A rare case of thalassaemia-intermedia involving a non-deletion alpha thalassemia point mutation in the alpha1-globin gene CD59 (GGC --> GAC) and a deletion alpha+ (-alpha(3.7)) thalassaemia in which use of high performance liquid chromatography (HPLC) C-gram Hb subtype profile and DNA molecular analysis helped establish the diagnosis.
A 246-nt variant of Coconut cadang-cadang viroid (CCCVd) has been identified and described from oil palms with orange spotting symptoms in Malaysia. Compared with the 246-nt form of CCCVd from coconut, the oil palm variant substituted C(31)→U in the pathogenicity domain and G(70)→C in the central conserved domain. This is the first sequence reported for a 246-nt variant of CCCVd in oil palms expressing orange spotting symptoms.
The possibility of using the resonant mirror biosensor to detect point substitutions in oligonucleotides was demonstrated with a fragment of the Helicobacter pylori 23S rRNA gene, point mutations in which are responsible for clarythromycin resistance. Conditions were optimized for the interaction of a probe immobilized on the sensing surface with targets containing various nucleotide substitutions. A probe allowing reliable discrimination of mutant targets was selected. The mismatch position in the probe was shown to affect the kinetic parameters (response) of hybridization with mutant targets, reporting not only the position, but also the character (G or C) of a substitution.
Chloroquine resistance (CQR) in falciparum malaria was identified to be associated with several mutations in the chloroquine resistance transporter gene (pfcrt) that encodes the transmembrane transporter in digestive vacuole membrane of the parasite. This study aimed to investigate the point mutations across the full-length pfcrt in Plasmodium falciparum isolates in Sabah, Malaysia. A total of 31 P. falciparum positive samples collected from Keningau, Kota Kinabalu, and Kudat, Sabah, were analyzed. pfcrt was PCR amplified and cloned prior to sequence analysis. This study showed that all the previously described 10 point mutations associated with CQR at codons 72, 74, 75, 76, 97, 220, 271, 326, 356, and 371 were found with different prevalence. Besides, two novel point mutations, I166V and H273N, were identified with 22.5% and 19.3%, respectively. Three haplotypes, namely, CVMNK (29%), CVIET (3.2%), and SVMNT (67.7%), were identified. High prevalence of SVMNT among P. falciparum isolates from Sabah showed that these isolates are closer to the P. falciparum isolates from Papua New Guinea rather than to the more proximal Southeast Asian CVIET haplotype. Full-length analysis of pfcrt showed that chloroquine resistant P. falciparum in Sabah is still prevalent despite the withdrawal of chloroquine usage since 1979.
A number of genetic risk factors have been implicated in the development of neonatal severe hyperbilirubinaemia. This includes mutations in the uridine glucoronosyl transferase 1A1 (UGT1A1) gene which is responsible for unconjugated hyperbilirubinemia in Gilbert's Syndrome. We studied the prevalence of UGT1A1 gene mutations in a group of Malay neonates to determine whether they are risk factors to severe neonatal jaundice. One hundred and twenty-five Malay neonates with severe hyperbilirubinemia were studied. Ninety-eight infants without severe hyperbilirubinaemia were randomly selected from healthy Malay term infants (controls). DNA from EDTA cord blood samples were examined for UGT1A1 mutations nt211G > A and nt247T > C using established Taqman SNP genotyping assays and the UGT1A1*28 variant was detected by the Agilent 2100 bioanalyzer. All samples were also screened for common Malay G6PD variants using established techniques. The frequency of UGT1A1 211G > A mutation is significantly higher in the severely hyperbilirubinemic group (13%) than the control group (4%; p = 0.015) and all the positive cases were heterozygous for the mutation. There was no significant difference in the frequency of UGT1A1*28 mutation between the severely hyperbilirubinemic (3.5%) and the control group (0.01%; p = 0.09). None of the neonates in both groups carried the nt247 T > C mutation. The prevalence of G6PD mutation was significantly higher in the severely jaundiced group than control (9% vs 4%; p = 0.04). In conclusion, nt 211 G > A alleles constitute at least 12% of UGT1A1 mutations underlying unconjugated hyperbilirubinemia and appears to be a significant independent risk factor associated with severe neonatal hyperbilirubinemia in the Malay newborns.
The non-stereospecific α-haloalkanoic acid dehalogenase E (DehE) degrades many halogenated compounds but is ineffective against β-halogenated compounds such as 3-chloropropionic acid (3CP). Using molecular dynamics (MD) simulations and site-directed mutagenesis we show here that introducing the mutation S188V into DehE improves substrate specificity towards 3CP. MD simulations showed that residues W34, F37, and S188 of DehE were crucial for substrate binding. DehE showed strong binding ability for D-2-chloropropionic acid (D-2CP) and L-2-chloropropionic acid (L-2CP) but less affinity for 3CP. This reduced affinity was attributed to weak hydrogen bonding between 3CP and residue S188, as the carboxylate of 3CP forms rapidly interconverting hydrogen bonds with the backbone amide and side chain hydroxyl group of S188. By replacing S188 with a valine residue, we reduced the inter-molecular distance and stabilised bonding of the carboxylate of 3CP to hydrogens of the substrate-binding residues. Therefore, the S188V can act on 3CP, although its affinity is less strong than for D-2CP and L-2CP as assessed by Km. This successful alteration of DehE substrate specificity may promote the application of protein engineering strategies to other dehalogenases, thereby generating valuable tools for future bioremediation technologies.
G6PD deficiency is the most common human enzymopathy and affects 200 million people worldwide. To date more than 400 biochemical variants and at least 60 different point mutations in the G6PD locus have been discovered. In Malaysia the overall incidence of G6PD deficiency among males is 3.1%, being more prevalent among the Chinese and Malays and less common among the Indians. As part of our initial effort to characterise G6PD deficiency in the Malaysian population, we investigated 18 G6PD deficient Chinese male neonates for the G6PD mutation G-->T at nt 1376, a common mutation seen among the Chinese in Taiwan and mainland China. The mutation was detected by a PCR-based technique using primers that artificially create a site for restriction enzyme Xho I. We found 61% (11 out of 18) of the Chinese G6PD deficient male neonates positive for this mutation. Study of enzyme electrophoretic mobility in 7 of the cases positive for this mutation revealed three different patterns of mobility. 107% (5 out of 7), 103% (1 out of 7) and 100% (1 out of 7). This study shows that mutation G-->T at nt 1376 is a common allele causing G6PD deficiency in Malaysians of Chinese origin. The finding of different patterns of electrophoretic mobility among the 7 cases positive for 1376 G-->T mutation supports the notion that diverse biochemical variants may share the same mutation.
Beta-thalassemia in West Malaysia is caused by 14 molecular defects with differing clinical severity. In Chinese patients from West Malaysia, the main beta-thalassemia mutations seen were (a) a 4 base pair-TCTT deletion in codon 41-42 [frameshift mutation (FSC 41-42)]; (b) a C to T substitution at the second intervening sequence (IVS2-654); (c) an A to G substitution in the TATA box [-28 (A to G)], and (d) an A to T substitution in codon 17[17 A to T]. In the Malays, the main mutations seen were (a) a G to C in nucleotide 5 at the intervening sequence I [IVS1-5 (G to C)]; (b) G to T substitution in nucleotide I at the intervening sequence I [IVS1-1 (G to T)]; (c) a A to T substitution in codon 17 (17 A to T); (d) removal of C from codon 35 [codon 35 (-C)], and (e) a 4 base pairs-TCTT deletion in codon 41-42 [frameshift mutation (FSC 41-42)]. A scoring system (Tha1 CS) has been formulated to predict clinical severity. It is the type of beta-thalassemia mutation present that decides on the clinical phenotype. The most severe beta-thalassemia mutation is assigned a score of 4. A score of 8 indicates severe thalassemia.
Trichohepatoenteric syndrome (THES) is a rare autosomal recessive disorder that is classically associated with intractable diarrhea with an onset within the first few months of life. Herein, we investigated and reported novel mutations in two causal genes in 3 Malaysian cases. Genomic DNA was extracted from peripheral blood obtained from patients in two Malaysian Chinese families. The exons of SKIV2L and TTC37 genes were amplified and sequenced by bi-directional sequencing to identify the point mutations within the coding sequence. Three Chinese boys from two families with characteristic features and clinical course were diagnosed with THES. In family-1, two point mutations were identified in the SKIV2L gene (c.1891G>A and c.3187C>T). In family-2, a single-nucleotide duplication (c.3426dupA) was found in the TTC37 gene. These mutations cause the production of abnormal non-functional gene product leading to the clinical manifestations in the patients. We reported three point mutations, which have not been previously described in other patients with THES in SKIV2L and TTC37 genes, including one nonsense, one frameshift, and one missense mutations.
Hemoglobin (Hb) Adana [HBA2: c179G>A (or HBA1); p.Gly60Asp] is a non-deletional α-thalassemia variant found in Malaysia. An improvement in the molecular techniques in recent years has made identification of Hb Adana much easier. For this study, a total of 26 Hb Adana α-thalassemia intermedia and 10 Hb Adana trait blood samples were collected from patients. Common deletional and non-deletional α-thalassemia genotypes were determined using multiplex gap polymerase chain reaction (PCR) and multiplex ARMS PCR techniques. Identification of the Hb Adana location on the α-globin gene was carried out using genomic sequencing and the location of the mutation was confirmed via restriction fragment length polymorphism-PCR. Among the 36 samples, 24 (66.7%) had the -α(3.7)/α(Cd59)α mutation, while the -α(3.7)/α(Cd59)α mutation accounted for 2 samples (5.6%) and the remaining 10 (27.8%) samples were α/α(Cd59)α. All 36 samples were found to have the Hb Adana mutation on the α2-globin gene. The position of the α-globin gene mutation found in our cases was similar to that reported in Indonesia (16%) but not to that in Turkey (0.6%). Our results showed that the Hb Adana mutation was preferentially present in the α2-globin genes in Malays compared to the other ethnicities in Malaysia. Thus, the Malays might have similar ancestry based on the similarities in the Hb Adana position.
Malaria cases persist in some remote areas in Sabah and Sarawak despite the ongoing and largely successful malaria control programme conducted by the Vector Borne Disease Control Programme, Ministry Of Health, Malaysia. Point mutations in the genes that encode the two enzymes involved in the folate biosynthesis pathway, dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) enzymes confer resistance to pyrimethamine and sulfadoxine respectively, in both Plasmodium falciparum and P. vivax. The aim of the current study was to determine the mutation on both pvdhfr at codon 13, 33, 57, 58, 61, 117, and 173 and pvdhps genes at codon 383 and 553, which are potentially associated with resistance to pyrimethamine and sulfadoxine in P. vivax samples in Sabah.
Introduction: Reduction or complete absence of α-globin chain production may result α-thalassemia. Alpha thalassemia carrier may have normal haemoglobin level and thus will be eligible as blood donor. Few complications may happen in which the carrier who donated the blood might be at risk of hypoxia and their blood components might not suitable for transfusion. Thus, it is important to screen for α-thalassemia to prevent any complications happen
after donation. The objective of this study is to investigate the interaction of red blood cell indices and α-globin genotypes among eligible blood donors in a private university, Universiti Tunku Abdul Rahman (UTAR), Malaysia. Methods: A total of 270 eligible blood donors were recruited for this study. Red cell indices were analysed using Horiba hematology analyser and α-globin genotyping was performed for seven alpha deletions, six alpha point mutations
and two alpha triplications. Results: Our study showed high prevalence of α-thalassemia carriers among the eligible blood donors (7.7%, 21/270), with all of them showed normal Hb level (>12 gm/dl). Five genotypes were detected consisting of 249 αα/αα (92.2%), 9 -α3.7/αα (3.3%), 9 --SEA/αα (3.3%), 2 -α4.2/αα (0.7%) and 1 ααCS/αα (0.4%). All α-globin genotypes showed normal Hb level with no significant difference between genotypes (p=0.167). Different
α-globin genotypes showed significant difference in RBC, MCV, MCH, MCHC, RDW and Hct/Hb ratio at the p
Introduction: Tuberculosis (TB) still remains a public health problem worldwide and the emergence of drug resistant TB (DR-TB) has worsened the situation as it is difficult and expensive to treat. The characterization of the genetic mutations underlying streptomycin resistance may be helpful in developing rapid detection methods which may guide clinicians in making therapeutic decisions. The aim of this study is to detect mutations causing streptomycin (STR) resistance in Mycobacterium tuberculosis isolates from Sabah. Methods: Susceptibility testing was carried out in MGIT system for 42 Mycobacterium tuberculosis clinical isolates. The drug resistant isolates were subject to whole genome sequencing and in-silico analysis was performed to detect the mutations in the sequence of the rpsL gene known to confer resistance to anti-tuberculous drugs. Results: Of the 42 positive isolates, 27 (64.3%) are shown to be susceptible towards first line drugs (FLDs) while 15 (35.7%) isolates were mono- and multiple resistant to the FLDs. Our findings reveal that the isolate 145 possess mutations at codon 43 within rpsL gene with amino acid change A to G (K43R). Conclusion: Findings from this study enable us to expand our knowledge of mutations causing drug resistance in Mycobacterium tuberculosis and the point mutations, which can be used as the potential marker for detection of drug resistant isolates.
Introduction: Tuberculosis (TB), commonly caused by Mycobacterium tuberculosis (Mtb), is one of the ten leading causes of death worldwide. The gold standard, microbiological culture for detection and differentiation of mycobac-teria are time-consuming and laborious. The use of fast, easy and sensitive nucleic acid amplification tests (NAATs) for diagnosis of TB remains challenging because there is a high degree of homology within Mtb complex (MTBC) members and absence of target genes in the genome of some strains. This study aimed to identify new candidate genetic marker and to design specific primers to detect Mtb using in silico methods. Methods: Using Basic Local Alignment Search Tool (BLAST) program, Mtb H37Rv chromosome reference genome sequence was mapped with other MTBC members and a single nucleotide polymorphism (SNP) at Rv1970 was found to be specific only for Mtb strains. Mismatch amplification mutation assay (MAMA) combine with polymerase chain reaction (PCR) was used as an alternative method to detect the point mutation. MAMA primers targeting the SNP were designed using Primer-BLAST and the PCR assay was optimized via Taguchi method. Results: The assay amplified a 112 bp gene fragment and was able to detect all Mtb strains, but not the other MTBC members and non-tuberculous Mycobacte-ria. The detection limit of the assay was 60 pg/μl. Conclusion: Bioinformatics has provided predictive identification of many new target markers. The designed primers were found to be highly specific at single-gene target resolution for detection of Mtb.
Haemoglobin (Hb)-M Hyde Park, also known as Hb-M Akita is a rare type of hereditary Hb M due to autosomal dominant mutation of CAC>TAC on codon 92 of β globin gene resulting in the replacement of histidine by tyrosine on β globin chain. This variant Hb has a tendency to form methaemoglobin (metHb). The iron ion in metHb is oxidized to ferric (Fe3+) which is unable to carry oxygen and the patients manifest as cyanosis clinically. A 9-year-old Malay girl was incidentally found to be cyanotic when she presented to a health clinic. Laboratory investigations revealed raised methaemoglobin levels and Hb analysis findings were consistent with Hb-M Hyde Park. β gene sequencing confirmed a point mutation of CAC>TAC on codon 92 in one of the β genes. The family study done on the individuals with cyanosis showed similar findings. A diagnosis of heterozygous Hb-M Hyde Park was made. Patients with this variant Hb usually presented with cyanosis with mild haemolysis and maybe misdiagnosed as congenital heart disease. No further treatment is needed as patients are relatively asymptomatic. Although the disease is harmless in the heterozygous carriers but the offspring of the carriers may suffer severe haemolytic anaemia when the offspring also inherit other β haemoglobinopathies/thalassemia. This can happen due to high prevalence of β thalassemia carrier (3.5-4 %) found in Malaysia. At the time of writing, this is the first case of hereditary Hb-M Hyde Park diagnosed in a Malay family living in Malaysia.
T1 Lipase is a thermostable secretary protein of Geobacillus zalihae strain previously expressed in a prokaryotic system and purified using three-step purification: affinity 1, affinity 2, and ion exchange chromatography (IEX). This approach is time consuming and offers low purity and recovery yield. In order to enhance the purification strategy of T1 lipase, affinity 2 was removed so that after affinity 1, the cleaved Glutathione S-transferase (GST) and matured T1 lipase could be directly separated through IEX. Therefore, a rational design of GST isoelectric point (pI) was implemented by prediction using ExPASy software in order to enhance the differences of pI values between GST and matured T1 lipase. Site-directed mutagenesis at two locations flanking the downstream region of GST sequences (H215R and G213R) was successfully performed. Double point mutations changed the charge on GST from 6.10 to 6.53. The purified lipase from the new construct GST tag mutant-T1 was successfully purified using two steps of purification with 6,849 U/mg of lipase specific activity, 33% yield, and a 44-fold increase in purification. Hence, the increment of the pI values in the GST tag fusion T1 lipase resulted in a successful direct separation through IEX and lead to successful purification.
Resistance to pyrethroid insecticides is widespread in Indonesian Aedes aegypti (Linnaeus), the primary vector of dengue viruses. This study aims to investigate the mutations in the voltage-gated sodium channel (Vgsc) conferring pyrethroid resistance against Ae. aegypti populations from Indonesia. Molecular genotyping of mutations using polymerase chain reaction assay and direct DNA sequencing were performed at positions 989 and 1,016 in IIS6 region, and 1,534 in IIIS6 region of the voltage-gated sodium channel (Vgsc) in nine populations of Indonesian Ae. aegypti. The V1016G and S989P genotyping identified the RR genotype to be predominant in six out of nine populations of Ae. aegypti, whereas the SS genotype occurred only in minority. Interestingly, co-occurrence of the V1016G and S989P mutations was detected in the aforementioned six populations with high frequency. Genotyping of F1534C showed all nine populations exhibited the SS genotype, with merely two individuals from a population were heterozygous (RS). Significant correlations were demonstrated between the allele frequencies of the V1016G mutation and the survivability rates as well as resistance ratios in pyrethroid adult bioassays. This signifies the V1016G can contribute more to the insensitivity of Vgsc than the F1534C. Homozygous 1016G mosquitoes were likelier to survive pyrethroid exposure. Identification of underlying mechanisms resulting in insecticide resistance is advantageous in developing effective mosquito control programs in Indonesia.