Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
Great progress has been made in unravelling the evolutionary history of Asian colobines, largely through the use of dated molecular phylogenies based on multiple markers. The Presbytis langurs are a case in point, with more allopatric species being identified, recognition of Presbytis thomasi from Sumatra rather than P. potenziani from the Mentawai Islands as being the most basal species of the group, and the discovery that P. rubicunda from Borneo is nested among the Sumatran species and only made it to Borneo in the last 1.3 million years. Based on variation in mitochondrial d-loop, it has recently been argued that Malaysia's P. femoralis femoralis is actually P. neglectus neglectus. Unfortunately, despite being available, sequences from the type locality, Singapore, were excluded from the analysis, and none of the newly generated sequences was deposited in GenBank. I manually reconstructed these sequences, which allowed me to present a molecular phylogeny that includes 8 additional sequences from West Malaysia and Singapore. P. neglectus from Malaysia and P. femoralis from Singapore form one monophyletic clade, with minimal divergence. I conclude that recognition of P. neglectus is erroneous and the name is a junior synonym of P. femoralis. Colobine taxonomy and systematics have advanced, and continue to advance, mostly by considering evidence from a wide range of individuals, species and data sets (molecular, behavioural and morphological) rather than focusing on single molecular markers from 1 or 2 species from one small geographic area. For an orderly taxonomic debate where evidence can be evaluated and reinterpreted it is essential that newly generated sequences are deposited in public repositories.
Matched MeSH terms: DNA, Mitochondrial; Sequence Analysis, DNA
Anopheles (Cellia) maculatus Theobald is a major malaria vector in southern Thailand and peninsular Malaysia, and previous population genetic studies suggested that mountain ranges act as barriers to gene flow. In this study, we examine the genetic variance among 12 collections of natural populations in southern Thailand by analyzing 7 microsatellite loci. Based on analysis of molecular variance (AMOVA), three geographic populations of An. maculatus are suggested. The southern population exists in western Thailand north of 12 degrees north latitude. Mosquitoes to the south fall into two genetic populations: 1) the middle southern collections located on the west side of the Phuket mountain range between 8 degrees and 10 degrees north latitude, and 2) the southern collections located on the east of the Phuket mountain range located between approximately 6.5 degrees and 11.5 degrees north latitude. AMOVA revealed significant genetic differentiation between northern and middle southern and southern populations. The middle southern population was moderately differentiated from the southern population. Furthermore, gene flow was restricted between proximal collections located on different sides of the Phuket mountain range. Collections separated by 50 km exhibited restriction of gene flow when separated by geographic barriers, whereas greater gene flow was evident among collections 650 km apart but without geographic barriers.
Tree species in the Aquilarieae tribe of the Thymelaeaceae family produce agarwood, a natural product highly valued for its fragrance, but the species are under threat due to indiscriminate harvesting. For conservation of these species, molecular techniques such as DNA profiling have been used. In this study, we assessed cross-amplification of microsatellite markers, initially developed for three Aquilaria species (A.crassna, A.malaccensis, and A.sinensis), on ten other agarwood-producing species, including members of Aquilaria (A.beccariana, A.hirta, A.microcarpa, A.rostrata, A.rugosa, A.subintegra, and A.yunnanensis) and Gyrinops (G.caudata, G.versteegii, and G.walla), both from the Aquilarieae tribe. Primers for 18 out of the 30 microsatellite markers successfully amplified bands of expected sizes in 1 sample each of at least 10 species. These were further used to genotype 74 individuals representing all the 13 studied species, yielding 13 cross-amplifiable markers, of which only 1 being polymorphic across all species. At each locus, the number of alleles ranged from 7 to 23, indicating a rather high variability. Four markers had relatively high species discrimination power. Our results demonstrated that genetic fingerprinting can be an effective tool in helping to manage agarwood genetic resources by potentially supporting the chain-of-custody of agarwood and its products in the market.
Matched MeSH terms: DNA Fingerprinting; DNA Primers
Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.
Matched MeSH terms: DNA; Random Amplified Polymorphic DNA Technique
Humans are constantly exposed to a wide range of reactive and toxic chemicals from the different sources in everyday life. Identification of the exposed chemical helps in the detection and understanding the exposure associated adverse health effects. Covalent adducts of proteins and DNA formed after xenobiotics exposure may serve as readily measurable indicators of these exposures. Measuring the exposed chemicals with focus on adducts resulting from the nucleophilic interactions with blood proteins is useful in the development of diagnostic markers. Particularly, the most abundant proteins such as albumin and hemoglobin acts as dominant scavengers for many reactive chemicals in blood and can serve as excellent diagnostic candidates to determine the type of chemical exposure. This review focuses on the potential application of an adductomics approach for the screening of bimolecular adducts of chemical warfare agents (CWAs). Recent incidents of CWAs use in Syria, Malaysia, and the UK illustrate the continuing threat of chemical warfare agents in the modern world. Detection of CWAs and their metabolites in blood or in other body fluids of victims depends on immediate access to victims. Concentrations of intact CWAs in body fluids of surviving victims may decline rapidly within a few days. Certain CWAs, particularly nerve agents and vesicants, form covalent bonds with certain amino acids to form CWA-protein adducts. Proteins that are abundant in the blood, including albumin and hemoglobin, may carry these adducts longer after the original exposure. We searched MEDLINE and ISI Web of Science databases using the key terms "adductomics" "adducts of CWAs," "CWAs adducts detection in the biological samples," "protein adducts of CWAs," alone and in combination with the keywords "detection" "intoxication" "exposure" "adverse effects" and "toxicity." We also included non-peer-reviewed sources such as text books, relevant newspaper reports, and applicable Internet resources. We screened bibliographies of identified articles for additional relevant studies including non-indexed reports. These searches produced 1931 citations of which only relevant and nonduplicate citations were considered for this review. The analysis of biomedical samples has several purposes including detecting and identifying the type of chemical agent exposed, understanding the biological mechanism, assists in giving adequate treatment, determining the cause of death and providing evidence in a court of justice for forensic investigations. Rapid advances in the mass spectrometry to acquire high-quality data with greater resolution enabled the analysis of protein and DNA adducts of xenobiotics including CWAs and place the rapidly advancing 'adductomics' next to the other "-omics" technologies. Adductomics can serve as a powerful bioanalytical tool for the verification of CWAs exposure. This review mostly describes the protein adducts for nerve agents and vesicants, outlines the procedures for measuring adducts, and suggests the evolving (or future) use of adducts in the detection and verification of CWAs.
Ancyronyx lianlabangorumsp. nov. (Coleoptera, Elmidae), a new spider riffle beetle from the Kelabit Highlands (Sarawak, northern Borneo), is described. Illustrations of the habitus and diagnostic characters of the new species and the similar, polymorphic A. pulcherrimus Kodada et al. are presented. Differences to closely related species, based on COI nucleotide sequences and morphological characters, are discussed. Ancyronyx pulcherrimus is here recorded from Sarawak for the first time, based on DNA barcoding.
The opportunistic pathogen Exophiala dermatitidis has been frequently isolated from tropical regions of the world. However, there is no report of environmental isolation of Exophiala spp. from Malaysia. The information regarding the ecology of this microbe is important for a better understanding of the opportunism. This study aims to conduct a survey of natural distribution of Exophiala spp. in Malaysia. Forty-seven strains of Exophiala-like was isolated by using selective media. These isolates from the fields were molecularly identified based on the ITS region. The biochemical activity of these microbes was tested by conducting various tests, i.e. DNase test, proteinase activity, and urea hydrolysis. Overall, 22 strains of E. dermatitidis were successfully obtained and identified from burnt tree bark, oil dripped soil sample, hot spring biofilm, railway track stones, tar road contaminated with petrol hydrocarbon, drain and deep mud of Sungai Pinang besides the new discovery from pigeon droppings. A single strain of E. heteromorpha was identified from tar road contaminated with petrol hydrocarbon. Genotypes of the isolated E. dermatitidis were identified by the neighbor-joining tree and grouped into Genotype A, A2 and B. The existence of new Genotype A4 was confirmed by a similar cladogram position in both neighbor-joining and maximum likelihood tree. The survival of E. dermatitidis in the hydrocarbon contaminated environment was studied by supplying engine oil and observing the growth pattern. The results of this study suggest that the opportunistic Exophiala spp. was isolated from nutrient limited and harsh conditions in the natural environment.
Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.
The identification of new virus strains is important for the study of infectious disease, but current (or existing) molecular biology methods are limited since the target sequence must be known to design genome-specific PCR primers. Thus, we developed a new method for the discovery of unknown viruses based on the cDNA--random amplified polymorphic DNA (cDNA-RAPD) technique. Getah virus, belonging to the family Togaviridae in the genus Alphavirus, is a mosquito-borne enveloped RNA virus that was identified using the Virus-Discovery-cDNA RAPD (VIDISCR) method.
Matched MeSH terms: DNA, Viral/genetics; DNA, Viral/chemistry; Sequence Analysis, DNA; DNA, Complementary/genetics*; Random Amplified Polymorphic DNA Technique/methods*
A new species of small, insular, forest floor skink, Sphenomorphus perhentianensis sp. nov., is described from Pulau Perhentian Besar of the Perhentian Archipelago, Peninsular Malaysia. This species is differentiated from all other 36 Sundaland species of Sphenomorphus based on a unique collection of morphological and colour pattern characteristics. These unique characteristics include a snout-vent length of 30.0 mm, 29 midbody scale rows, smooth as opposed to striated dorsal scales, 65 paravertebrals, 61 ventrals, 4 supraoculars, parietals contacting the posterior-most supraocular, 1 medially projecting superciliary scale, 2 loreals, 6 supralabials and infralabials, 10 lamellae beneath the fourth toe, smooth subdigital lamellae, enlarged preanal scales, no body bands, a dark brown, diffuse, dorsolateral stripe extending to just past the axilla, a cream coloured dorsolateral stripe on the nape and anterior-most portion of the body, and no cream coloured postorbital stripe. The discovery of a second endemic reptile in the Perhentian Archipelago underscores the unrealized biodiversity of its herpetofauna. Additional works will describe two additional species from the Perhentian Archipelago.
A lipase producer psychrophilic microorganism isolated from Arctic sample was
studied. The genomic DNA of the isolate was extracted using modified CTAB method.
Identification of the isolate by morphological and 16S rRNA sequence analysis revealed
that the isolate is closely related to Arthrobacter gangotriensis (97% similarity).
A. gangotriensis was determined as positive lipase producer based on the plate screening
using specific and sensitive plate assay of Rhodamine B. The PCR result using
Arthrobacter sp.’s full lipase gene sequence as the template primers emphasised a
possible lipase gene at 900 bp band size. The gene is further cloned in a suitable vector
system for expression of lipase.
Indonesia is home to several tree taxa that are harvested for agarwood. This highly valuable oleoresin ironically was the cause for some species to become vulnerable due to gluttonous human activity. However, information on the genetic diversity of these endangered trees is limited. In this study, 28 specimens representing eight species from two genera, Aquilaria and Gyrinops, were collected from ex-situ and in-situ populations in Indonesia. Phylogenetic analysis conducted on DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS) and the trnL-trnF intergenic spacer regions, revealed that Aquilaria and Gyrinops are paraphyletic when Aquilaria cumingiana is excluded. The phylogenetic analysis for ITS and trnL-trnF showed capability to categorise agarwood-producing species based on their regions: East Indonesia and West Indonesia, using Wallace's Line as the divider. In addition, we discuss challenges in species identification and taxonomy of agarwood-producing genera, and their conservation efforts in Indonesia.
Materials that can enhance the sensitivity and selectivity of a biosensor are greatly in demand. The nanocomposition of thionine (Th) and graphene can increase the electroconductivity of the working electrode used. Graphene is a very good electrical conductor but is also hydrophobic in nature. Composition with thionine gives it the capability to disperse well in water. Plus, thionine provides the opportunity for DNA probes to be immobilized due to the presence of the amino group in its structure. In this research, the thionine-graphene (Th-G) nanocomposite was synthesized through filtration and characterised using scanning electron microscopy (SEM) to distinguish different elements coexist in the nanocomposite and to investigate the microstructure changes of the nanocomposite to confirm the composition. Different elements were analyzed to test the presence of both thionine and graphene in the composition. Physical characterisation through SEM proved the nanocomposition was a success.
Mushroom can be used as a biological indicator in assessing radiological impact on the
environment. Radiological effect would be reflected through morphological changes as well as
those changes at molecular level. For this purpose, a preliminary work was conducted, which
included DNA isolation, optimization of PCR parameters for Inter-Simple Sequence Repeat (ISSR)
and primers screening on Pleurotus sajor caju mushroom strains from Nuclear Malaysia’s
Sterifeed Mushrooms Collection Centre. In this work, DNA isolation technique from cap and stalk
of fruit body were optimized and quantified. It was found that stalk produced highest amount of
genomic DNA at 304.01ng/µl and cap at 149.00ng/µl. A total of 100 ISSR primers were tested and
51 primers were successfully amplified. These primers will be used further for dose response
evaluation and molecular profiling in mushroom species.
In this study, RAPD-PCR and ERIC-PCR were used to study the epidemiology of V. parahaemolyticus isolated from cockles in Padang, Indonesia. The Gold Oligo OPAR3 primer produced bands ranged from 1-8 with sizes from 0.2 – 5.0 kb and the Gold Oligo OPAR8 primer produced 1-7 bands with sizes 0.7 – 1.5 kb. Both primers produced twenty five RAPD patterns with a few isolates failed to produce any products. Based on phylogenetic dendrogram, all the isolates can be divided into 6 major clusters with similarity between 0 to 52%. For the ERIC primer, it produced bands ranged from 3-15 with sizes from 0.1 – 5.0 kb and twenty seven different ERIC patterns. Construction of the phylogenetic dendogram showed the isolates can be divided into 4 major clusters with similarity between 56 to 86%. The high diversity of both processes may be due to the multiple contamination sources of V. parahaemolyticus.
Matched MeSH terms: DNA Primers; Random Amplified Polymorphic DNA Technique
A total of 78 samples comprising different types of street foods, sold in different locations in Malaysia, were examined for the presence of Enterobacter cloacae. E. cloacae contamination was recorded in 9% of the samples examined. Tests for susceptibility to 12 different antibiotics showed that all were resistant to six or more antibiotics, but susceptible to chloramphenicol and gentamicin. Plasmids of four different sizes were detected from the three plasmid positive isolates. RAPD analysis using four primers yielded completely different banding patterns for all E. cloacae studied. In Malaysia, no published information on street foods in the epidemiological investigation of E.cloacae related disease is available. However, their occurrences have provided compelling evidence that the risk of disease transmission caused by E. cloacae through street foods is moderate.
Matched MeSH terms: DNA Primers; Random Amplified Polymorphic DNA Technique
DNA damaging effect of the salted and fermented food products (salted fishes, dried shrimps and shrimp pastes) collected from three different locations in Malacca namely Pantai Puteri, Batang Tiga and Kelemak on the DNA of the Chang liver cells were evaluated via Alkaline Comet Assay. Treatment at 62.5 mg/ml following 24 hours of incubation was used based on the preliminary cytotoxicity data. Percentage of damage to the DNA was calculated using software for scoring based on the tail moment and tail intensity (severity of the DNA damage). Hydrogen peroxide was used as positive control at 0.1 mM following 30 minutes of incubation in 4 C. The results showed that the methanol extracts of shrimp pastes and salted fish from Pantai Puteri, exhibited a higher DNA damage (shrimp pastes - TM - 8.33 ± 2.19; TI - 31.67 ± 5.84, salted fishes - TM - 2.25 ± 0.86; TI - 9.25 ± 1.55) and were expressed as (shrimp pastes) 56.66 ± 8.74% of DNA damage and methanol salted fish extracts from the same location showed 13.00 ± 2.84% of the DNA damage on Chang liver cells compared to the other extracts. Values for methanol extract of shrimp pastes from Pantai Puteri were comparable to the positive control - Hydrogen peroxide (TM- 9.50 ± 1.50; TI - 30.50 ± 2.50). On the other hand, aqueous salted fishes extract from Pantai Puteri (TM - 1.33 ± 0.42; TI - 8.67 ± 2.42) and shrimp pastes extracts from Kelemak (methanol extract - TM -1.75 ± 0.15; TI -7.50 ± 0.50, aqueous extract - TM - 1.00 ± 0.00; TI - 5.00 ± 0.00) showed slightly high value for tail moment and tail intensity as compared to negative control (TM - 0.29 ± 0.05; TI - 2.50 ± 0.29). Values for methanol extracts of shrimp pastes from Pantai Puteri were comparable to the positive control (TM- 9.50 ± 1.50; TI - 30.50 ± 2.50). In conclusion, our results demonstrate genotoxic damage induced by few salted and fermented food extracts in Chang liver cell.
In Malaysia, harmful algal blooms often occur along the coastal waters of west Sabah, where one of the causative organisms is the toxin-producing dinoflagellate, Pyrodinium bahamense var. compressum. A total of five P. bahamense var. compressum isolates were obtained from four locations and were cultured in f/2 medium. A Polymerase Chain Reaction (PCR) based technique was developed and used to screen for the presence of the dinoflagellate, P. bahamense var. compressum. A dinoflagellate-specific primer pair was designed based on sequences of P. bahamense var. compressum to amplify the 18S small subunit ribosomal DNA (rDNA) sequences. The rDNA of the P. bahamense var. compressum isolates were obtained. A species-specific primer pair was designed to target a 600 bp rDNA sequence of the target dinoflagellate. The primer pair targeting P. bahamense var. compressum did not yield any product with the fifteen algae cultures used as negative controls, but only amplified the rDNA of P. bahamense var. compressum cultures. The PCR method for identification of P. bahamense var. compressum was also applied on twenty field samples collected with plankton net. P. bahamense var. compressum cells were detected by PCR in five field samples and were confirmed by direct sequencing. From this study, a species-specific primer pair was obtained to identify the target species, P. bahamense var. compressum, among the natural complex communities of seawater.
The combtooth blenny (Blenniidae) genus Omobranchus contains small, cryptobenthic fishes common to nearshore habitats throughout the Indo-West Pacific. Recent molecular systematic studies have resolved Omobranchus as monophyletic but little research has been done to resolve species-level relationships. Herein, phylogenetic analyses of one mitochondrial (CO1) and four nuclear (ENC1, myh6, sreb2, and tbr1) genes provide evidence for the monophyly of Omobranchus and support for the elongatus and banditus species group. Sampling of multiple individuals from widespread species (O. ferox, O. punctatus, and O. elongatus) suggested that the Thai-Malay Peninsula is a phylogeographic break that may be a historic barrier to gene flow. Additionally, common meristics and other morphological characters are used to describe an early life history stage of O. ferox and O. punctatus.
Matched MeSH terms: DNA, Mitochondrial; Sequence Analysis, DNA