MyMedR

Displaying publications 1 - 20 of 928 in total

Abstract:

Sort:

'Babesia gibsoni' of dogs from North America and Asia belong to different species

Zahler M, Rinder H, Zweygarth E, Fukata T, Maede Y, Schein E, et al.

Parasitology, 2000 Apr;120 ( Pt 4):365-9.
PMID: 10811277

18S rDNA sequences from 4 isolates of Babesia gibsoni originating from Japan, Malaysia and Sri Lanka were compared with a previously published, 0.5 kb portion of the 18S rDNA from a B. gibsoni isolate from California, USA, and with the corresponding 18S rDNA sequences of other Babesia spp. Distance, parsimony and maximum likelihood analyses showed almost identical genotypes among the small canine Babesia from Asia, but an unexpectedly distant genetic relationship to that from the USA. While the American isolate segregated together with B. equi, the Asian isolates showed a close relationship to B. divergens and B. odocoilei. These results indicate that small Babesia of dogs originating from North America and Asia belong to different, genetically distantly related species.

Matched MeSH terms: Molecular Sequence Data
'Candidatus Phytoplasma malaysianum', a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus)

Nejat N, Vadamalai G, Davis RE, Harrison NA, Sijam K, Dickinson M, et al.

Int J Syst Evol Microbiol, 2013 Feb;63(Pt 2):540-548.
PMID: 22523165 DOI: 10.1099/ijs.0.041467-0

This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytoplasma distinguished the phytoplasma from all previously described 'Candidatus Phytoplasma' species. Pairwise sequence similarity scores, calculated through alignment of full-length 16S rRNA gene sequences, revealed that the MaPV phytoplasma 16S rRNA gene shared 96.5 % or less sequence similarity with that of previously described 'Ca. Phytoplasma' species, justifying the recognition of the MaPV phytoplasma as a reference strain of a novel taxon, 'Candidatus Phytoplasma malaysianum'. The 16S rRNA gene F2nR2 fragment from the MaPV phytoplasma exhibited a distinct restriction fragment length polymorphism (RFLP) profile and the pattern similarity coefficient values were lower than 0.85 with representative phytoplasmas classified in any of the 31 previously delineated 16Sr groups; therefore, the MaPV phytoplasma was designated a member of a new 16Sr group, 16SrXXXII. Phytoplasmas affiliated with this novel taxon and the new group included diverse strains infecting periwinkle, coconut palm and oil palm in Malaysia. Three phytoplasmas were characterized as representatives of three distinct subgroups, 16SrXXXII-A, 16SrXXXII-B and 16SrXXXII-C, respectively.

Matched MeSH terms: Molecular Sequence Data
3'-UTR variations and G6PD deficiency

Amini F, Ismail E

J Hum Genet, 2013 Apr;58(4):189-94.
PMID: 23389243 DOI: 10.1038/jhg.2012.155

The combination of two silent mutations, c.1311C>T in exon 11 and IVS11 T93C (glucose-6-phosphate dehydrogenase (G6PD) 1311T/93C), with unknown mechanism, have been reported in G6PD-deficient individuals in Asian populations including Malaysian aboriginal group, Negrito. Here, we report the screening of G6PD gene in 103 Negrito volunteers using denaturing high-performance liquid chromatography (dHPLC) and direct sequencing. A total of 48 individuals (46.6%) were G6PD deficient, 83.3% of these carried G6PD 1311T/93C with enzyme activity ranging from 1.8 to 4.8 U gHb(-1). Three novel single-nucleotide polymorphisms (SNPs), rs112950723, rs111485003 and rs1050757, were found in the G6PD 3'-untranslated region (UTR). Strong association was observed between haplotype 1311T/93C and rs1050757G, which is located inside the 35 bp AG-rich region. In silico analysis revealed that the transition of A to G at position rs1050757 makes significant changes in the G6PD mRNA secondary structure. Moreover, putative micro (mi)RNA target sites were identified in 3'-UTR of G6PD gene, two of these in the region encompassing rs1050757. It could be speculated that rs1050757 have a potential functional effect on the downregulation of mRNA and consequently G6PD deficiency either by affecting mRNA stability and translation or mirRNA regulation process. This is the first report of biochemical association of an SNP in 3'-UTR of G6PD gene and the possible role of mRNA secondary structure.

Matched MeSH terms: Molecular Sequence Data
Fulltext 4'-O-substitutions determine selectivity of aminoglycoside antibiotics

Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, et al.

Nat Commun, 2014;5:3112.
PMID: 24473108 DOI: 10.1038/ncomms4112

Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.

Matched MeSH terms: Molecular Sequence Data
Fulltext A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence

Lou H, Lu Y, Lu D, Fu R, Wang X, Feng Q, et al.

Am J Hum Genet, 2015 Jul 02;97(1):54-66.
PMID: 26073780 DOI: 10.1016/j.ajhg.2015.05.005

Tibetan high-altitude adaptation (HAA) has been studied extensively, and many candidate genes have been reported. Subsequent efforts targeting HAA functional variants, however, have not been that successful (e.g., no functional variant has been suggested for the top candidate HAA gene, EPAS1). With WinXPCNVer, a method developed in this study, we detected in microarray data a Tibetan-enriched deletion (TED) carried by 90% of Tibetans; 50% were homozygous for the deletion, whereas only 3% carried the TED and 0% carried the homozygous deletion in 2,792 worldwide samples (p < 10(-15)). We employed long PCR and Sanger sequencing technologies to determine the exact copy number and breakpoints of the TED in 70 additional Tibetan and 182 diverse samples. The TED had identical boundaries (chr2: 46,694,276-46,697,683; hg19) and was 80 kb downstream of EPAS1. Notably, the TED was in strong linkage disequilibrium (LD; r(2) = 0.8) with EPAS1 variants associated with reduced blood concentrations of hemoglobin. It was also in complete LD with the 5-SNP motif, which was suspected to be introgressed from Denisovans, but the deletion itself was absent from the Denisovan sequence. Correspondingly, we detected that footprints of positive selection for the TED occurred 12,803 (95% confidence interval = 12,075-14,725) years ago. We further whole-genome deep sequenced (>60×) seven Tibetans and verified the TED but failed to identify any other copy-number variations with comparable patterns, giving this TED top priority for further study. We speculate that the specific patterns of the TED resulted from its own functionality in HAA of Tibetans or LD with a functional variant of EPAS1.

Matched MeSH terms: Molecular Sequence Data
A 35 kDa antigenic protein from Shigella flexneri: in silico structural and functional studies

Yung-Hung RL, Ismail A, Lim TS, Choong YS

Biochem Biophys Res Commun, 2011 Nov 18;415(2):229-34.
PMID: 21982766 DOI: 10.1016/j.bbrc.2011.09.116

Shigella flexneri serotype 2a is a major public health concern in the developing and under-developed countries which contributes to shigellosis endemic and mortality. Thus, there is an urgent need for a rapid diagnostic test for effective therapy and disease management. Previous study showed that a ∼35 kDa antigenic protein from S. flexneri is a potential biomarker. We therefore modelled the three-dimensional structure of the antigen to probe its functionality which could aid in the development of an antigen-based diagnostic. Results showed that the antigen is a transmembrane protein consists of OmpA and OmpA-like domains. The OmpA domain is a beta-barrel embedded in the outer membrane with four surface-exposed extracellular loops. The OmpA-like domain is linked to the OmpA domain with a 17 amino acids linker and located in the periplasmic. Docking of peptidoglycan into the groove of OmpA-like domain might help in catalyzing the bacterial cell wall formation. Both domains are expected to be involved in the virulence, structural stability, pathogenesis and survival of Shigella thus made the 35 kDa protein a suitable shigellosis diagnostic biomarker. This structural elucidation will also enable a better identification of the epitope regions for the development of specific binders to the 35 kDa antigen.

Matched MeSH terms: Molecular Sequence Data
A MALDI TOF MS-based minisequencing method for rapid detection of TEM-type extended-spectrum beta-lactamases in clinical strains of Enterobacteriaceae

Ikryannikova LN, Shitikov EA, Zhivankova DG, Il'ina EN, Edelstein MV, Govorun VM

J Microbiol Methods, 2008 Dec;75(3):385-91.
PMID: 18694787 DOI: 10.1016/j.mimet.2008.07.005

A minisequencing method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) was developed for rapid identification of single nucleotide polymorphisms at bla(TEM) gene codons 104, 164 and 238 associated with extended-spectrum activity on TEM-type beta-lactamases. The method was validated by testing the Escherichia coli and Klebsiella pneumoniae strains possessing the known bla(TEM) gene sequences.

Matched MeSH terms: Molecular Sequence Data
Fulltext A Sco protein among the hypothetical proteins of Bacillus lehensis G1: Its 3D macromolecular structure and association with Cytochrome C Oxidase

Tan SH, Normi YM, Leow AT, Salleh AB, Karjiban RA, Murad AM, et al.

BMC Struct Biol, 2014 Mar 19;14:11.
PMID: 24641837 DOI: 10.1186/1472-6807-14-11

BACKGROUND: At least a quarter of any complete genome encodes for hypothetical proteins (HPs) which are largely non-similar to other known, well-characterized proteins. Predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. The present study highlights the primary effort to classify and cluster 1202 HPs of Bacillus lehensis G1 alkaliphile to serve as a platform to mine and select specific HP(s) to be studied further in greater detail.
RESULTS: All HPs of B. lehensis G1 were grouped according to their predicted functions based on the presence of functional domains in their sequences. From the metal-binding group of HPs of the cluster, an HP termed Bleg1_2507 was discovered to contain a thioredoxin (Trx) domain and highly-conserved metal-binding ligands represented by Cys69, Cys73 and His159, similar to all prokaryotic and eukaryotic Sco proteins. The built 3D structure of Bleg1_2507 showed that it shared the βαβαββ core structure of Trx-like proteins as well as three flanking β-sheets, a 310 -helix at the N-terminus and a hairpin structure unique to Sco proteins. Docking simulations provided an interesting view of Bleg1_2507 in association with its putative cytochrome c oxidase subunit II (COXII) redox partner, Bleg1_2337, where the latter can be seen to hold its partner in an embrace, facilitated by hydrophobic and ionic interactions between the proteins. Although Bleg1_2507 shares relatively low sequence identity (47%) to BsSco, interestingly, the predicted metal-binding residues of Bleg1_2507 i.e. Cys-69, Cys-73 and His-159 were located at flexible active loops similar to other Sco proteins across biological taxa. This highlights structural conservation of Sco despite their various functions in prokaryotes and eukaryotes.
CONCLUSIONS: We propose that HP Bleg1_2507 is a Sco protein which is able to interact with COXII, its redox partner and therefore, may possess metallochaperone and redox functions similar to other documented bacterial Sco proteins. It is hoped that this scientific effort will help to spur the search for other physiologically relevant proteins among the so-called "orphan" proteins of any given organism.

Matched MeSH terms: Molecular Sequence Data
A case of beta-thalassemia with a C----T substitution at position 654 of the second intervening sequence of the beta-globin gene

Jo T, Momita S, Sadamori N, Tomonaga M, Fucharoem S, Fukumaki Y, et al.

Intern. Med., 1992 Feb;31(2):269-72.
PMID: 1600278

A 26-year-old Chinese-Malaysian female patient with beta-thalassemia is presented. The main hematological values found in this patient were as follows: 1) normocytic hypochromic anemia (RBC 444 x 10(4)/microliters, Hb 11.8 g/dl) with marked anisopoikilocytosis, 2) erythroid hyperplasia, and 3) increased HbF (HbA 41.4%, HbA2 2.9%, HbF 48.9%). DNA obtained from peripheral leukocytes was analyzed using dot blot hybridization of the polymerase chain reaction (PCR)-amplified DNA with allele-specific oligonucleotide probes. A C----T substitution at position 654 of the second intervening sequence (IVS-2) was detected in her beta-globin clone.

Matched MeSH terms: Molecular Sequence Data
A combination of evolutionary trace method, molecular surface accessibility and hydrophobicity analysis to design a high hydrophobicity laccase

Mohamad SB, Ong AL, Khairuddin RF, Ripen AM

In Silico Biol. (Gedrukt), 2010;10(3):145-53.
PMID: 22430288 DOI: 10.3233/ISB-2010-0423

Laccases are industrially attractive enzymes and their applications have expanded to the field of bioremediation. The challenge of today's biotechnology in enzymatic studies is to design enzymes that not only have a higher activity but are also more stable and could fit well with the condition requirements. Laccases are known to oxidize non-natural substrates like polycyclic aromatic hydrocarbons (PAHs). We suppose by increasing the hydrophobicity of laccase, it would increase the chance of the enzyme to meet the hydrophobic substrates in a contamination site, therefore increasing the bioremediation efficacy of PAHs from environment. In this attempt, the applications of evolutionary trace (ET), molecular surface accessibility and hydrophobicity analysis on laccase sequences and laccase's crystal structure (1KYA) are described for optimal design of an enzyme with higher hydrophobicity. Our analysis revealed that Q23A, Q45I, N141A, Q237V, N262L, N301V, N331A, Q360L and Q482A could be promising exchanges to be tested in mutagenesis experiments.

Matched MeSH terms: Molecular Sequence Data
A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1

Noor YM, Samsulrizal NH, Jema'on NA, Low KO, Ramli AN, Alias NI, et al.

Gene, 2014 Jul 25;545(2):253-61.
PMID: 24811681 DOI: 10.1016/j.gene.2014.05.012

Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99 Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium-proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes.

Matched MeSH terms: Molecular Sequence Data
A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling

Razmara J, Deris SB, Parvizpour S

Comput Biol Med, 2013 Oct;43(10):1614-21.
PMID: 24034753 DOI: 10.1016/j.compbiomed.2013.07.022

The structural comparison of proteins is a vital step in structural biology that is used to predict and analyse a new unknown protein function. Although a number of different techniques have been explored, the study to develop new alternative methods is still an active research area. The present paper introduces a text modelling-based technique for the structural comparison of proteins. The method models the secondary and tertiary structure of proteins in two linear sequences and then applies them to the comparison of two structures. The technique used for pairwise comparison of the sequences has been adopted from computational linguistics and its well-known techniques for analysing and quantifying textual sequences. To this end, an n-gram modelling technique is used to capture regularities between sequences, and then, the cross-entropy concept is employed to measure their similarities. Several experiments are conducted to evaluate the performance of the method and compare it with other commonly used programs. The assessments for information retrieval evaluation demonstrate that the technique has a high running speed, which is similar to other linear encoding methods, such as 3D-BLAST, SARST, and TS-AMIR, whereas its accuracy is comparable to CE and TM-align, which are high accuracy comparison tools. Accordingly, the results demonstrate that the algorithm has high efficiency compared with other state-of-the-art methods.

Matched MeSH terms: Molecular Sequence Data
A diminutive new species of cave-dwelling Wolf Snake (Colubridae: Lycodon Boie, 1826) from Peninsular Malaysia

Grismer LL, Quah ES, Anuar M S S, Muin MA, Wood PL, Nor SA

Zootaxa, 2014.
PMID: 24943599 DOI: 10.11646/zootaxa.3815.1.3

A newly discovered, diminutive, cave-dwelling, lowland species of the colubrid snake genus Lycodon Boie is described from a limestone cave along the Thai-Malaysian border in the state of Perlis, northwestern Peninsular Malaysia. Lycodon cavernicolus sp. nov. is most closely related to L. butleri Boulenger, an endemic, upland, forest-dwelling species from Peninsular Malaysia of the fasciatus group but is separated from L. butleri and all other species of the L. fasciatus group and the closely related L. ruhstrati group by having the combination of 245 (male) and 232 (female) ventral scales; 113 (male) and 92 (female) paired, subcaudal scales; a single precloacal plate; nine or 10 supralabials; 10 or 11 infralabials; a maximum total length of 508 mm (female); a relative tail length of 0.25-0.27; an immaculate venter in juveniles and dark-brown, posterior, ventral scale margins in adults; and dorsal and caudal bands in juveniles white. The discovery of L. cavernicolus sp. nov. adds to a rapidly growing list of newly discovered reptiles from karst regions and limestone forests of Peninsular Malaysia, underscoring the fact that these areas should be studied before they are quarried as they harbor a significant portion of the Peninsular Malaysia's herpetological diversity.

Matched MeSH terms: Molecular Sequence Data
A ferulic acid ester of sucrose and other constituents of Bhesa paniculata

Harrison LJ, Sia GL, Sim KY, Tan HT, Connolly JD, Lavaud C, et al.

Phytochemistry, 1995 Apr;38(6):1497-500.
PMID: 7786481

A novel derivative of sucrose, beta-(3,6-di-O-feruloyl)-fructofuranosyl-alpha-(2,3,4,6-tetra-O-ac etyl)- glucopyranoside, was isolated from the wood of Bhesa paniculata. Its structure was determined by a combination of 2D 1H-1H and 1H-13C correlation NMR spectroscopy. The known compounds, glycerol 1-9',12'-octadecadienoate, beta-sitosterol, (+/-)-pinoresinol, methyl 3,4-dihydroxybenzoate, 4-hydroxy-3-methoxybenzoic acid, anofinic acid and 2-(1'-methylethenyl)-benzofuran-5-carboxylic acid were also isolated.

Matched MeSH terms: Molecular Sequence Data
A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences

Othman RM, Deris S, Illias RM

J Biomed Inform, 2008 Feb;41(1):65-81.
PMID: 17681495

A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms. The genetic similarity algorithm combines semantic similarity measure algorithm with parallel genetic algorithm. The semantic similarity measure algorithm is used to compute the similitude strength between the Gene Ontology terms. Then, the parallel genetic algorithm is employed to perform batch retrieval and to accelerate the search in large search space of the Gene Ontology graph. The genetic similarity algorithm is implemented in the Gene Ontology browser named basic UTMGO to overcome the weaknesses of the existing Gene Ontology browsers which use a conventional approach based on keyword matching. To show the applicability of the basic UTMGO, we extend its structure to develop a Gene Ontology -based protein sequence annotation tool named extended UTMGO. The objective of developing the extended UTMGO is to provide a simple and practical tool that is capable of producing better results and requires a reasonable amount of running time with low computing cost specifically for offline usage. The computational results and comparison with other related tools are presented to show the effectiveness of the proposed algorithm and tools.

Matched MeSH terms: Molecular Sequence Data
A human adenovirus species B subtype 21a associated with severe pneumonia

Hage E, Huzly D, Ganzenmueller T, Beck R, Schulz TF, Heim A

J Infect, 2014 Nov;69(5):490-9.
PMID: 24975176 DOI: 10.1016/j.jinf.2014.06.015

Between 2005 and 2013 six severe pneumonia cases (all requiring mechanical ventilation, two fatal outcomes) caused by human adenovirus type 21 (HAdV-B21) were observed in Germany. So far, HAdV-B21 was mainly associated with non-severe upper and lower respiratory tract infections. However, a few highly virulent HAdV types, e.g. HAdV-B14p1, were previously associated with severe, fatal pneumonia. Complete genomic sequences of the German HAdV-B21 pneumonia isolates formed a single phylogenetic cluster with very high sequence identity (≥ 99.897%). Compared to the HAdV-B21 prototype (only 99.319% identity), all isolates had a unique 15 amino acid deletion and a 2 amino acid insertion in the RGD loop of the penton base which may affect binding to the secondary receptor on the host cells. Moreover, a recombinant E4 gene region derived of HAdV-B3 was identified by bootscan analysis. Thus, the highly virulent, pneumotropic HAdV-B21 was denominated as subtype 21a. Surprisingly, there was 99.963% identity with agent Y/SIBU97 (only 13.4 kb available in GenBank of the 35.4 kb genome) which was associated with 10 fatalities due to cardiopulmonary failure in Sarawak, Malaysia, in 1997. In conclusion, a HAdV-B21 subtype (21a) associated with severe pneumonia in Germany was phylogenetically linked to an adenovirus isolated in Malaysia.

Matched MeSH terms: Molecular Sequence Data
A molecular epidemiological study targeting the glycoprotein gene of rabies virus isolates from China

Meng SL, Yan JX, Xu GL, Nadin-Davis SA, Ming PG, Liu SY, et al.

Virus Res, 2007 Mar;124(1-2):125-38.
PMID: 17129631

A group of 31 rabies viruses (RABVs), recovered primarily from dogs, one deer and one human case, were collected from various areas in China between 1989 and 2006. Complete G gene sequences determined for these isolates indicated identities of nucleotide and amino acid sequences of >or=87% and 93.8%, respectively. Phylogenetic analysis of these and some additional Chinese isolates clearly supported the placement of all Chinese viruses in Lyssavirus genotype 1 and divided all Chinese isolates between four distinct groups (I-IV). Several variants identified within the most commonly encountered group I were distributed according to their geographical origins. A comparison of representative Chinese viruses with other isolates retrieved world-wide indicated a close evolutionary relationship between China group I and II viruses and those of Indonesia while China group III viruses formed an outlying branch to variants from Malaysia and Thailand. China group IV viruses were closely related to several vaccine strains. The predicted glycoprotein sequences of these RABVs variants are presented and discussed with respect to the utility of the anti-rabies biologicals currently employed in China.

Matched MeSH terms: Molecular Sequence Data
A multi-locus approach resolves the phylogenetic relationships of the Simulium asakoae and Simulium ceylonicum species groups in Malaysia: evidence for distinct evolutionary lineages

Low VL, Takaoka H, Adler PH, Ya'cob Z, Norma-Rashid Y, Chen CD, et al.

Med Vet Entomol, 2015 Sep;29(3):330-7.
PMID: 25968459 DOI: 10.1111/mve.12120

A multi-locus approach was used to examine the DNA sequences of 10 nominal species of blackfly in the Simulium subgenus Gomphostilbia (Diptera: Simuliidae) in Malaysia. Molecular data were acquired from partial DNA sequences of the mitochondria-encoded cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA genes, and the nuclear-encoded 18S rRNA and 28S rRNA genes. No single gene, nor the concatenated gene set, resolved all species or all relationships. However, all morphologically established species were supported by at least one gene. The multi-locus sequence analysis revealed two distinct evolutionary lineages, conforming to the morphotaxonomically recognized Simulium asakoae and Simulium ceylonicum species groups.

Matched MeSH terms: Molecular Sequence Data
A new HLA-B*35 allele, B*3589, detected in a Malaysian individual

Phipps M, Jinam T

Tissue Antigens, 2009 Mar;73(3):279-80.
PMID: 19144089 DOI: 10.1111/j.1399-0039.2008.01195.x

A novel human leukocyte antigen-B allele officially named B*3589, was found in an indigenous individual of Jehai ethnicity when sequencing was performed to investigate human genome variation in a research project. B*3589 differs form B*3505 in a point mutation at codon 169 (CGC to TGC) resulting in an amino acid change from Arg to Cys.

Matched MeSH terms: Molecular Sequence Data
A new method for FMR1 gene methylation screening by multiplex methylation-specific real-time polymerase chain reaction

Elias MH, Ankathil R, Salmi AR, Sudhikaran W, Limprasert P, Zilfalil BA

Genet Test Mol Biomarkers, 2011 Jun;15(6):387-93.
PMID: 21329465 DOI: 10.1089/gtmb.2010.0191

Fragile X Syndrome (FXS) is the most common form of inherited mental retardation in men. It is caused by abnormalities in the FMR1 gene that are associated with CGG repeat expansion and the hypermethylation status of its promoter. Methylated alleles lead to transcriptional inhibition and consequent loss of Fragile X Mental Retardation Protein. Chemical modification of cytosine to uracil by bisulfite treatment has proved to be an attractive method for DNA methylation studies that precludes labor-intensive Southern blot analysis, which is the gold standard test for FXS. In this report, bisulfite-treated DNA samples were amplified using real-time multiplex methylation-specific polymerase chain reaction followed by melting curve analysis. Our results show that all control samples with known CGG repeat numbers and methylation statuses were correctly diagnosed. The samples from 43 male patients were also successfully diagnosed, which were in complete agreement with the results of Southern blotting. By such means, 39 patients were found to have an unmethylated allele; 3, a fully mutated allele; and 1, both methylated and unmethylated alleles, thus implying a diagnosis of mosaicism. In conclusion, we find our method to be convenient for screening a large number of male patients with FXS, because it is rapid and easy to perform, especially when there is a low quantity of DNA that must be sensitively and accurately assayed.

Matched MeSH terms: Molecular Sequence Data

Filters

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

External Links