize emerging viruses in bat species, and to provide a detailed overview of the current technologies and methodologies used in these studies.
    Matched MeSH terms: DNA Viruses/classification; DNA Viruses/genetics; DNA Viruses/isolation & purification
  12. Genetic characterization of Giardia duodenalis in wild rats in China: Identification of a divergent lineage lineage within Assemblage B
    Yin C, Zhou YL, Shu M, Liu X, Chen GL
    Trop Biomed, 2026 Sep 01;43(3):359-362.
    PMID: 42960656 DOI: 10.47665/tb.43.3.016
    Giardia duodenalisis a zoonotic intestinal protozoan parasite that causes gastrointestinal disease in both humans and a wide range of animals. This study investigated the prevalence and genetic diversity of G. duodenalisin wild rats in China to assess the potential role of these wild rats in zoonotic transmission. Fecal samples were collected from 228 wild rats in Chongqing Municipality and Guangdong Province. The parasite was detected and characterized by nested PCR amplification, sequencing, and phylogenetic analysis of the b-giardin (bg), glutamate dehydrogenase (gdh), and triosephosphate isomerase (tpi) genes. A distinct genetic lineage of G. duodenalis Assemblage B was identified in wild rats, with an overall prevalence of 6.6%. Phylogenetic analysis revealed that these isolates formed a unique, strongly supported clade within Assemblage B, showing significant genetic divergence from previously documented subtypes. No other assemblages were detected in this study. These findings highlight the presence of a divergent lineage G. duodenalis lineage in wild rats and underscore the need for further research to determine the prevalence and molecular detection status and genetic diversity of this parasite in rodent populations across China.
    Matched MeSH terms: DNA, Protozoan/genetics; DNA, Protozoan/chemistry; Sequence Analysis, DNA
  13. Fulltext Definition of Mafa-A and -B haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis)
    Otting N, Doxiadis GG, Bontrop RE
    Immunogenetics, 2009 Dec;61(11-12):745-53.
    PMID: 19937015 DOI: 10.1007/s00251-009-0412-9
    The major histocompatibility complex (MHC) class I B gene/allelic repertoire was investigated in a pedigreed population of cynomolgus macaques of mixed Indonesian/Malaysian origin. The Mafa-B alleles detected in this cohort are mostly specific for a given geographic area, and only a small number of alleles appears to be shared with other populations. This suggests the fast evolution of Mafa-B alleles due to adaptation to new environments. In contrast to humans, the B locus in Old World monkeys displays extensive copy number variation. The Mafa-B and previously defined -A gene combinations segregate in families and thus allowed the definition of extended haplotypes. In many cases it was possible to assign a particular Mafa-I allele to one of these Mafa-A/B haplotypes as well. The presence of a large number of stable haplotypes in this cohort of animals, which was pedigreed for up to eight generations, looks promising for developing discriminative MHC typing tools that are less cumbersome. Furthermore, the discovery of 53 unreported Mafa-B sequences expands the lexicon of alleles significantly, and may help in understanding the complex organisation of the macaque B region.
    Matched MeSH terms: Sequence Analysis, DNA; DNA, Complementary/genetics; DNA, Complementary/chemistry
  14. Genetic diversity in the C-terminus of merozoite surface protein 1 among Plasmodium knowlesi isolates from Selangor and Sabah Borneo, Malaysia
    Yap NJ, Goh XT, Koehler AV, William T, Yeo TW, Vythilingam I, et al.
    Infect Genet Evol, 2017 10;54:39-46.
    PMID: 28634105 DOI: 10.1016/j.meegid.2017.06.019
    Plasmodium knowlesi, a malaria parasite of macaques, has emerged as an important parasite of humans. Despite the significance of P. knowlesi malaria in parts of Southeast Asia, very little is known about the genetic variation in this parasite. Our aim here was to explore sequence variation in a molecule called the 42kDa merozoite surface protein-1 (MSP-1), which is found on the surface of blood stages of Plasmodium spp. and plays a key role in erythrocyte invasion. Several studies of P. falciparum have reported that the C-terminus (a 42kDa fragment) of merozoite surface protein-1 (MSP-142; consisting of MSP-119 and MSP-133) is a potential candidate for a malaria vaccine. However, to date, no study has yet investigated the sequence diversity of the gene encoding P. knowlesi MSP-142 (comprising Pk-msp-119 and Pk-msp-133) among isolates in Malaysia. The present study explored this aspect. Twelve P. knowlesi isolates were collected from patients from hospitals in Selangor and Sabah Borneo, Malaysia, between 2012 and 2014. The Pk-msp-142 gene was amplified by PCR and directly sequenced. Haplotype diversity (Hd) and nucleotide diversity (л) were studied among the isolates. There was relatively high genetic variation among P. knowlesi isolates; overall Hd and л were 1±0.034 and 0.01132±0.00124, respectively. A total of nine different haplotypes related to amino acid alterations at 13 positions, and the Pk-MSP-119 sequence was found to be more conserved than Pk-msp-133. We have found evidence for negative selection in Pk-msp-42 as well as the 33kDa and 19kDa fragments by comparing the rate of non-synonymous versus synonymous substitutions. Future investigations should study large numbers of samples from disparate geographical locations to critically assess whether this molecule might be a potential vaccine target for P. knowlesi.
    Matched MeSH terms: DNA, Protozoan/genetics; Sequence Analysis, DNA
  15. Fulltext Rapid Detection of Plasmodium knowlesi by Isothermal Recombinase Polymerase Amplification Assay
    Lai MY, Ooi CH, Lau YL
    Am J Trop Med Hyg, 2017 Nov;97(5):1597-1599.
    PMID: 28820700 DOI: 10.4269/ajtmh.17-0427
    In this study, we developed a recombinase polymerase amplification (RPA) assay for specific diagnosis of Plasmodium knowlesi. Genomic DNA was extracted from whole blood samples using a commercial kit. With incubation at 37°C, the samples were successfully amplified within 20 minutes. The end product of RPA was further examined by loading onto agarose gel and a specific band was observed with a size of 128 bp. The RPA assay exhibited high sensitivity with limits of detection down to one copy of the plasmid. From the specificity experiments, it was demonstrated that all P. knowlesi samples (N = 45) were positive while other Plasmodium spp. (N = 42) and negative samples (N = 6) were negative. Therefore, the RPA assay is a highly promising approach with the potential to be used in resource-limited settings. This assay can be further optimized for bedside and on field application.
    Matched MeSH terms: DNA, Protozoan/blood; DNA, Protozoan/isolation & purification*
  16. Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan
    Amin AKMR, Tanaka M, Al-Saari N, Feng G, Mino S, Ogura Y, et al.
    Syst Appl Microbiol, 2017 Jul;40(5):290-296.
    PMID: 28648725 DOI: 10.1016/j.syapm.2017.04.003
    Two phylogenetically distinct Vibrionaceae strains C4II189Tand C4V358Tisolated from reef seawater off Ishigaki Island, Japan, in 2014 were studied with advanced genome-based taxonomy approaches. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and the number of core genes) cohesions between the two identified species were high enough to propose them as members of a new genus within the family Vibrionaceae. Consequently, an eighth genus Thaumasiovibrio gen. nov. is proposed that contains two new species Thaumasiovibrio occultus sp. nov. strain C4II189T(=DSM 101554T=JCM 31629T) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358T(=DSM 101555T=JCM 31630T). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent O/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus.
    Matched MeSH terms: DNA, Bacterial/genetics; Sequence Analysis, DNA
  17. Fulltext Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax
    Beck SV, Carvalho GR, Barlow A, Rüber L, Hui Tan H, Nugroho E, et al.
    PLoS One, 2017;12(7):e0179557.
    PMID: 28742862 DOI: 10.1371/journal.pone.0179557
    The complex climatic and geological history of Southeast Asia has shaped this region's high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.
    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA
  18. Taxonomic assignment of the benthic toxigenic dinoflagellate Gambierdiscus sp. type 6 as Gambierdiscus balechii (Dinophyceae), including its distribution and ciguatoxicity
    Dai X, Mak YL, Lu CK, Mei HH, Wu JJ, Lee WH, et al.
    Harmful Algae, 2017 07;67:107-118.
    PMID: 28755713 DOI: 10.1016/j.hal.2017.07.002
    Recent molecular phylogenetic studies of Gambierdiscus species flagged several new species and genotypes, thus leading to revitalizing its systematics. The inter-relationships of clades revealed by the primary sequence information of nuclear ribosomal genes (rDNA), however, can sometimes be equivocal, and therefore, in this study, the taxonomic status of a ribotype, Gambierdiscus sp. type 6, was evaluated using specimens collected from the original locality, Marakei Island, Republic of Kiribati; and specimens found in Rawa Island, Peninsular Malaysia, were further used for comparison. Morphologically, the ribotype cells resembled G. scabrosus, G. belizeanus, G. balechii, G. cheloniae and G. lapillus in thecal ornamentation, where the thecal surfaces are reticulate-foveated, but differed from G. scabrosus by its hatchet-shaped Plate 2', and G. belizeanus by the asymmetrical Plate 3'. To identify the phylogenetic relationship of this ribotype, a large dataset of the large subunit (LSU) and small subunit (SSU) rDNAs were compiled, and performed comprehensive analyses, using Bayesian-inference, maximum-parsimony, and maximum-likelihood, for the latter two incorporating the sequence-structure information of the SSU rDNA. Both the LSU and SSU rDNA phylogenetic trees displayed an identical topology and supported the hypothesis that the relationship between Gambierdiscus sp. type 6 and G. balechii was monophyletic. As a result, the taxonomic status of Gambierdiscus sp. type 6 was revised, and assigned as Gambierdiscus balechii. Toxicity analysis using neuroblastoma N2A assay confirmed that the Central Pacific strains were toxic, ranging from 1.1 to 19.9 fg P-CTX-1 eq cell-1, but no toxicity was detected in a Western Pacific strain. This suggested that the species might be one of the species contributing to the high incidence rate of ciguatera fish poisoning in Marakei Island.
    Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Ribosomal/chemistry
  19. Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide
    Balakrishnan KN, Abdullah AA, Bala J, Abba Y, Sarah SA, Jesse FFA, et al.
    Infect Genet Evol, 2017 10;54:81-90.
    PMID: 28642159 DOI: 10.1016/j.meegid.2017.06.020
    BACKGROUND: Rat cytomegalovirus ALL-03 (Malaysian strain) which was isolated from a placenta and uterus of a house rat, Rattus rattus diardii has the ability to cross the placenta and infecting the fetus. To further elucidate the pathogenesis of the Malaysian strain of Rat Cytomegalovirus ALL-03 (RCMV ALL-03), detailed analysis on the viral genome sequence is crucial.

    METHODS: Genome sequencing of RCMV ALL-03 was carried out in order to identify the open reading frame (ORF), homology comparison of ORF with other strains of CMV, phylogenetic analysis, classifying ORF with its corresponding conserved genes, and determination of functional proteins and grouping of gene families in order to obtain fundamental knowledge of the genome.

    RESULTS: The present study revealed a total of 123 Coding DNA sequences (CDS) from RCMV ALL-03 with 37 conserved ORF domains as with all herpesvirus genomes. All the CDS possess similar function with RCMV-England followed by RCMV-Berlin, RCMV-Maastricht, and Human CMV. The phylogenetic analysis of RCMV ALL-03 based on conserving genes of herpes virus showed that the Malaysian RCMV isolate is closest to RCMV-English and RCMV-Berlin strains, with 99% and 97% homology, respectively. Similarly, it also demonstrated an evolutionary relationship between RCMV ALL-03 and other strains of herpesviruses from all the three subfamilies. Interestingly, betaherpesvirus subfamily, which has been shown to be more closely related with gammaherpesviruses as compared to alphaherpesviruses, shares some of the functional ORFs. In addition, the arrangement of gene blocks for RCMV ALL-03, which was conserved among herpesvirus family members was also observed in the RCMV ALL-03 genome.

    CONCLUSION: Genomic analysis of RCMV ALL-03 provided an overall picture of the whole genome organization and it served as a good platform for further understanding on the divergence in the family of Herpesviridae.

    Matched MeSH terms: DNA, Viral/genetics; Sequence Analysis, DNA
  20. DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods
    Ayoib A, Hashim U, Gopinath SCB, Md Arshad MK
    Appl Microbiol Biotechnol, 2017 Nov;101(22):8077-8088.
    PMID: 28942548 DOI: 10.1007/s00253-017-8493-0
    This review covers a developmental progression on early to modern taxonomy at cellular level following the advent of electron microscopy and the advancement in deoxyribonucleic acid (DNA) extraction for expatiation of biological classification at DNA level. Here, we discuss the fundamental values of conventional chemical methods of DNA extraction using liquid/liquid extraction (LLE) followed by development of solid-phase extraction (SPE) methods, as well as recent advances in microfluidics device-based system for DNA extraction on-chip. We also discuss the importance of DNA extraction as well as the advantages over conventional chemical methods, and how Lab-on-a-Chip (LOC) system plays a crucial role for the future achievements.
    Matched MeSH terms: DNA/genetics; DNA/isolation & purification*
Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links