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Displaying publications 521 - 540 of 928 in total

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DNA sequence analysis of a small cryptic plasmid from Lactococcus lactis subsp. lactis M14

Raha AR, Hooi WY, Mariana NS, Radu S, Varma NR, Yusoff K

Plasmid, 2006 Jul;56(1):53-61.
PMID: 16675013

A small plasmid designated pAR141 was isolated from Lactococcus lactis subsp. lactis M14 and its complete 1,594 base pair nucleotide sequence was determined. Analysis of the sequence indicated that this plasmid does not carry any industrially important determinants besides the elements involved in plasmid replication and control. The transcriptional repressor CopG and replication initiation protein RepB appeared as a single operon. A small countertranscribed RNA (ctRNA) coding region was found between the copG and repB genes. The double strand origin (dso) and single strand origin (sso) of rolling circle replicating (RCR) plasmids were also identified in pAR141, suggesting that this plasmid replicates by rolling circle (RC) mode. This observation was supported by S1 nuclease and Southern hybridization analyses.

Matched MeSH terms: Molecular Sequence Data
Neutralization of Burkholderia pseudomallei protease by Fabs generated through phage display

Nathan S, Rader C, Barbas CF

Biosci Biotechnol Biochem, 2005 Dec;69(12):2302-11.
PMID: 16377887

The isolation of therapeutic and functional protease inhibitors in vitro via combinatorial chemistry and phage display technology has been described previously. Here we report the construction of a combinatorial mouse-human chimeric antibody fragment (Fab) antibody library targeted against the protease of the tropical pathogen, Burkholderia pseudomallei. The resulting library was biopanned against the protease, and selected clones were analyzed for their ability to function as protease inhibitors. Three families of Fabs were identified by restriction fingerprinting, all of which demonstrated high specificity towards the protease of B. pseudomallei. Purified Fabs also demonstrated the capacity to inhibit B. pseudomallei protease activity in vitro, and this inhibitory property was exclusive to the pathogenic protease. Thus these recombinant antibodies are candidates for immunotherapy and tools to aid in further elucidation of the mechanism of action of the B. pseudomallei protease.

Matched MeSH terms: Molecular Sequence Data
Heteroplasmy, length, and sequence characterization of the mitochondrial control region in Tomistoma schlegelii

Kaur T, Ong AH

Biochem Genet, 2011 Oct;49(9-10):562-75.
PMID: 21461907 DOI: 10.1007/s10528-011-9431-y

This study describes the organization of the repetitive pattern in the mtDNA control region of Tomistoma schlegelii. Using newly designed primers, we detected length variations of approximately 50-100 bp among individuals, and only one individual showed a heteroplasmic band. Sequencing the region after CSB III revealed two main patterns: a repeat motif and a variable number tandem repeat (VNTR) pattern. The VNTR region, with a core unit of 104 bp, consisting of four motifs and a short AT chain, is implicated in the length variation seen among individuals of Tomistoma. A conserved motif seen in a family unit indicated that the repeat pattern was stably inherited from the maternal parent to all offspring. A combination of VNTR patterns specific to different crocodilians was seen in Tomistoma, and the overall secondary structure was shown to be similar to that in Crocodylus and Gavialis.

Matched MeSH terms: Molecular Sequence Data
Ecological diversification in a group of Indomalayan pitvipers (Trimeresurus): convergence in taxonomically important traits has implications for species identification

Sanders KL, Malhotra A, Thorpe RS

J Evol Biol, 2004 Jul;17(4):721-31.
PMID: 15271071

We analyse molecular and phenotypic evolution in a group of taxonomically problematic Indomalayan pitvipers, the Trimeresurus sumatranus group. Mitochondrial DNA sequencing provides a well-resolved phylogeny, with each species representing a distinct lineage. Multivariate morphological analysis reveals a high level of phenotypic differentiation, which is congruent between the sexes but does not reflect phylogenetic history. An adaptive explanation for the observed pattern of differentiation is supported by independent contrasts analysis, which shows significant correlations between current ecology and the characters that most account for the variation between taxa, including those that are presently used to identify the species. Reduced precipitation and altitude, and increased temperature, are correlated with higher numbers of scales on the head, body and tail. It is hypothesized that scale number plays an important role in heat and water exchange by influencing the area of exposed of interstitial skin, and that colour pattern variation reflects selection pressures involving camouflage and thermoregulation. Ecological convergence in traits used for classification is found to have important implications for species identification where taxa are distributed over varying environments.

Matched MeSH terms: Molecular Sequence Data
Fulltext Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater

Foong CP, Lau NS, Deguchi S, Toyofuku T, Taylor TD, Sudesh K, et al.

BMC Microbiol, 2014;14:318.
PMID: 25539583 DOI: 10.1186/s12866-014-0318-z

Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host.

Matched MeSH terms: Molecular Sequence Data
Fulltext Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population

Tay CY, Mitchell H, Dong Q, Goh KL, Dawes IW, Lan R

BMC Microbiol, 2009;9:126.
PMID: 19538757 DOI: 10.1186/1471-2180-9-126

Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture.

Matched MeSH terms: Molecular Sequence Data
Hydrophobic protein in colorectal cancer in relation to tumor stages and grades

Yeoh LC, Loh CK, Gooi BH, Singh M, Gam LH

World J Gastroenterol, 2010 Jun 14;16(22):2754-63.
PMID: 20533595

AIM: To identify differentially expressed hydrophobic proteins in colorectal cancer.
METHODS: Eighteen pairs of colorectal cancerous tissues in addition to tissues from normal mucosa were analysed. Hydrophobic proteins were extracted from the tissues, separated using 2-D gel electrophoresis and analysed using Liquid Chromatography Tandem Mass Spectrometry (LC/MS/MS). Statistical analysis of the proteins was carried out in order to determine the significance of each protein to colorectal cancer (CRC) and also their relation to CRC stages, grades and patients' gender.
RESULTS: Thirteen differentially expressed proteins which were expressed abundantly in either cancerous or normal tissues were identified. A number of these proteins were found to relate strongly with a particular stage or grade of CRC. In addition, the association of these proteins with patient gender also appeared to be significant.
CONCLUSION: Stomatin-like protein 2 was found to be a promising biomarker for CRC, especially in female patients. The differentially expressed proteins identified were associated with CRC and may act as drug target candidates.

Matched MeSH terms: Molecular Sequence Data
The evolving molecular epidemiology of HIV type 1 among injecting drug users (IDUs) in Malaysia

Tee KK, Saw TL, Pon CK, Kamarulzaman A, Ng KP

AIDS Res Hum Retroviruses, 2005 Dec;21(12):1046-50.
PMID: 16379608

Earlier studies in the 1990s indicate that human immunodeficiency virus type 1 (HIV-1) subtype B has been the predominant subtype among injecting drug users (IDUs) in Malaysia. More recent studies performed between 2003 and 2004, however, show a high prevalence of unique CRF01_AE/B intersubtype recombinants among IDUs. To determine the subtype distribution among IDUs in Kuala Lumpur prior to the emergence of CRF01_AE/B intersubtype recombinants, the gag-pol or the reverse transcriptase gene was sequenced from IDUs who were diagnosed as HIV positive between 1993 and 2002. Subtype B was present at 50.0% followed by CRF01_AE/B recombinant at 41.7%, with more CRF01_AE/B recombinants detected between 2000 and 2002. All CRF01_AE/B recombinants shared similar recombination patterns. Interestingly, we found that this potential new candidate of circulating recombinant form (CRF) could have emerged as early as the mid-1990s. The results showed evidence of changing HIV-1 molecular epidemiology toward the predominance of CRF01_AE/B intersubtype recombinants among IDUs in Kuala Lumpur.

Matched MeSH terms: Molecular Sequence Data
HIV type 1 gag subtype A is predominant in Malaysian intravenous drug users

Kasper P, Chalwatzis N, Duraisamy G, Ofenloch-Hähnle B, Faatz E

AIDS Res Hum Retroviruses, 1997 Sep 20;13(14):1251-3.
PMID: 9310293
Matched MeSH terms: Molecular Sequence Data
HIV type 1 subtypes in Malaysia include B, C, and E

Brown TM, Robbins KE, Sinniah M, Saraswathy TS, Lee V, Hooi LS, et al.

AIDS Res Hum Retroviruses, 1996 Nov 20;12(17):1655-7.
PMID: 8947304
Matched MeSH terms: Molecular Sequence Data
Epitope mapping of the Sta58 major outer membrane protein of Rickettsia tsutsugamushi

Lachumanan R, Devi S, Cheong YM, Rodda SJ, Pang T

Infect Immun, 1993 Oct;61(10):4527-31.
PMID: 7691753

Binding studies of 160 overlapping, synthetic octapeptides from the hydrophilic regions of the Sta58 major outer membrane protein of Rickettsia tsutsugamushi with sera from patients with scrub typhus revealed 15 immunodominant peptides which are recognized by all the sera tested. Further analysis of the specificity of peptide binding with five of these peptides indicated that the peptides showed significantly stronger binding to scrub typhus patients' sera than they did to sera from patients with other febrile illnesses common in the region, i.e., malaria, dengue fever, typhoid fever, and leptospirosis. The main antibody class binding to these peptides appears to be immunoglobulin M, and there appears to be little correlation between reactivity with peptides and antibody titers measured by the indirect immunoperoxidase test.

Matched MeSH terms: Molecular Sequence Data
Sequence analysis of Malaysian infectious bursal disease virus isolate and the use of reverse transcriptase nested polymerase chain reaction enzyme-linked immunosorbent assay for the detection of VP2 hypervariable region

Phong SF, Hair-Bejo M, Omar AR, Aini I

Avian Dis, 2003 Jan-Mar;47(1):154-62.
PMID: 12713171

The VP2 hypervariable region of P97/302 local infectious bursal disease virus (IBDV) isolate was amplified by the reverse transcriptase (RT) nested polymerase chain reaction (PCR) and cloned. This region of P97/302 local isolate was sequenced and compared with eight other reported IBDV sequences. The result showed that P97/302 IBDV was most identical to the reported very virulent IBDV strains because it has amino acid substitutions at positions 222, 256, 294, and 299, which encode alanine, isoleucine, isoleucine, and serine, respectively. This region can be digested with restriction enzymes of Taq1, Sty1, Ssp1 but not with Sac1. The P97/302 isolate was then used for the optimization of RT nested PCR enzyme-linked immunosorbent assay (ELISA). The RT nested PCR ELISA was able to detect 10(-4) dilution of the infected bursa homogenates and was 10 times more sensitive when compared with the agarose gel detection method. The RT nested PCR ELISA can detect up to 0.48 ng of the PCR product. The specificity of this nested PCR ELISA was also high (100%).

Matched MeSH terms: Molecular Sequence Data
Fulltext Regulation of embryonic hematopoiesis by a cytokine-inducible SH2 domain homolog in zebrafish

Lewis RS, Noor SM, Fraser FW, Sertori R, Liongue C, Ward AC

J Immunol, 2014 Jun 15;192(12):5739-48.
PMID: 24835394 DOI: 10.4049/jimmunol.1301376

Cytokine-inducible SH2 domain-containing protein (CISH), a member of the suppressor of cytokine signaling family of negative feedback regulators, is induced by cytokines that activate STAT5 and can inhibit STAT5 signaling in vitro. However, demonstration of a definitive in vivo role for CISH during development has remained elusive. This study employed expression analysis and morpholino-mediated knockdown in zebrafish in concert with bioinformatics and biochemical approaches to investigate CISH function. Two zebrafish CISH paralogs were identified, cish.a and cish.b, with high overall conservation (43-46% identity) with their mammalian counterparts. The cish.a gene was maternally derived, with transcripts present throughout embryogenesis, and increasing at 4-5 d after fertilization, whereas cish.b expression commenced at 8 h after fertilization. Expression of cish.a was regulated by the JAK2/STAT5 pathway via conserved tetrameric STAT5 binding sites (TTCN3GAA) in its promoter. Injection of morpholinos targeting cish.a, but not cish.b or control morpholinos, resulted in enhanced embryonic erythropoiesis, myelopoiesis, and lymphopoiesis, including a 2- 3-fold increase in erythrocytic markers. This occurred concomitantly with increased activation of STAT5. This study indicates that CISH functions as a conserved in vivo target and regulator of STAT5 in the control of embryonic hematopoiesis.

Matched MeSH terms: Molecular Sequence Data
Biological properties of TW01 cells expressing latent membrane protein-1 gene of EBV-derived from nasopharyngeal carcinoma cells at different stages of malignancy

Tan EL, Sam CK

Exp Oncol, 2007 Sep;29(3):166-74.
PMID: 18004239

Epstein-Barr virus (EBV), a human gammaherpesvirus is intimately associated with nasopharyngeal carcinoma (NPC), with the incidence of the virus detected in malignant tissues being close to 100% in NPC endemic areas. The viral latent gene, latent membrane protein 1 (LMP1), has all the typical characteristics of an oncogene and extensive studies have shown beyond doubt its abilities in cellular transformation giving rise to malignant phenotypes. The present study compares the gene sequence and biological properties of LMP1 gene derived from two patients with different stages of NPC--one presented with dysplastic, pre-malignant lesion and the other with malignant lesion.

Matched MeSH terms: Molecular Sequence Data
Regional and accelerated molecular evolution in group I snake venom gland phospholipase A2 isozymes

Chuman Y, Nobuhisa I, Ogawa T, Deshimaru M, Chijiwa T, Tan NH, et al.

Toxicon, 2000 Mar;38(3):449-62.
PMID: 10669032

In accordance with detection of a few phospholipase A2 (PLA2) isozyme genes by Southern blot analysis, only two cDNAs, named NnkPLA-I , and NnkPLA-II, encoding group I PLA2s, NnkPLA-I and NnkPLA-II, respectively, were isolated from the venom gland cDNA library of Elapinae Naja naja kaouthia of Malaysia. NnkPLA-I and NnkPLA-II showed four amino acid substitutions, all of which were brought about by single nucleotide substitution. No existence of clones encoding CM-II and CM-III, PLA2 isozymes which had been isolated from the venom of N. naja kaouthia of Thailand, in Malaysian N. naja kaouthia venom gland cDNA library was verified by dot blot hybridization analysis with particular probes. NnkPLA-I and NnkPLA-II differed from CM-II and CM-III with four and two amino acid substitutions, respectively, suggesting that their molecular evolution is regional. The comparison of NnkPLA-I, NnkPLA-II and cDNAs encoding other group I snake venom gland PLA2s indicated that the 5'- and 3'-untranslated regions are more conserved than the mature protein-coding region and that the number of nucleotide substitutions per nonsynonymous site is almost equal to that per synonymous site in the protein-coding region, suggesting that accelerated evolution has occurred in group I venom gland PLA2s possibly to acquire new physiological functions.

Matched MeSH terms: Molecular Sequence Data
Fulltext Isolation and molecular characterization of Brucella melitensis from seropositive goats in Peninsula Malaysia

Bamaiyi PH, Hassan L, Khairani-Bejo S, Zainal Abidin M, Ramlan M, Krishnan N, et al.

Trop Biomed, 2012 Dec;29(4):513-8.
PMID: 23202595

A study was carried out to isolate Brucella melitensis using established bacteriological and PCR techniques in Brucella seropositive goats in farms in Selangor, Negeri Sembilan, Melaka and Pulau Pinang. Brucella melitensis was isolated from 7 of 134 reactors with the highest isolation from the vaginal swabs (57.14%) followed by the spleen (28.57%), uterine fluid (14.29%). No Brucella was isolated from the lymph nodes. PCR confirmed all the seven isolates as B. melitensis and isolates were phylogenetically related to other isolates from India, Iran, and Israel but most closely related to isolates from Singapore.

Matched MeSH terms: Molecular Sequence Data
Fulltext DNA typing of Calliphorids collected from human corpses in Malaysia

Kavitha R, Tan TC, Lee HL, Nazni WA, Sofian-Azirun M

Trop Biomed, 2013 Mar;30(1):119-24.
PMID: 23665717 MyJurnal

Estimation of post-mortem interval (PMI) is crucial for time of death determination. The advent of DNA-based identification techniques forensic entomology saw the beginning of a proliferation of molecular studies into forensically important Calliphoridae (Diptera). The use of DNA to characterise morphologically indistinguishable immature calliphorids was recognised as a valuable molecular tool with enormous practical utility. The local entomofauna in most cases is important for the examination of entomological evidences. The survey of the local entomofauna has become a fundamental first step in forensic entomological studies, because different geographical distributions, seasonal and environmental factors may influence the decomposition process and the occurrence of different insect species on corpses. In this study, calliphorids were collected from 13 human corpses recovered from indoors, outdoors and aquatic conditions during the post-mortem examination by pathologists from the government hospitals in Malaysia. Only two species, Chrysomya megacephala and Chrysomya rufifacies were recovered from human corpses. DNA sequencing was performed to study the mitochondrial encoded COI gene and to evaluate the suitability of the 1300 base pairs of COI fragments for identification of blow fly species collected from real crime scene. The COI gene from blow fly specimens were sequenced and deposited in GenBank to expand local databases. The sequenced COI gene was useful in identifying calliphorids retrieved from human corpses.

Matched MeSH terms: Molecular Sequence Data
Fulltext Simulium (Nevermannia) chomthongense, a new species of black fly (Diptera: Simuliidae) from Chiang Mai, Thailand

Takaoka H, Srisuka W, Saeung A, Otsuka Y, Choochote W

Trop Biomed, 2012 Sep;29(3):381-90.
PMID: 23018501

Simulium (Nevermannia) chomthongense sp. nov. is described from female, male, pupal and larval specimens collected from Doi Inthanon National Park and Doi Phahompok National Park, Chiang Mai, Thailand. This new species, first reported as S. (Eusimulium) sp. A, and later regarded as S. (N.) caudisclerum Takaoka & Davies, described from peninsular Malaysia, is distinguished from S. (N.) caudisclerum in the male by the number of enlarged upper-eye facets and the relative size of the hind basitarsus against the hind tibia and femur, and in the pupa by the relative length of the stalks of paired filaments against the common basal stalk and the color of the dorsal surface of abdominal segments 1- 3 (or 4). Taxonomic and molecular notes are provided to separate this new species from four other known species of the vernum species-group, which share an accessory sclerite on the larval abdomen, a rare characteristic in this species-group.

Matched MeSH terms: Molecular Sequence Data
Fulltext Sequence analysis on the mitochondrial COXI gene of recent clinical isolates of Plasmodium knowlesi in Klang Valley, peninsular Malaysia

Fong MY, Lau YL, Chin LC, Al-Mekhlafi AM

Trop Biomed, 2011 Aug;28(2):457-63.
PMID: 22041769

The cytochrome oxidase subunit I (COXI) gene sequences of three recent (2007-2008) clinical Plasmodium knowlesi isolates from Klang Valley, peninsular Malaysia, were determined and compared with those of older (1960's) peninsular Malaysia, recent isolates from Sarawak (on Borneo Island), and an isolate from Thailand. Multiple alignment of the sequences showed that the three clinical isolates were more similar to the older peninsular Malaysia isolates than to those from Sarawak and Thailand. Phylogenetic tree based on the COXI sequences revealed three distinct clusters of P. knowlesi. The first cluster consisted of isolates from peninsular Malaysia, the second consisted of Sarawak isolates and the third composed of the Thailand isolate. The findings of this study highlight the usefulness of mitochondrial COXI gene as a suitable marker for phylogeographic studies of P. knowlesi.

Matched MeSH terms: Molecular Sequence Data
Fulltext Plasmodium falciparum 19 kDa of merozoite surface protein-1 (MSP-1(19)) expressed in Mycobacterium bovis bacille Calmette Guerin (BCG) is reactive with an inhibitory but not a blocking monoclonal antibody

Nurul AA, Rapeah S, Norazmi MN

Trop Biomed, 2010 Apr;27(1):60-7.
PMID: 20562815

Proteins on the surface of Plasmodium falciparum merozoites are good targets for vaccine development against malaria because they are accessible to antibodies in the plasma. The 19 kDa C-terminus of merozoite surface protein-1 (MSP-1(19)) has been shown to induce both inhibitory as well as blocking antibodies, the latter blocking the protective effects of the former. Inhibitory antibodies bind to MSP-1(19) and inhibit merozoite invasion of red blood cells (RBC) but the binding of blocking antibodies can prevent binding of inhibitory antibodies thereby allowing the parasite to invade RBC. We constructed a synthetic version of the MSP-1(19) of the P. falciparum using mycobacterium codon usage by assembly PCR. The synthetic MSP-1(19) was mutated at various sites to promote the production of inhibitory but not blocking antibodies as previously reported. The native and mutated MSP-1(19) were cloned and expressed in Mycobacterium bovis bacille Calmette-Guerin (BCG) and the expressions of the recombinant proteins were detected by specific monoclonal antibodies (mAbs) namely, 12.10 and 1E1 against MSP-1(19) using Western blotting. The mutated MSP-1(19) protein reacted with the inhibitory mAb, 12.10, but not the blocking mAb, 1E1, paving the way for the construction of a potential recombinant BCG (rBCG) blood stage vaccine against malaria.

Matched MeSH terms: Molecular Sequence Data

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