A new haemoglobin, Haemoglobin Malay is described in a 22 year old Malay. Structural analysis showed a AAC----AGC mutation in codon 17, with the production of an abnormal beta chain (beta Malay) that has an Asn----Ser substitution at position beta 19. This haemoglobin variant could not be detected by conventional procedures.
Polycyclic aromatic hydrocarbons (PAHs) are persistent pollutants and chemically a class of structurally similar chemical compounds characterized by the presence of fused aromatic rings. This research was undertaken to find out immunotoxic effects produced by pyrene, phenanthrene and fluoranthene. These chemicals were injected into developing chicks at three dose levels (0.2, 2 and 20 mg per kg) through allantioc route to rule out possible mechanisms involved in immunotoxicity. DNA adduct produced by PAHs in immune organs were analyzed by DNA adduct enzyme-linked immunosorbent assay (ELISA) kit and DNA damage was assessed by comet assay. A significant increase in the DNA adduct levels was found in thymus and bursa in 2 mg and 20 mg dose levels of pyrene, fluoranthene and phenanthrene treated groups, whereas those in spleen simulated the value of controls. Comet assay indicated that PAHs especially pyrene, fluoranthene and phenanthrene were capable of inducing increased level of comet parameters in thymus at all the dose levels. Bursa of Fabricius and spleen also showed a gradual rise in comet parameters corresponding to all dose levels, but the increase was more marked as in thymus. Thus, it can be concluded that DNA adducts produced by PAHs lead to single-strand breaks and reduced DNA repair, which ultimately begin a carcinogenic process. Hence, this experiment can be considered as a strong evidence of genotoxic potential of PAHs like pyrene, phenanthrene and fluoranthene in developing chicks.
Matched MeSH terms: DNA Damage*; DNA Adducts/metabolism*
The distribution patterns of tropical ectomycorrhizal (ECM) fungi along altitudinal gradients remain largely unknown. Furthermore, despite being an iconic site for biodiversity research, virtually nothing is known about the diversity and spatial patterns of fungi on Mt Kinabalu and neighbouring mountain ranges. We carried out deep DNA sequencing of soil samples collected between 425 and 4000 m above sea level to compare richness and community composition of ECM fungi among altitudinal forest types in Borneo. In addition, we tested whether the observed patterns are driven by habitat or by geometric effect of overlapping ranges of species (mid-domain effect). Community composition of ECM fungi was strongly correlated with elevation. In most genera, richness peaked in the mid-elevation montane forest zone, with the exception of tomentelloid fungi, which showed monotonal decrease in richness with increasing altitude. Richness in lower-mid- and mid-elevations was significantly greater than predicted under the mid-domain effect model. We provide the first insight into the composition of ECM fungal communities and their strong altitudinal turnover in Borneo. The high richness and restricted distribution of many ECM fungi in the montane forests suggest that mid-elevation peak richness is primarily driven by environmental characteristics of this habitat and not by the mid-domain effect.
Background: MDM2 and p53 are involved in a negative feedback loop where p53 regulates MDM2 at the transcriptional level. MDM2, in turn, downregulates p53. This co-ordinated interaction between these proteins is set to play an important role in the regulation of cell cycle progression following DNA damage to cells. The over-expression of both p53 and MDM2 has been reported in various cancers. However there are only few studies discussing the co-expression of MDM2 with p53 in oral squamous cell carcinoma Aim: The purpose of this study was to determine the correlation of co-expression of p53, MDM2, and Ki-67 proteins with clinico-pathological factors in oral squamous cell carcinoma (OSCC) and to conduct a systematic review of the co-expression of p53/MDM2.
Method: This is a retrospective descriptive study and a systematic review. Formalin-fixed paraffinembedded tissues from 45 OSCC cases were stained by immunohistochemistry (IHC) for p53, MDM2, and Ki-67 proteins.
Results: Immuno-reactivity for p53, MDM2, and Ki-67 was seen in 75.6%, 97.8%, and 62.2% cases of OSCC respectively. The co-expression of p53 and MDM2 (p53/MDM2) was detected in 97.1%, however there was no significant correlation between p53 and MDM2 expression. Notably, p53/MDM2 coexpression was significantly associated with tumour differentiation (p-value = 0.045). The Ki-67LI was not significantly associated with neither MDM2 nor p53/MDM2 co-expression (p-value = 0.268, 0.916 respectively).
Conclusion: The expression of MDM2 was not signif icantly associated with p53 expression suggesting that MDM2 expression is mediated by p53-independent pathways or mutated p53 could not induce the expression of MDM2 in this set of OSCCs. The only clinico-pathological parameter that correlates significantly with co-expression of p53/MDM2 is tumour differentiation where it is suggestive that the co-expression of these 2 proteins is indicative of aggressive tumour behavior.
The aim of this study was to determine the genotoxicity of a locally produced nanocomposite by Universiti Sains Malaysia, Malaysia using Comet assay. Stem cells from human exfoliated deciduous teeth (SHED) were treated with the nanocomposite at five different concentrations (0.006, 0.0125, 0.025, 0.05, and 0.1 mg/ml) along with concurrent negative (medium alone) and positive control (zinc sulfate heptahydrate) and incubated at 37°C for 24 hours in an incubator at 5% CO2. The tail moment was used to assess the extent of DNA damage. The tail moment for the group of SHED treated with nanocomposite (for all the five different concentrations) was not statistically significant as compared to the negative control, suggesting that the locally produced dental nanocomposite did not induce any DNA damage. Hence, it can be concluded that the locally produced nanocomposite is non-genotoxic on stem cells from human exfoliated deciduous teeth.
Thirty one Vibrio cholera isolates recovered from cholera outbreak in Bintulu, Sarawak (Malaysia) were detected with the presence of ctx gene by using specific PCR. These isolates were further characterized and differentiated by using the Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) and BOX-PCR to determine their genomic fingerprints. The specific PCR result confirmed the identities of 27 isolates out of 31 as pathogenic V. cholerae. The ERIC-PCR generated several genetic profiles consisting of 4-6 bands with sizes in the range of 100 to 600 bp, while the BOX-PCR produced profiles numbering 2-7 bands in the sizes between 200 to 1000 bp. Based on the dendrogram generated from the DNA fingerprinting profiles (ERIC-PCR and BOX-PCR), all of the isolates can be divided into 2 main clusters that is further divided into 2 sub-clusters. The low genetic diversity of the isolates indicated the outbreak of V. cholerae in the study area was due to the contamination from a single or few sources of V. cholerae.
The genus Streptomonospora is a group of extremely halophilic filamentous actinomycetes that form a distinct branch in the 16S rRNA gene phylogenetic tree adjacent to the genera Nocardiopsis and Thermobifida, family Norcadiopsaceae. To date, genus Streptomonospora only contain two validly described species which are Streptomonospora salina and Streptomonospora alba. During a biodiversity study on halophilic filamentous actinomycetes from 18 co-ordinates in Barrientos Island, Antarctic, numerous actinomycetes strains were isolated. To identify whether these isolates were members of the genus Streptomonospora, a genus specific primer that allow the rapid detection of the genus Streptomonospora by means of PCR amplification was used. Furthermore molecular cloning was performed to make identical and multiple copies of the target gene. In addition, morphological characteristic identification was performed to validate isolates with positive amplification during PCR.
The paper examines the propagation direction and speed of large scale travelling ionospheric disturbances (LSTIDs) obtained from GPS observations of extreme geomagnetic storms during the 23rd solar cycle; these are the October 2003 and November 2003 geomagnetic storms. In the analysis, the time delay between total electron content (TEC) structures at Scott Base station (SBA) (Lat. –77.85º, Long. 166.76º), McMurdo (McM4), (Lat. –77.84º, Long. 166.95º), Davis (DAV1), (Lat. –68.58º, Long. 77.97º) and Casey station (CAS1) (Lat. –66.28º, Long. 110.52º) GPS stations as well as the distance between these stations were employed in the analysis. The measurements during the October 2003 storm showed obvious time delay between the TEC enhancement occurrences at SBA/MCM4, DAV1 and CAS1 stations. The time delay indicated a movement of the ionospheric structures from higher to lower latitudes in a velocity ranging between 0.8 km/s – 1.2 km/s. The first sudden TEC enhancement was observed at SBA/McM4 (Lat. –75.84º) followed by CAS1 station (Lat. –66.28º) and the final TEC enhancement was seen at DAV1 station (Lat. –68.58º) with TEC magnitude decreasing while moving from higher to lower latitudes. One important observation was that although the latitude of the CAS1 station was lower than the DAV1 station, the TEC enhancement was firstly seen at the CAS1 station due to the shorter distance between SBA and CAS1 compared with the distance between SBA and CAS1 of about 500 km. The TEC measurements during the November 2003 storm showed an opposite propagation direction (i.e. poleward direction from lower to higher latitudes) which was seen with a velocity ranging between 0.3 km/s – 0.4 km/s. As similar response was observed using vertical TEC measurements obtained from individual PRN satellites but with higher velocity ranges (1.2 km/s – 2.4 km/s during October
and 0.5 km/s – 0.7 km/s during November). The equatorward or poleward expansion of LSTIDs during the October and November 2003 storms was probably caused by the disturbances in the neutral temperature which occurred close to the dayside convection throat or due to the neutral wind oscillation induced by atmospheric gravity waves launched from the aurora region.
Researchers have developed and modified DNA biosensor techniques to provide a fast, simple and sensitive method for detection of human diseases, bacterial food contamination, forensic and environmental research. This study describes the physical characterization of screen-printed carbon electrodes using the scanning electron microscope.
Basal stem rot (BSR) caused by species Ganoderma, is one of the most serious disease of oil palm in Malaysia. As far as the disease problem to oil palm in Malaysia is concerned, BSR is the only disease requiring urgent solution. The BSR is not new to Malaysia, it has been known to attack oil palm since the early years when the crop was introduced into this country. There is an indication that there are differences in susceptibility to basal stem rot between germplasm materials from different genetic origin [2]. This provides hope in generating oil palm varieties with reduced level of susceptibility using existing genetic materials. There is also interest in developing diagnostic tools such as using PCR primers for detection of the pathogen in oil palms [1]. Altered expression of several classes of genes was observed in plants in response to fungal infection. These include genes associated with cell maintenance and development, genes involved in biosynthesis of lignin and phenolics and genes implicated in oxidative burst, programmed cell death or hypersensitive response [5].
Microsatellites or simple sequence repeats (SSRs) are tandem repeats of DNA of 1-6 bp long. They ubiquitously occur in both eukaryotic and prokaryotic genomes. Because of their abundance,
they have widespread applications in both animal and plant sciences; such as varietal identification, genetic mapping, QTL mapping, phylogenetic and diversity studies. Thus, SSRs have become valuable DNA markers for molecular biologists and geneticists. Microsatellites are markers
of choice for many molecular geneticists because of their hypervariability, codominant
inheritance, multi-allelism and PCR-based assaying of variations that are amenable to automation and high throughput assay. However, the utilization of microsatellite markers in the past was
hampered by its laborious de novo isolations and species-specific nature.
The objective of the present study was to develop a rapid, reliable and yet inexpensive protocol for genomic DNA extraction from frozen and ethanol-preserved Asian green-lipped mussels for random amplified microsatelite (RAM) analysis. The procedure comprised of three major steps: (1) Tissue degradation by boiling in 6% Chelex 100 resin in TE buffer; (2) Protein digestion by Proteinase K; and (3) DNA precipitation by adding 2 volumes of cold absolute ethanol. The entire procedure can be completed within two hours. The resulting RAM profiles were clear and reproducible. Our results demonstrate that the combined protocol of Chelex 100-Proteinase K-ethanol precipitation is a powerful yet economical DNA isolation method for population genetic studies involving a large sample size.
In this study polymerase chain reaction (PCR) was used to identify yeast in domestic ragi obtained
from two local markets in Sarawak and Pahang. These ragi are normally used as a dry starter in food fermentation (tapai) for Pahang (ST2) and Sarawak (ST3) and tuak (ST1) which is an alcoholic drink in Sarawak. Universal primer, NL1 and NL4 were used as a primer in this study to amplify D1/D2 fragment. Based on the result from the sequencing and after the BLAST search of the nucleotide sequences, the strain was confirmed as Candida glabrata (FN424108.) partial 26S rRNA gene, strain IMUFRJ 51955 for ST1, Saccharomyces cerevisiae(EU285514.1) isolate 35 26S ribosomal RNA gene, partial sequence for ST2 sample and Candida glabrata (FN393990.1) partial 26S rRNA gene, strain MUCL 51244 for ST3. All these strains were found in domestic ragi used for food fermentation.
The main source of E. coli 0157:H7 is cattle, but recent studies showed high percentage of outbreaks
contributed by contaminated water. The occurrence of E. coli O157:H7 in environmental water samples poses a potential threat to human health. The aim of this study was to establish a protocol for the detection of the pathogen E. coli O157:H7 and E. coli virulence genes (eaeA, rfbE, hly, stx1, and stx2) in a multiplex PCR protocol using six specific primer pairs. The target genes produced species-specific amplicons at 625 bp, 397 bp, 296 bp, 166 bp, 210 bp and 484 bp for E. coli O157:H7 (fliCh7 gene) and virulence genes (eaeA, rfbE, hly, stx1, and stx2) respectively. The results obtained show that the established PCR protocol is suitable for a rapid and specific analysis of the pathogenic E. coli O157:H7 in environmental water samples for the assessment of microbiological risks.
The introduction of new agricultural commodities and products derived from modernbiotechnology may have an impact on human and animal health, the environment and economiesof countries. As more Genetically Modified Organisms (GMO) enter markets worldwide, themonitoring of GMOs is being preferred for obvious reasons such as determination of seed purity,verification of non-GMO status of agricultural crops and fulfilling GMO labeling provisions, tomention a few. Numerous GMO analytical methods which include screening, identification andquantification have been developed to reliably determine the presence and/or amount of GMOin agricultural commodities, in raw agricultural materials and in processed and refined ingredients.The detection of GMOs relies on the detection of transgenic DNA or protein material. For routineanalysis, a good sample preparation technique should reproducibly generate DNA/protein ofsufficient quality, purity and yield while minimizing the effects of inhibition andcontamination.
The key sample preparation steps include homogenization, pretreatment, extraction andpurification. Due to the fact that analytical laboratories receive samples that are often processedand refined, the quality and quantity of transgenic target analyte (e.g. protein and DNA) frequentlychallenge the sensitivity of any detection method. With the development of GMO analysistechniques, the Polymerase Chain Reaction (PCR) technique has been the mainstay for GMOdetection, and the real-time PCR is the most effective and important method for GMOquantification. The choice of target sequence; for example a promoter, a terminator, a gene, or ajunction between two of these elements, is the single most important factor controlling the specificity of the PCR method. Recent developments include event-specific methods, particularlyuseful for identification and quantification of GM content. Although PCR technology has obvious
limitations, the potentially high degree of sensitivity and specificity explains why PCR in its various
formats, is currently the leading analytical technology employed in GMO analysis. Comparatively, immunoassays are becoming attractive tools for rapid field monitoring for the integrity of agricultural commodities in identity preservation systems, whereby non-specialised personnel can employ them in cost-effective manner. This review discusses various popular extraction methodologies and summarises the current status of the most widely used and easily applicable GMO analysis technologies in laboratories, namely the PCR and immunoassay technologies.
Mitochondrial DNA (mtDNA) deletions are a major cause of chronic progressive external ophthalmoplegia (CPEO) and Kearns-Sayre syndrome (KSS). We analyzed single mtDNA deletions in 11 CPEO and one KSS patients by means of Southern blot and long polymerase chain reaction (PCR) assays. The deletion sizes ranged from 3.4 kb to 6.9 kb whereas the heteroplasmy level varied from 18.8% to 85.5%. Two unique deletions sized 4320 bp and 4717 bp were found. This study represents the first genetic screen of mtDNA disorders in Malaysia, and it follows the data seen in other published reports on CPEO and KSS genetic aetiology.
Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use of peptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study of biological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries of existing disciplines. Many self-assembling systems are range from bi- and tri-block copolymers to DNA structures as well as simple and complex proteins and peptides. The ultimate goal is to harness molecular self-assembly such that design and control of bottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes of life and non-life science applications. Such aspirations can be achieved through understanding the fundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.
Genetically modified organisms (GMO) are increased remarkably from year to year and the estimated global area cultivated with genetically modified (GM) crops reached 125 million hectares in year 2008. However, insect resistance maize based on Bacillus thuringienses (Bt) is of the most cultivated GM crop in worldwide. Bacillus thuringiensis (Bt) is an aerobic, gram-positive bacterium that synthesize one or more Cry protein that are toxic to various types crop and forestry insects pests. To date, several cry genes have been introduced into GM plant to combat with various type of insect. Worldwide commercialization of GM crops has raised the customers’ concern about the Biosafety issues, and thus, many countries have implemented the labeling legislations for GM food and their derivatives. In this study, we introduced the quantitative analysis method based on the recombinant plasmid DNA as calibrators that can be used to determine the percentage of GMO content in various types of food and feed samples. Therefore, we have reported 7.5% (6/80) of the samples were contained StarLink maize and 1.25% (1/80) samples were contained Bt176 maize. Additionally, the percentage of GM content in each positive sample were further determined with the developed quantitative method. The percentage of the StarLink corns that present in the positive samples were varies from 0.09% to 2.53% and Bt176 corn that present in the positive sample was 16.90%. The present study demonstrated that the recombinant plasmid DNA that used in quantitative real-time method as good alternative quantitative analysis of GM content.
Application of surface plasmon resonance (SPR) biosensor in detection of genetically modified organism (GMO) is demonstrated. A total of four biotinylated probes namely Tnosb, P35Sb, LECb and TSQb were successfully immobilized onto the SA chip. Results analysis indicated that the SPR system with the sensor chip immobilized with the Tnosb, P35Sb, LECb and TSQb biotinylated probes potentially detect complementary standard fragments as low as 1 nM. Biospecific interaction analysis (BIA), employing surface plasmon resonance (SPR) and biosensor technologies provide easy, rapid and automatable approach in detection of GMOs. Short assay times, label free DNA hybridization reaction and no toxic compounds are required, i.e. ethidium bromide, and the reusability of the sensor surface are some of the factors that contribute to the general advantages of the surface plasmon resonance (SPR) biosensor system in detection of GMOs.
Spinal Muscular Atrophy (SMA) is a heredity neuromuscular disorder and is one of the most common genetic causes of childhood fatality. SMA is classified into three groups based on age of onset and achieved motor milestone. Survival Motor Neuron (SMN) gene has been identified as the responsible gene for SMA. From August 2003 until Feb 2007 we have received 93 samples for SMN1 gene deletion analysis from various hospitals in Malaysia. All the patients except for 3 patients were Malaysian (71 Malays, 5 Indians, 9 Chinese and 5 patients are mixed ethnicity). DNA were extracted from blood samples using DNA extraction kit and subjected to SMN/ gene deletion analysis by PCR-RE. Forty nine out of 93 samples (20 type I, 21 type II, and 8 type III) were found to have homozygous deletion of at least exon 7 of the SMN1 gene. Twelve patients (7 type I, 4 type II, 1 type III) showed the presence of the SMN1 gene and the rest were excluded as they did not fulfill the criteria of International SMA Consortium. Deletion analysis of exon 7 of the SMN gene can be an alternative to the existing diagnostic modalities of SMA.