As a health-beneficial fruit, litchi is widely accepted by people in subtropical and tropical regions. However, the critical chemicals responsible for the health benefits are not clear yet. As a large amount of polysaccharides are present in litchi, they might play an important role in the health benefits. In this work, the main water-soluble polysaccharide (LPPBa) was purified from litchi pulp. The chemical structure was characterized as arabinogalactan by gas chromatography and nuclear magnetic resonance spectrometry (NMR). NMR data revealed the glycosidic linkages and their locations in backbone and branches. The precise structure was putatively identified as below, and it was different to those commonly occurred arabinogalactans. The molecular weight was determined to be 2.4 × 10(6)Da by gel permeation chromatography.
We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680 bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A + T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254 bp in length with the A + T content of 55.09% and four replicates of a 76-bp repeat within this region.
The ciliated protozoan parasite Cryptocaryon irritans infecting marine fishes in Taiwan is described. Developmental characteristics and sequences of the ribosomal DNA regions such as part of 18 S, the entire first internal transcribed spacer, and part of 5.8 S of various Taiwan isolates of C. irritans were investigated. A total of 5 isolates was obtained from different fish-host species and localities, the majority from cultured fish species. C. irritans from Taiwan is able to shift its developmental characteristics, i.e. from non-adherent to adherent tomonts, from individualistic to aggregate-forming tomonts, from infection of the gills only to infection of the gills and body. Thus, it is not possible to classify strains of C. irritans on the basis of these parameters. Premature tomonts that developed from dead fishes were able to produce theronts that could infect fish host. Isolates from Pingtung and the USA had identical nucleotide sequences while an isolate from Malaysia was identical to an Israel isolate. Percentage variation among pairs of Taiwan isolates showed a higher degree of variation than isolate sequences listed in GenBank. Sequence analysis revealed highly aberrant isolates in Taiwan, and a phylogenetic tree distinguished a marine and a low-salinity variant. C. irritans from marine fishes in Taiwan, therefore, display some characteristics not previously reported. Since manipulation of salinity in brackishwater ponds and marine cage sites is not feasible, there is a need to develop new strategies for the control and prevention of cryptocaryoniasis.
The present study was done to determine the molecular epidemiology of rabies virus (RV) in Vietnam. The nucleoprotein (N) and glycoprotein (G) genes of RVs were amplified from the brains of ten rabid dogs of Ho Chi Minh City, Vietnam. The nucleotide sequences of these genes were compared with those of other Asian strains to find the possible relationship among them. Phylogenetic analysis revealed that the Asian N gene segregated into three main branches, namely South-East Asia 1 (SEA 1), South-East Asia 2 (SEA 2) and Indian subcontinent (ISC) genotypes. The SEA 1 genotype comprised RVs from Malaysia, Vietnam and Thailand. The SEA 2 genotype contained strains from the Philippines, and the ISC genotype comprised strains from Sri Lanka and India. Phylogenetically G genes of RVs from Vietnam and Thailand were clustered together. Our study suggests that Vietnamese and Thai RVs are closely related and might have originated from a common ancestor.
Burkholderia pseudomallei is an opportunistic pathogen and the causative agent of melioidosis. It is able to adapt to harsh environments and can live intracellularly in its infected hosts. In this study, identification of transcriptional factors that associate with the β' subunit (RpoC) of RNA polymerase was performed. The N-terminal region of this subunit is known to trigger promoter melting when associated with a sigma factor. A pull-down assay using histidine-tagged B. pseudomallei RpoC N-terminal region as bait showed that a hypothetical protein BPSS1356 was one of the proteins bound. This hypothetical protein is conserved in all B. pseudomallei strains and present only in the Burkholderia genus. A BPSS1356 deletion mutant was generated to investigate its biological function. The mutant strain exhibited reduced biofilm formation and a lower cell density during the stationary phase of growth in LB medium. Electron microscopic analysis revealed that the ΔBPSS1356 mutant cells had a shrunken cytoplasm indicative of cell plasmolysis and a rougher surface when compared to the wild type. An RNA microarray result showed that a total of 63 genes were transcriptionally affected by the BPSS1356 deletion with fold change values of higher than 4. The expression of a group of genes encoding membrane located transporters was concurrently down-regulated in ΔBPSS1356 mutant. Amongst the affected genes, the putative ion transportation genes were the most severely suppressed. Deprivation of BPSS1356 also down-regulated the transcriptions of genes for the arginine deiminase system, glycerol metabolism, type III secretion system cluster 2, cytochrome bd oxidase and arsenic resistance. It is therefore obvious that BPSS1356 plays a multiple regulatory roles on many genes.
Specific human papillomavirus (HPV) types have been implicated in the development of cervical carcinoma worldwide. Novel molecular techniques have facilitated the detection and typing of HPV in cervical lesions. DNA preparations from a series of 23 histopathologically confirmed cervical carcinoma patients were analyzed by polymerase chain reaction (PCR) using degenerate primers for the presence of HPV DNA sequences. A total of 22 of 23 cases studied (95.7%) were found positive for HPV DNA sequences. Further studies by DNA hybridization with viral specific probe and restriction enzyme analysis demonstrated the presence of HPV 16 in 73.9% (17/23) and HPV 18 in 65.2% (15/23) of the cases examined. Interestingly, the uncommon HPV 31 and 33 were also found but with a lower percentage (16.9%). It was noted that HPV 16 frequency in the carcinoma increased with age but HPV 18 was evenly present at all ages investigated. We found that HPV was frequently associated with the majority of the cervical carcinomas, and in all but one case, oncogenic high risk HPV genotypes were present. We conclude that HPV infection of the genital tract has an important role in the development of the disease in Malaysia.
A Gram-stain-positive, endospore-forming, rod-shaped bacterial strain, designated D5(T), was isolated from seawater collected from a sandy beach in a southern state of Malaysia and subjected to a polyphasic taxonomic study. Sequence analysis of the 16S rRNA gene demonstrated that this isolate belongs to the genus Jeotgalibacillus, with 99.87% similarity to Jeotgalibacillus alimentarius JCM 10872(T). DNA-DNA hybridization of strain D5(T) with J. alimentarius JCM 10872(T) demonstrated 26.3% relatedness. The peptidoglycan type was A1α linked directly to L-lysine as the diamino acid. The predominant quinones identified in strain D5(T) were menaquinones MK-7 and MK-8.The major fatty acids were iso-C15:0 and anteiso-C15:0. The G+C content of its DNA was 43.0 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and sulfoquinovosyl diacylglycerol, as well as two unknown phospholipids and three unknown lipids. The phenotypic, chemotaxonomic and genotypic data indicated that strain D5(T) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus malaysiensis sp. nov. is proposed (type strain D5(T) = DSM 28777(T) = KCTC33550(T)). An emended description of the genus Jeotgalibacillus is also provided.
Living fossils are lineages that have retained plesiomorphic traits through long time periods. It is expected that such lineages have both originated and diversified long ago. Such expectations have recently been challenged in some textbook examples of living fossils, notably in extant cycads and coelacanths. Using a phylogenetic approach, we tested the patterns of the origin and diversification of liphistiid spiders, a clade of spiders considered to be living fossils due to their retention of arachnid plesiomorphies and their exclusive grouping in Mesothelae, an ancient clade sister to all modern spiders. Facilitated by original sampling throughout their Asian range, we here provide the phylogenetic framework necessary for reconstructing liphistiid biogeographic history. All phylogenetic analyses support the monophyly of Liphistiidae and of eight genera. As the fossil evidence supports a Carboniferous Euramerican origin of Mesothelae, our dating analyses postulate a long eastward over-land dispersal towards the Asian origin of Liphistiidae during the Palaeogene (39-58 Ma). Contrary to expectations, diversification within extant liphistiid genera is relatively recent, in the Neogene and Late Palaeogene (4-24 Ma). While no over-water dispersal events are needed to explain their evolutionary history, the history of liphistiid spiders has the potential to play prominently in vicariant biogeographic studies.
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.
A taxonomic study was carried out on strain A-11-3(T), which was isolated from an oil-enriched consortia from the surface seawater of Hong-Deng dock in the Straits of Malacca and Singapore. Cells were aerobic, Gram-negative, non-spore-forming irregular rods. The strain was catalase- and oxidase-negative. It grew on a restricted spectrum of organic compounds, including some organic acids and alkanes. 16S rRNA gene sequence comparisons showed that strain A-11-3(T) was most closely related to the type strains of Alcanivorax jadensis (96.8 % sequence similarity), Alcanivorax borkumensis (96.8 %), Alcanivorax dieselolei (94.8 %), Alcanivorax venustensis (94.2 %) and Alcanivorax balearicus (94.0 %). The predominant fatty acids were C(16 : 0) (31.2 %), C(18 : 1)omega7c (24.8 %), C(18 : 0) (9.6 %), C(12 : 0) (8.3 %), C(16 : 1)omega7c (8.3 %) and C(16 : 0) 3-OH (5.1 %). The G+C content of the genomic DNA was 54.7 mol%. Moreover, the strain produced lipopeptides as its surface-active compounds. According to physiological and biochemical tests, DNA-DNA hybridization results and sequence comparisons of the 16S-23S internal transcribed spacer, the gyrB gene and the alkane hydroxylase gene alkB1, strain A-11-3(T) was affiliated with the genus Alcanivorax but could be readily distinguished from recognized Alcanivorax species. Therefore strain A-11-3(T) represents a novel species of the genus Alcanivorax for which the name Alcanivorax hongdengensis sp. nov. is proposed. The type strain is A-11-3(T) (=CGMCC 1.7084(T)=LMG 24624(T)=MCCC 1A01496(T)).
The whole-genome sequence of Mycobacterium bolletii M24, isolated from the bronchoalveolar lavage fluid of a Malaysian patient, is reported here. The circular chromosome of 5,507,730 bp helped to clarify the taxonomic position of this organism within the M. abscessus complex and revealed the presence of proteins potentially important for pathogenicity in a human host.
The drug release characteristics of beads made of poly(methyl vinyl ether-co-maleic acid) using Zn2+ as the crosslinking agent were investigated with respect to the influence of microwave irradiation. The beads were prepared by an extrusion method with sodium diclofenac as a model water-soluble drug. They were subjected to microwave irradiation at 80W for 5 and 20 min, and at 300W for 1 min 20s and 5 min 20s. The profiles of drug dissolution, drug content, drug-polymer interaction and polymer-polymer interaction were determined by dissolution testing, drug content assay, differential scanning calorimetry and Fourier transform infrared spectroscopy. Treatment of beads by microwave at varying intensities of irradiation can aid to retard the drug release with a greater reduction extent through treating the beads for a longer duration of irradiation. The treatment of beads by microwave induced the formation of multiple polymeric domains of great strength and extent of polymer-polymer and drug-polymer interaction. The release of drug from beads was retarded via the interplay of O-H, N-H, C-H, (CH2)n and C-O functional groups of these domains, and was mainly governed by the state of polymer relaxation of the matrix unlike that of the untreated beads of which the release of drug was effected via drug diffusion and polymer relaxation. In comparison to Ca2+ crosslinked matrix which exhibited inconsistent drug release retardation behavior under the influence of microwave, the extent and rate of drug released from the Zn2+ crosslinked beads were greatly reduced by microwave and the release of drug from these beads was consistently retarded in response to both high and low intensity microwaves.
Discriminatory typing methods are invaluable in the investigation of outbreaks of infectious diseases. Single primers were used to generate randomly amplified polymorphic DNA (RAPD) profiles from Klebsiella pneumoniae isolates of various serotype and K. pneumoniae isolates from cases of sepsis at a Malaysian hospital and two English hospitals. RAPD profiles of acceptable reproducibility, a maximum of three minor band variations, were produced using a rapid DNA extraction method. RAPD typing of K. pneumoniae was shown to be as discriminatory as restriction fragment length polymorphism analysis using pulsed field gel electrophoresis yet quicker and less costly. The findings suggest that RAPD typing may be a useful tool for the epidemiological typing of K. pneumoniae.
Klebsiella pneumoniae is a Gram-negative, cylindrical rod shaped opportunistic pathogen that is found in the environment as well as existing as a normal flora in mammalian mucosal surfaces such as the mouth, skin, and intestines. Clinically it is the most important member of the family of Enterobacteriaceae that causes neonatal sepsis and nosocomial infections. In this work, a combination of protein sequence analysis, structural modeling and molecular docking simulation approaches were employed to provide an understanding of the possible functions and characteristics of a hypothetical protein (KPN_02809) from K. pneumoniae MGH 78578. The computational analyses showed that this protein was a metalloprotease with zinc binding motif, HEXXH. To verify this result, a ypfJ gene which encodes for this hypothetical protein was cloned from K. pneumoniae MGH 78578 and the protein was overexpressed in Escherichia coli BL21 (DE3). The purified protein was about 32 kDa and showed maximum protease activity at 30 °C and pH 8.0. The enzyme activity was inhibited by metalloprotease inhibitors such as EDTA, 1,10-phenanthroline and reducing agent, 1,4-dithiothreitol (DTT). Each molecule of KPN_02809 protein was also shown to bind one zinc ion. Hence, for the first time, we experimentally confirmed that KPN_02809 is an active enzyme with zinc metalloprotease activity.
Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants.
Most Proteobacteria produce N-acylhomoserine lactones for bacterial cell-to-cell communication, a process called quorum sensing. Interference of quorum sensing, commonly known as quorum quenching, represents an important way to control quorum sensing. This work reports the isolation of quorum quenching bacterium strain 2WS8 from Malaysia tropical wetland water (2°11'8"N, 102°15'2"E, in 2007) by using a modified version of a previously reported KG medium. Strain 2WS8 was isolated based on its ability to utilize N-(3-oxohexanoyl)-L-homoserine lactone (3-oxo-C6-HSL) as the sole source of energy. This bacterium clustered closely to Pseudomonas aeruginosa PAO1. Strain 2SW8 possesses both quiP and pvdQ homologue acylase genes. Rapid Resolution Liquid Chromatography analysis confirmed that strain 2SW8 preferentially degraded N-acylhomoserine lactones with 3-oxo group substitution but not those with unsubstituted groups at C3 position in the acyl side chain. Strain 2SW8 also showed 2-heptyl-3-hydroxy-4-quinolone production.
A cryptic plasmid, pMWHK1 recovered from an Antarctic bacterium Pedobacter cryoconitis BG5 was sequenced and characterised. The plasmid is a circular 6206bp molecule with eight putative open reading frames designated as orf1, orf2, orf3, orf4, orf5, orf6, orf7 and orf8. All the putative open reading frames of pMWHK1 are found to be actively transcribed. Proteins encoded by orf2 and orf4 are predicted to be responsible for the mobilization and replication of the plasmid respectively. orf4 shares 55% and 61% identities with the theta-type Rep proteins from two strains of Riemerella anatipestifer. This suggests that pMWHK1 could be a member of the theta-type replicating plasmid. The origin of replication is located within the AT-rich region upstream of orf4. orf5 and orf6 encode bacterial toxin-antitoxin proteins predicted to maintain plasmid stability. orf3 encodes an entry exclusion protein that is hypothetically involved in reducing the frequency of DNA transfer through conjugation. orf1, orf7 and orf8 encode proteins with unknown functions. Plasmid, pMWHK1 is stably maintained in P. cryoconitis BG5 at 20°C.
The structural gene of elastase strain K (elastase from Pseudomonas aeruginosa strain K), namely HindIII1500PstI, was successfully sequenced to contain 1497 bp. The amino acid sequence, deduced from the nucleotide sequence, revealed that the mature elastase consists of 301 amino acids, with a molecular mass of 33.1 kDa, and contains a conserved motif HEXXH, zinc ligands and residues involved in the catalysis of elastase strain K. The structural gene was successfully cloned to a shuttle vector, pUCP19, and transformed into Escherichia coli strains TOP10, KRX, JM109 and Tuner™ pLacI as well as P. aeruginosa strains PA01 (A.T.C.C. 47085) and S5, with detection of significant protein expression. Overexpression was detected from transformants KRX/pUCP19/HindIII1500PstI of E. coli and PA01/pUCP19/HindIII1500PstI of P. aeruginosa, with increases in elastolytic activity to 13.83- and 5.04-fold respectively relative to their controls. In addition, recombinant elastase strain K showed considerable stability towards numerous organic solvents such as methanol, ethanol, acetone, toluene, undecan-1-ol and n-dodecane, which typically pose a detrimental effect on enzymes; our finding provides further information to support the potential application of the enzyme in synthetic industries, particularly peptide synthesis.
The distribution in Thailand of antibody to a recently discovered variant of circumsporozoite proteins of Plasmodium vivax was determined by enzyme-linked immunosorbent assay (ELISA). The ELISA capture antigens were a synthetic peptide of the principal variant sequence ANGAGNQPG and a candidate P vivax vaccine that contained the predominant repeat sequence GDRAA/DGQPA. Serological evidence of recent inoculation with the variant was found throughout Thailand and in migrants from Cambodia, Malaysia, and Burma. IgG antibody to the two P vivax circumsporozoite proteins was detected in 217 of 804 test sera (27%). Within the regions studied the proportion of positive sera specific for the variant epitope ranged from 28% to 66%. A vaccine against the predominant repeat domain may rapidly select for the variant, which already appears to be widespread within Thailand.