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  1. Newly developed mRNA vaccines induce immune responses in Litopenaeus vannamei shrimps during primary vaccination
    See SA, Bhassu S, Tang SS, Yusoff K
    Dev Comp Immunol, 2025 Jan;162:105264.
    PMID: 39299363 DOI: 10.1016/j.dci.2024.105264
    White spot syndrome virus (WSSV) causes highly destructive infection in crustacean aquaculture, often resulting in 100% mortality within a week. However, there is lack of studies addressing the safety issues of WSSV vaccines in shrimps. In this study, WSSV VP28 mRNA vaccines were developed using codon deoptimization approach. These vaccines were administered to Litopenaeus vannamei shrimps at various dosages to access their safety and the shrimps' immune responses using quantification PCR (qPCR). The findings of this study indicate that the expression level of codon deoptimized VP28 mRNA vaccines are lower compared to the wild type VP28 vaccines, as observed through a comparison of bioinformatic predictions and experimental results. Additionally, the total haemocyte count (THC) in shrimps injected with codon deoptimized VP28 vaccine was higher than those injected with wild type VP28 vaccines. Furthermore, the expression of immune-related genes differed between codon deoptimized and wild type VP28 vaccines. In summary, the results suggest that 0.01 μg codon deoptimized VP28-D1 mRNA vaccine is the most promising WSSV mRNA vaccine, displaying low pathogenicity and expression in shrimps. To the best of our knowledge, this research represents the first attempt to attenuate WSSV using codon deoptimization method and development of a potential mRNA vaccine for shrimp purpose. The study addresses an important gap in shrimp vaccine research, offering potential solutions for WSSV control in shrimps.
    Matched MeSH terms: DNA Virus Infections/immunology
  2. Intraspecific genetic diversity with unrestricted gene flow in the domoic acid-producing diatom Nitzschia navis-varingica (Bacillariophyceae) from the Western Pacific
    Tan SN, Kotaki Y, Teng ST, Lim HC, Gao C, Lundholm N, et al.
    Harmful Algae, 2025 Jan;141:102769.
    PMID: 39645396 DOI: 10.1016/j.hal.2024.102769
    The benthic pennate diatom Nitzschia navis-varingica, known for producing domoic acid (DA) and its isomers, is widely distributed in the Western Pacific (WP) region. To investigate the genetic differentiation and gene flow patterns among the populations in the WP, the genetic diversity of 354 strains of N. navis-varingica was analysed using two nuclear-encoded rDNA loci: the large subunit rDNA (LSU rDNA) and the internal transcribed spacer 2 (ITS2). Frustule morphology of each strain was examined by TEM. The LSU rDNA phylogeny revealed a monophyletic lineage encompassing all strains, with sequence divergences of <0.9 %. Phylogenetic and population genetic analyses of ITS2 identified eight distinct clades (designated as Groups A to H) with moderate to high genetic heterogeneity (0.5-19.7 %). The low genetic differentiations between the geographically separated populations (pairwise FST of <0.03) suggested high gene flow and lack of spatial genetic structuring. Molecular clock analysis of the ITS2 phylogeny traced the evolutionary history of N. navis-varingica to the Eocene Epoch, and the split between clades likely occurred from the mid-Miocene to Pleistocene Epochs (10.8-1.2 Ma). The population dispersal in the WP were likely influenced by historical events like the Quarternary glacial cycles during the period, contributing to its homogenous distributions in the region.
    Matched MeSH terms: DNA, Ribosomal/genetics
  3. Ancient DNA analysis of elite nomadic warrior from Chinge-Tey I funerary commemorative complex in the "Valley of the Kings", Tuva
    Nedoluzhko A, Vergasova E, Sharko F, Agapitova N, Kharitonov D, Sukhanova X, et al.
    BMC Genomics, 2025 Mar 05;26(1):220.
    PMID: 40045199 DOI: 10.1186/s12864-025-11361-y
    BACKGROUND: In the Ist millennium BC bearers of the Scythian-type nomadic cultures inhabited the steppes of Eurasia, from Northern China to the Carpathians. According to archaeological data, the origin of nomadic life style and economy can be traced to the eastern part of this steppe "corridor", primarily to the territory of the present-day Republic of Tuva in Russia. Here, in the Turan-Uyuk Basin, also known as the "Valley of the Kings", some of the earliest known Scythian-type archaeological sites called Arzhan-1, Arzhan-2, Chinge-Tey I, Tunnug 1 were studied. Each of them is a large-scale funerary commemorative complex with burials of tribal nomadic leaders, surrounded by graves of supposed members of their families or associates. All these people belonged to the societies which are associated with the earliest nomadic cultures in Asia. Representatives of similar cultures will later be known and described as the Scythians/the Saka in Assyrian, Achaemenid, and Greek sources. Arzhan 2 and Chinge-Tey I elite level sites as well as ordinary pastoralist burials of the early-Scythian period in Tuva are attributed to the Aldy-Bel archaeological culture of the Early Iron Age (8th- 6th century BC). Taking the first step to shed light on the genetic origin of Aldy-Bel elites, we carried out a comparative genome-wide analysis of an elite level person buried in grave 9 at Chinge-Tey I (7th- 6th centuries BC) and two published earlier genomes of individuals, whose burials (graves 14 and 22) accompanied the 'royal couple' (grave 5) at Arzhan-2. This study aims also at checking a hypothesis of genetic kinship between human individuals buried in the large-scale burial complexes of the "Valley of the Kings" and brings up the issue of possible dynastic connections of local elites, buried under different kurgans of the valley.

    RESULTS: First, ancient DNA analysis of an elite nomadic warrior from Chinge-Tey I has been carried out, thus a third wide-genome dataset for Aldy-Bel culture- one of the earliest nomadic cultures in Asia, is presented in this study. Second, we undertook a comparative analysis of genome-wide data of three mentioned Aldy-Bel culture representatives and individuals of the other Bronze and Early Iron Age population groups of Asia to estimate their possible genetic connections. Then, kinship analysis was undertaken for these three Aldy-Bel culture individuals. Finally, mitochondrial and Y-chromosome haplogroups of Chinge-Tey princely person were compared to those of other Aldy-Bel culture representatives and to individuals of subsequent Scythian-type Uyuk-Sagly culture in Tuva.

    CONCLUSION: (1) Generating the third wide-genome of the enabled us to undertake its comparison with two other genomes of Aldy-Bel culture representatives (Arzhan-2, graves 14 and 22) and with other Bronze and Early Iron Age population groups in Asia to trace the origin and genetic connection of Aldy-Bel population, representing one of the earliest Scythian-type nomadic group. (2) The results obtained show that the princely individual from Chinge-Tey I and two 'king's associates' from Arzhan-2 were genetically close to nomads of simultaneous Tasmola culture in Eastern and Central Kazakhstan and pastoralists buried in the Early Iron Age cemeteries of present-day Xinjiang (first of all, Abusanteer archaeological site). Aldy-Bel culture representatives appeared also close to individuals of the Middle Bronze Age Okunevo culture in the Minusinsk Basin. Besides, Aldy-Bel pastoralists turned out genetically close to nomads of the subsequent Uyuk-Sagly culture in Mongolia (5th - 3rd centuries BC). (3) Ancient DNA kinship analyses, undertaken for three Aldy-Bel culture individuals pointed out to the absence of their tribe kinship. (4) On the other hand, Chinge-Tey warrior's mitochondrial haplogroup G was previously described in two (graves 14 and 5) individuals from Arzhan-2, including a female individual from the "royal" tomb 5. This result provided a possibility of maternal kinship among this so called 'queen' from Arzhan-2 and the princely person from Chinge-Tey I. This possibility supported a hypothesis of their family ties suggested on archaeological materials. Y-chromosome haplogroup Q1b1, revealed for the princely person, was widely distributed among local people of Aldy-Bel and subsequent Uyuk-Sagly cultures.

    Matched MeSH terms: DNA, Mitochondrial/genetics
  4. Mitochondrial Replacement Therapy: An Islamic Perspective
    Ibrahim AH, Rahman NNA, Saifuddeen SM
    J Bioeth Inq, 2023 Sep;20(3):485-495.
    PMID: 37440155 DOI: 10.1007/s11673-023-10279-y
    Mitochondrial replacement technology (MRT) is an emerging and complex bioethical issue. This treatment aims to eliminate maternal inherited mitochondrial DNA (mtDNA) disorders. For Muslims, its introduction affects every aspect of human life, especially the five essential interests of human beings-namely, religion, life, lineage, intellect, and property. Thus, this technology must be assessed using a comprehensive and holistic approach addressing these human essential interests. Consequently, this article analyses and assesses tri-parent baby technology from the perspective of Maqasidic bioethics-that is, Islamic bioethics based on the framework of Maqasid al-Shariah. Using this analysis, this article suggests that tri-parent baby technology should not be permitted for Muslims due to the existence of third-party cell gametes which lead to lineage mixing and due to the uncertain safety of the therapy itself and because the major aim of the technology is to fulfil the affected couples interest to conceive their own genetically healthy child, not to treat and cure mtDNA disorders sufferers.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  5. Unraveling Bacterial Single-Stranded Sequence Specificities: Insights from Molecular Dynamics and MMPBSA Analysis of Oligonucleotide Probes
    Pirojsirikul T, Lee VS, Nimmanpipug P
    Mol Biotechnol, 2024 Apr;66(4):582-591.
    PMID: 38374320 DOI: 10.1007/s12033-024-01082-0
    We utilized molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) free energy calculations to investigate the specificity of two oligonucleotide probes, namely probe B and probe D, in detecting single-stranded DNA (ssDNA) within three bacteria families: Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. Due to the limited understanding of molecular mechanisms in the previous research, we have extended the discussion to focus specifically on investigating the binding process of bacteria-probe DNA duplexes, with an emphasis on analyzing the binding free energy. The role of electrostatic contributions in the specificity between the oligonucleotide probes and the bacterial ssDNAs was investigated and found to be crucial. Our calculations yielded results that were highly consistent with the experimental data. Through our study, we have successfully exhibited the benefits of utilizing in-silico approaches as a powerful virtual-screening tool, particularly in research areas that demand a thorough comprehension of molecular interactions.
    Matched MeSH terms: DNA, Bacterial/genetics
  6. Characterization and Genomic Analysis of a Lytic Vibriophage vB_VneS_S3 of Infecting Vibrio neocaledonicus
    Yang Q, Sun S, Shao H, Su Y, Wang N, Chen X, et al.
    Curr Microbiol, 2025 Apr 19;82(6):251.
    PMID: 40252093 DOI: 10.1007/s00284-025-04239-5
    Vibrio is a prevalent marine bacteria, distinguished by their remarkable genomic flexibility. Although Vibrio neocaledonicus is well known for effectively inhibiting carbon steel corrosion, nothing is known about its viruses. This study identified a new lytic vibriophage vB_VneS_S3. Transmission electron microscopy analysis showed that vB_VneS_S3 is a siphoviral morphology with an icosahedral head and long non-contractile tail. It is a linear, dsDNA with a length of 76,083 bp and a G + C content of 48.97%, encodes 101 ORFs. Average nucleotide sequence identification and phylogenetic analysis demonstrated that phage vB_VneS_S3 is a new species within the genus of Mardecavirus. Biogeographic analysis revealed that vB_VneS_S3 was exclusively identified in the Arctic, where it exhibited low abundance. In conclusion, our results provided basic information about the interaction between V. neocaledonicus and viruses, increased our knowledge of phylogenetic diversity, genomic characteristics, and distribution of the novel phage.
    Matched MeSH terms: DNA, Viral/genetics
  7. Fulltext Nanoparticle-Encapsulated Camptothecin: Epigenetic Modulation in DNA Repair Mechanisms in Colon Cancer Cells
    Farhana A, Koh AE, Tong JB, Alsrhani A, Kumar Subbiah S, Mok PL
    Molecules, 2021 Sep 06;26(17).
    PMID: 34500845 DOI: 10.3390/molecules26175414
    Molecular crosstalk between the cellular epigenome and genome converge as a synergistic driver of oncogenic transformations. Besides other pathways, epigenetic regulatory circuits exert their effect towards cancer progression through the induction of DNA repair deficiencies. We explored this mechanism using a camptothecin encapsulated in β-cyclodextrin-EDTA-Fe3O4 nanoparticles (CPT-CEF)-treated HT29 cells model. We previously demonstrated that CPT-CEF treatment of HT29 cells effectively induces apoptosis and cell cycle arrest, stalling cancer progression. A comparative transcriptome analysis of CPT-CEF-treated versus untreated HT29 cells indicated that genes controlling mismatch repair, base excision repair, and homologues recombination were downregulated in these cancer cells. Our study demonstrated that treatment with CPT-CEF alleviated this repression. We observed that CPT-CEF exerts its effect by possibly affecting the DNA repair mechanism through epigenetic modulation involving genes of HMGB1, APEX1, and POLE3. Hence, we propose that CPT-CEF could be a DNA repair modulator that harnesses the cell's epigenomic plasticity to amend DNA repair deficiencies in cancer cells.
    Matched MeSH terms: DNA Polymerase III/genetics; DNA Polymerase III/metabolism; DNA Repair/drug effects*; DNA-Binding Proteins/genetics; DNA-Binding Proteins/metabolism
  8. Metagenomics profiling for assessing microbial diversity in both active and closed landfills
    Zainun MY, Simarani K
    Sci Total Environ, 2018 Mar;616-617:269-278.
    PMID: 29117585 DOI: 10.1016/j.scitotenv.2017.10.266
    The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×107 and 1.50×107, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.
    Matched MeSH terms: DNA, Bacterial/isolation & purification; DNA, Archaeal/isolation & purification
  9. The complete mitochondrial genome of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae)
    Shen KN, Loh KH, Chen CH, Hsiao CD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4122-4123.
    PMID: 25585497
    In this study, the complete mitogenome sequence of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,533 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Blue-face angelfish is 28.7% for A, 28.9% for C, 15.9% for G, 26.6% for T and show 84% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Blue-face angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA/methods
  10. Enhanced DNA double-strand break repair of microbeam targeted A549 lung carcinoma cells by adjacent WI38 normal lung fibroblast cells via bi-directional signaling
    Kobayashi A, Tengku Ahmad TAF, Autsavapromporn N, Oikawa M, Homma-Takeda S, Furusawa Y, et al.
    Mutat Res, 2017 10;803-805:1-8.
    PMID: 28689138 DOI: 10.1016/j.mrfmmm.2017.06.006
    Understanding the mechanisms underlying the radiation-induced bystander effect (RIBE) and bi-directional signaling between irradiated carcinoma cells and their surrounding non-irradiated normal cells is relevant to cancer radiotherapy. The present study investigated propagation of RIBE signals between human lung carcinoma A549 cells and normal lung fibroblast WI38 cells in bystander cells, either directly or indirectly contacting irradiated A549 cells. We prepared A549-GFP/WI38 co-cultures and A549-GFP/A549 co-cultures, in which A549-GFP cells stably expressing H2BGFP were co-cultured with either A549 cells or WI38 cells, respectively. Using the SPICE-NIRS microbeam, only the A549-GFP cells were irradiated with 500 protons per cell. The level of γ-H2AX, a marker for DNA double-strand breaks (DSB), was subsequently measured for up to 24h post-irradiation in three categories of cells: (1) "targeted"/irradiated A549-GFP cells; (2) "neighboring"/non-irradiated cells directly contacting the "targeted" cells; and (3) "distant"/non-irradiated cells, which were not in direct contact with the "targeted" cells. We found that DSB repair in targeted A549-GFP cells was enhanced by co-cultured WI38 cells. The bystander response in A549-GFP/A549 cell co-cultures, as marked by γ-H2AX levels at 8h post-irradiation, showed a decrease to non-irradiated control level when approaching 24h, while the neighboring/distant bystander WI38 cells in A549-GFP/WI38 co-cultures was maintained at a similar level until 24h post-irradiation. Surprisingly, distant A549-GFP cells in A549-GFP/WI38 co-cultures showed time dependency similar to bystander WI38 cells, but not to distant cells in A549-GFP/A549 co-cultures. These observations indicate that γ-H2AX was induced in WI38 cells as a result of RIBE. WI38 cells were not only involved in rescue of targeted A549, but also in the modification of RIBE against distant A549-GFP cells. The present results demonstrate that radiation-induced bi-directional signaling had extended a profound influence on cellular sensitivity to radiation as well as the sensitivity to RIBE.
    Matched MeSH terms: DNA Repair*; DNA Breaks, Double-Stranded*
  11. Fulltext A new species group in the genus Dichaetophora, with descriptions of six new species from the Oriental region (Diptera, Drosophilidae)
    Yang JH, Toda MJ, Suwito A, Hashim R, Gao JJ
    Zookeys, 2017.
    PMID: 28769630 DOI: 10.3897/zookeys.665.11609
    The genus Dichaetophora Duda comprises 61 described species classified into four species groups: agbo, tenuicauda, acutissima and sinensis. This genus is distributed exclusively in the Old World, and is rich in species in the tropical and subtropical areas of the Oriental, Australasian, and Afrotropical regions. In this paper, a new species group, the trilobita group, is established for six new species discovered from the Oriental region. The delimitation of these species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI and COII (cytochrome c oxydase, subunits I and II, respectively) genes, considering also their respective geographical origins. Then, the new species (trilobita Yang & Gao, sp. n., heterochroma Yang & Gao, sp. n., flatosternata Yang & Gao, sp. n., borneoensis Yang & Gao, sp. n., javaensis Yang & Gao, sp. n., and sumatraensis Yang & Gao, sp. n.) are described, and a key, based on not only morphological but also molecular information, is provided.
    Matched MeSH terms: DNA
  12. Fulltext Fructose-1,6-bisphosphatase deficiency as a cause of recurrent hypoglycemia and metabolic acidosis: Clinical and molecular findings in Malaysian patients
    Moey LH, Abdul Azize NA, Yakob Y, Leong HY, Keng WT, Chen BC, et al.
    Pediatr Neonatol, 2018 08;59(4):397-403.
    PMID: 29203193 DOI: 10.1016/j.pedneo.2017.11.006
    BACKGROUND: Fructose-1,6-bisphosphatase (FBPase) deficiency is a rare autosomal recessive inborn error of gluconeogenesis. We reported the clinical findings and molecular genetic data in seven Malaysian patients with FBPase deficiency.

    METHODS: All patients diagnosed with FBPase deficiency from 2010 to 2015 were included in this study. Their clinical and laboratory data were collected retrospectively.

    RESULTS: All the patients presented with recurrent episodes of hypoglycemia, metabolic acidosis, hyperlactacidemia and hepatomegaly. All of them had the first metabolic decompensation prior to 2 years old. The common triggering factors were vomiting and infection. Biallelic mutations in FBP1 gene (MIM*611570) were identified in all seven patients confirming the diagnosis of FBPase deficiency. In four patients, genetic study was prompted by detection of glycerol or glycerol-3-phosphate in urine organic acids analysis. One patient also had pseudo-hypertriglyceridemia. Seven different mutations were identified in FBP1, among them four mutations were new: three point deletions (c.392delT, c.603delG and c.704delC) and one splice site mutation (c.568-2A > C). All four new mutations were predicted to be damaging by in silico analysis. One patient presented in the neonatal period and succumbed due to sepsis and multi-organ failure. Among six survivors (current age ranged from 4 to 27 years), four have normal growth and cognitive development. One patient had short stature and another had neurological deficit following status epilepticus due to profound hypoglycemia.

    CONCLUSION: FBPase deficiency needs to be considered in any children with recurrent hypoglycemia and metabolic acidosis. Our study expands the spectrum of FBP1 gene mutations.

    Matched MeSH terms: DNA Helicases/genetics*; DNA-Binding Proteins/genetics*
  13. Fulltext Genetic analyses favour an ancient and natural origin of elephants on Borneo
    Sharma R, Goossens B, Heller R, Rasteiro R, Othman N, Bruford MW, et al.
    Sci Rep, 2018 01 17;8(1):880.
    PMID: 29343863 DOI: 10.1038/s41598-017-17042-5
    The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Altogether the data support a natural colonization of Bornean elephants at a time when large terrestrial mammals could colonise from the Sunda shelf when sea levels were much lower. Our results are important not only in understanding the unique history of the colonization of Borneo by elephants, but also for their long-term conservation.
    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA/methods
  14. Fulltext Synthesis and Characterization of Polyaniline/Graphene Composite Nanofiber and Its Application as an Electrochemical DNA Biosensor for the Detection of Mycobacterium tuberculosis
    Mohamad FS, Mat Zaid MH, Abdullah J, Zawawi RM, Lim HN, Sulaiman Y, et al.
    Sensors (Basel), 2017 Dec 02;17(12).
    PMID: 29207463 DOI: 10.3390/s17122789
    This article describes chemically modified polyaniline and graphene (PANI/GP) composite nanofibers prepared by self-assembly process using oxidative polymerization of aniline monomer and graphene in the presence of a solution containing poly(methyl vinyl ether-alt-maleic acid) (PMVEA). Characterization of the composite nanofibers was carried out by Fourier transform infrared (FTIR) and Raman spectroscopy, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). SEM images revealed the size of the PANI nanofibers ranged from 90 to 360 nm in diameter and was greatly influenced by the proportion of PMVEA and graphene. The composite nanofibers with an immobilized DNA probe were used for the detection of Mycobacterium tuberculosis by using an electrochemical technique. A photochemical indicator, methylene blue (MB) was used to monitor the hybridization of target DNA by using differential pulse voltammetry (DPV) method. The detection range of DNA biosensor was obtained from of 10-6-10-9 M with the detection limit of 7.853 × 10-7 M under optimum conditions. The results show that the composite nanofibers have a great potential in a range of applications for DNA sensors.
    Matched MeSH terms: DNA
  15. Notes on Amanita section Caesareae from Malaysia
    Tang LP, Lee SS, Zeng NK, Cai Q, Zhang P, Yang ZL
    Mycologia, 2017 12 04;109(4):557-567.
    PMID: 29200380 DOI: 10.1080/00275514.2017.1394789
    Some Amanita specimens collected from Malaysia are critically investigated by morphological examination and molecular analysis of two gene fragments, the nuc rDNA partial 28S (28S) gene and the internal transcriber spacer (ITS1-5.8S-ITS2 = ITS) regions. Six phylogenetic species of Amanita section Caesareae are recognized among the studied collections. One of them is described as new, A. malayensis. Four of the phylogenetic species correspond with existing morphology-based taxa: A. aporema, A. javanica, A. princeps, and A. similis. The remaining species is not described because of the paucity of material. Detailed descriptions and the distribution of these southeastern Asian species are provided, along with a key to the species of section Caesareae from Malaysia.
    Matched MeSH terms: DNA, Fungal/genetics; DNA, Ribosomal Spacer/genetics
  16. Morphology and phylogeny of Prorocentrum caipirignum sp. nov. (Dinophyceae), a new tropical toxic benthic dinoflagellate
    Nascimento SM, Mendes MCQ, Menezes M, Rodríguez F, Alves-de-Souza C, Branco S, et al.
    Harmful Algae, 2017 12;70:73-89.
    PMID: 29169570 DOI: 10.1016/j.hal.2017.11.001
    A new species of toxic benthic dinoflagellate is described based on laboratory cultures isolated from two locations from Brazil, Rio de Janeiro and Bahia. The morphology was studied with SEM and LM. Cells are elliptical in right thecal view and flat. They are 37-44μm long and 29-36μm wide. The right thecal plate has a V shaped indentation where six platelets can be identified. The thecal surface of both thecal plates is smooth and has round or kidney shaped and uniformly distributed pores except in the central area of the cell, and a line of marginal pores. Some cells present an elongated depression on the central area of the apical part of the right thecal plate. Prorocentrum caipirignum is similar to Prorocentrum lima in its morphology, but can be differentiated by the general cell shape, being elliptical while P. lima is ovoid. In the phylogenetic trees based on ITS and LSU rDNA sequences, the P. caipirignum clade appears close to the clades of P. lima and Prorocentrum hoffmannianum. The Brazilian strains of P. caipirignum formed a clade with strains from Cuba, Hainan Island and Malaysia and it is therefore likely that this new species has a broad tropical distribution. Prorocentrum caipirignum is a toxic species that produces okadaic acid and the fast acting toxin prorocentrolide.
    Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Protozoan/genetics
  17. Advancements in electrochemical DNA sensor for detection of human papilloma virus - A review
    Rasouli E, Shahnavaz Z, Basirun WJ, Rezayi M, Avan A, Ghayour-Mobarhan M, et al.
    Anal Biochem, 2018 09 01;556:136-144.
    PMID: 29981317 DOI: 10.1016/j.ab.2018.07.002
    Human papillomavirus (HPV) is one of the most common sexually transmitted disease, transmitted through intimate skin contact or mucosal membrane. The HPV virus consists of a double-stranded circular DNA and the role of HPV virus in cervical cancer has been studied extensively. Thus it is critical to develop rapid identification method for early detection of the virus. A portable biosensing device could give rapid and reliable results for the identification and quantitative determination of the virus. The fabrication of electrochemical biosensors is one of the current techniques utilized to achieve this aim. In such electrochemical biosensors, a single-strand DNA is immobilized onto an electrically conducting surface and the changes in electrical parameters due to the hybridization on the electrode surface are measured. This review covers the recent developments in electrochemical DNA biosensors for the detection of HPV virus. Due to the several advantages of electrochemical DNA biosensors, their applications have witnessed an increased interest and research focus nowadays.
    Matched MeSH terms: DNA, Single-Stranded/analysis*; DNA, Viral/analysis*
  18. Isolation and Quantification of Mimivirus-Like and Marseillevirus-Like Viruses from Soil Samples in An Aboriginal (Orang asli) Village in Peninsular Malaysia
    Tan YF, Lim CY, Chong CW, Lim PKC, Yap IKS, Leong PP, et al.
    Intervirology, 2018;61(2):92-95.
    PMID: 30121676 DOI: 10.1159/000491602
    BACKGROUND: The giant amoebal viruses of Mimivirus and Marseillevirus are large DNA viruses and have been documented in water, soil, and sewage samples. The trend of discovering these giant amoebal viruses has been increasing throughout Asia with Japan, India, and Saudi Arabia being the latest countries to document the presence of these viruses. To date, there have been no reports of large amoebal viruses being isolated in South East Asia.

    OBJECTIVE: In this study, we aim to discover these viruses from soil samples in an aboriginal village (Serendah village) in Peninsular -Malaysia.

    METHOD AND RESULTS: We successfully detected and isolated both Mimivirus-like and Marseillevirus-like viruses using Acanthamoeba castellanii. Phylogeny analysis identified them as Mimivirus and Marseillevirus, respectively.

    CONCLUSION: The ubiquitous nature of both Mimivirus and Marseillevirus is further confirmed in our study as they are detected in higher quantity in soil that is near to water vicinities in an aboriginal village in Peninsular Malaysia. However, this study is limited by our inability to investigate the impact of Mimivirus and Marseillevirus on the aboriginal villagers. More studies on the potential impact of these viruses on human health, especially on the aborigines, are warranted.

    Matched MeSH terms: DNA Viruses/classification*; DNA Viruses/genetics*; DNA Viruses/isolation & purification
  19. Fulltext Identification and ultrastructural characterization of Acanthamoeba bacterial endocytobionts belonging to the Alphaproteobacteria class
    Chan LL, Mak JW, Ambu S, Chong PY
    PLoS One, 2018;13(10):e0204732.
    PMID: 30356282 DOI: 10.1371/journal.pone.0204732
    The detection and identification of two endocytobiotic bacterial strains, one affiliated to the "Candidatus Caedibacter acanthamoebae"/"Ca. Paracaedimonas acanthamoeba", and another to the endosymbiont of Acanthamoeba UWC8 and "Ca. Jidaibacter acanthamoeba" are described. For endocytobiont screening, we developed a PCR method with a set of broad-range bacterial 16S rRNA primers to substitute the commonly used but technically demanding fluorescent in situ hybridization technique. Our PCR test alone without sequencing failed to discriminate the endocytobiont-containing and endocytobiont-free Acanthamoeba sp. due to the presence of mismatched primers to host mitochondrial DNA. We highlighted the need to perform bacterial primer checking against the Acanthamoeba genome to avoid false positive detection in PCR. Although the genetic aspect of "Ca. Caedibacter acanthamoebae"/"Ca. Paracaedimonas acanthamoeba" and the endosymbiont of Acanthamoeba UWC8/"Ca. Jidaibacter acanthamoeba" are well studied, knowledge pertaining to their morphologies are quite vague. Hence, we used transmission electron microscopy to examine our endocytobionts which are affiliated to previously described intracellular bacteria of Acanthamoeba sp. We used good-quality TEM images for the localization and the fate of the current endocytobionts inside different life stages of the hosts. Furthermore, to the best of our knowledge, our TEM findings are the first to provide morphological evidence for the clearance of defective Acanthamoeba endocytobionts via an autophagic-like process.
    Matched MeSH terms: DNA, Bacterial/genetics; DNA, Mitochondrial/genetics
  20. Fulltext Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides)
    Tan CK, Natrah I, Suyub IB, Edward MJ, Kaman N, Samsudin AA
    Microbiologyopen, 2019 05;8(5):e00734.
    PMID: 30353678 DOI: 10.1002/mbo3.734
    AIMS: The aim of this study was to identify and compare the gut microbial community of wild and captive Tor tambroides through 16S rDNA metagenetic sequencing followed by functions prediction.

    METHODS AND RESULTS: The library of 16S rDNA V3-V4 hypervariable regions of gut microbiota was amplified and sequenced using Illumina MiSeq. The sequencing data were analyzed using Quantitative Insights into Microbial Ecology (QIIME) pipeline and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The most abundant bacterial phyla in both wild and captive T. tambroides were Firmicutes, Proteobacteria, Fusobacteria and Bacteroidetes. Cetobacterium spp., Peptostreptococcaceae family, Bacteroides spp., Phosphate solubilizing bacteria PSB-M-3, and Vibrio spp. were five most abundant OTU in wild T. tambroides as compared to Cetobacterium spp., Citrobacter spp., Aeromonadaceae family, Peptostreptococcaceae family and Turicibacter spp. in captive T. tambroides.

    CONCLUSION: In this study, the specimens of the wild T. tambroides contain more diverse gut microbiota than of the captive ones. The results suggested that Cetobacterium spp. is one of the core microbiota in guts of T. tambroides. Besides, high abundant Bacteroides spp., Citrobacter spp., Turicibacter spp., and Bacillus spp. may provide important functions in T. tambroides guts.

    SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study provide significant information of T. tambroides gut microbiota for further understanding of their physiological functions including growth and disease resistance.

    Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Ribosomal/chemistry; Sequence Analysis, DNA
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