The large-scale genomic resource for kelampayan was generated from a developing xylem cDNA library. A total of 6,622 high quality expressed sequence tags (ESTs) were generated through high-throughput 5' EST sequencing of cDNA clones. The ESTs were analyzed and assembled to generate 4,728 xylogenesis unigenes distributed in 2,100 contigs and 2,628 singletons. About 59.3 % of the ESTs were assigned with putative identifications whereas 40.7 % of the sequences showed no significant similarity to any sequences in GenBank. Interestingly, most genes involved in lignin biosynthesis and several other cell wall biosynthesis genes were identified in the kelampayan EST database. The identified genes in this study will be candidates for functional genomics and association genetic studies in kelampayan aiming at the production of high value forests.
Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd(+)) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd(+) E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands.
Duabanga moluccana (or locally known as sawih) is an indigenous fast growing tropical tree species that confers various advantages for the timber industry and for planted forests development. In this paper, we isolated and characterized 8 polymorphic microsatellite markers from the D. moluccana genome using ISSR-suppression PCR techniques. The number of alleles and PIC values ranged from 3 to 8 alleles per locus and from 0.488 to 0.792, respectively. Three microsatellite loci were deviated from Hardy-Weinberg equilibrium (P
Energy is widely used in industry for heating and cooling, with natural gas (NG) being the largest primary energy source in Malaysia, closely followed by coal. Renewable energy, such as biogas upgrading to biomethane, could cut the use of fossil fuels by supplementing NG usage due to their similar physicochemical and thermochemical characteristics. Biogas production plants in Malaysia are more commonly seen in waste-to-energy scenarios, with the technology anaerobic digestion, and their deployment is supported via feed-in tariffs (FiT) for power generation. Other potential applications such as the conversion of biogas into biomethane, injection into the natural gas grid or transportation through a virtual pipeline may still need further technical development. This paper presents spatial techno economic optimisation modelling using BeWhere to determine decentralised biomethane production plants using feedstock from multiple sources of biogas, including palm oil mill effluent (POME), food waste, cattle manure and chicken manure. This model considered potential configurations and sizes of the biomethane plants, the transportation of biomethane using a virtual pipeline (at 250 psig) and demand in one of the states in Malaysia, namely Johor. It was found that two to four biomethane plants with capacities ranging between 125 and 700 m3/h were located in densely populated areas or heavier industrial consumers when the carbon tax was implemented at 167.71 EUR/tCO2 (800 MYR/tCO2). Sensitivity analysis suggested that biomethane production increases with the increasing country renewable energy share target to beyond 2080 MW. It is recommended that specific policy regulations and Feed-in Tariff (FiT) mechanisms are used to expand the biomethane market share in the country.
Postweaning diarrhea caused by pathogenic Escherichia coli, in particular verotoxigenic E. coli (VTEC), has caused significant economic losses in the pig farming industry worldwide. However, there is limited information on VTEC in Malaysia. The objective of this study was to characterize pathogenic E. coli isolated from post-weaning piglets and growers with respect to their antibiograms, carriage of extended-spectrum beta-lactamases, pathotypes, production of hemolysins and fimbrial adhesins, serotypes, and genotypes.
Escherichia coli is an important etiologic agent of lower respiratory tract infections (LRTI). Multidrug-resistant E. coli EC302/04 was isolated from a tracheal aspirate, and its genome sequence is expected to provide insights into antimicrobial resistance as well as adaptive and virulence mechanisms of E. coli involved in LRTI.
Extraintestinal pathogenic Escherichia coli (ExPEC) that causes extraintestinal infections often harbor plasmids encoding fitness traits such as resistance and virulence determinants that are of clinical importance. We determined the complete nucleotide sequence of plasmid pEC302/04 from a multidrug-resistant E. coli EC302/04 which was isolated from the tracheal aspirate of a patient in Malaysia. In addition, we also performed comparative sequence analyses of 18 related IncFIIA plasmids to determine the phylogenetic relationship and diversity of these plasmids. The 140,232 bp pEC302/04 is a multireplicon plasmid that bears three replication systems (FII, FIA, and FIB) with subtype of F2:A1:B1. The plasmid is self-transmissible with a complete transfer region. pEC302/04 also carries antibiotic resistance genes such as bla TEM-1 and a class I integron containing sul1, cml and aadA resistance genes, conferring multidrug resistance (MDR) to its host, E. coli EC302/04. Besides, two iron acquisition systems (SitABCD and IutA-IucABCD) which are the conserved virulence determinants of ExPEC-colicin V or B and M (ColV/ColBM)-producing plasmids were identified in pEC302/04. Multiple toxin-antitoxin (TA)-based addiction systems (i.e., PemI/PemK, VagC/VagD, CcdA/CcdB, and Hok/Sok) and a plasmid partitioning system, ParAB, and PsiAB, which are important for plasmid maintenance were also found. Comparative plasmid analysis revealed only one conserved gene, the repA1 as the core genome, showing that there is an extensive diversity among the IncFIIA plasmids. The phylogenetic relationship of 18 IncF plasmids based on the core regions revealed that ColV/ColBM-plasmids and non-ColV/ColBM plasmids were separated into two distinct groups. These plasmids, which carry highly diverse genetic contents, are also mosaic in nature. The atypical combination of genetic materials, i.e., the MDR- and ColV/ColBM-plasmid-virulence encoding regions in a single ExPEC plasmid is rare but of clinical importance. Such phenomenon is bothersome when the plasmids are transmissible, facilitating the spread of virulence and resistance plasmids among pathogenic bacteria. Notably, certain TA systems are more commonly found in particular ExPEC plasmid types, indicating the possible relationships between certain TA systems and ExPEC pathogenesis.
Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus sequence typing (MLST) is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2) co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC, and tviD that may explain the variations that differentiate between seemingly successful (widespread) and unsuccessful (poor dissemination) S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.
E.coli, an important vector distributing antimicrobial resistance in the environment, was found to be multi-drug resistant, abundant, and genetically diverse in the Matang mangrove estuaries, Malaysia. One-third (34%) of the estuarine E. coli was multi-drug resistant. The highest antibiotic resistance prevalence was observed for aminoglycosides (83%) and beta-lactams (37%). Phylogenetic groups A and B1, being the most predominant E. coli, demonstrated the highest antibiotic resistant level and prevalence of integrons (integron I, 21%; integron II, 3%). Detection of phylogenetic group B23 downstream of fishing villages indicates human fecal contamination as a source of E. coli pollution. Enteroaggregative E. coli (1%) were also detected immediately downstream of the fishing village. The results indicated multi-drug resistance among E. coli circulating in Matang estuaries, which could be reflective of anthropogenic activities and aggravated by bacterial and antibiotic discharges from village lack of a sewerage system, aquaculture farms and upstream animal husbandry.
The emergence of Escherichia coli resistant to extended-spectrum cephalosporins (ESCs) is of concern as ESC is often used to treat infections by Gram-negative bacteria. One-hundred and ten E. coli strains isolated in 2009-2010 from children warded in a Malaysian tertiary hospital were analyzed for their antibiograms, carriage of extended-spectrum beta-lactamase (ESBL) and AmpC genes, possible inclusion of the beta-lactamase genes on an integron platform, and their genetic relatedness. All E. coli strains were sensitive to carbapenems. About 46% of strains were multidrug resistant (MDR; i.e., resistant to ≥3 antibiotic classes) and almost half (45%) were nonsusceptible to ESCs. Among the MDR strains, high resistance rates were observed for ampicillin (98%), tetracycline (75%), and trimethoprim/sulfamethoxazole (73%). Out of 110 strains, bla(TEM-1) (49.1%), bla(CTX-M) (11.8%), and bla(CMY-2) (6.4%) were detected. Twenty-one strains were ESBL producers. CTX-M-15 was the predominant CTX-M variant found and this is the first report of a CTX-M-27-producing E. coli strain from Malaysia. Majority (3.1%) of the strains harbored class 1 integron-encoded integrases with a predominance of aadA and dfr genes within the integron variable region. No gene cassette encoding ESBL genes was found and integrons were not significantly associated with ESBL or non-ESBL producers. Possible clonal expansion was observed for few CTX-M-15-positive strains but the O25-ST131 E. coli clone known to harbor CTX-M-15 was not detected while CMY-2-positive strains were genetically diverse.
The rapidly increasing generation of municipal solid waste (MSW) threatens the environmental integrity and well-being of humans at a global level. Incineration is regarded as a technically sound technology for the management of MSW. However, the effective management of the municipal solid waste incineration (MSWI) ashes remains a challenge. This article presents the global dynamics of MSWI ashes research from 1994 to 2018 based on a bibliometric analysis of 1810 publications (research articles and conference proceedings) extracted from the Web of Science database, followed by a comprehensive summary on the research developments in the field. The results indicate the rapid growth of annual publications on MSWI ashes research, with China observed as the most productive country within the study period. Waste Management, Journal of Hazardous Materials, Chemosphere and Waste Management & Research, which accounted for 35.42% of documents on MSWI research, are the most prominent journals in the field. The most critical thematic areas on this topic are MSWI ashes characterisation, dioxin emissions from fly ash, valorisation of bottom ash and heavy metal removal. The evolution of MSWI ashes treatment technologies is also discussed, together with the challenges and future research directions. This is the first bibliometric analysis on global MSWI ashes research based on a sufficiently large dataset, which could provide new insights for researchers to initiate further research with leading institutions/authors and ultimately advance this research field.
Rapid population growth and urbanisation have generated large amount of municipal solid waste (MSW) in many cities. Up to 40-60% of Malaysia's MSW is reported to be food waste where such waste is highly putrescible and can cause bad odour and public health issue if its disposal is delayed. In this study, the implementation of community composting in a village within Iskandar Malaysia is presented as a case study to showcase effective MSW management and mitigation of GHG emission. The selected village, Felda Taib Andak (FTA), is located within a palm oil plantation and a crude palm oil processing mill. This project showcases a community-composting prototype to compost food and oil palm wastes into high quality compost. The objective of this article is to highlight the economic and environment impacts of a community-based composting project to the key stakeholders in the community, including residents, oil palm plantation owners and palm oil mill operators by comparing three different scenarios, through a life cycle approach, in terms of the greenhouse gas emission and cost benefit analysis. First scenario is the baseline case, where all the domestic waste is sent to landfill site. In the second scenario, a small-scale centralised composting project was implemented. In the third scenario, the data obtained from Scenario 2 was used to do a projection on the GHG emission and costing analysis for a pilot-scale centralised composting plant. The study showed a reduction potential of 71.64% on GHG emission through the diversion of food waste from landfill, compost utilisation and significant revenue from the compost sale in Scenario 3. This thus provided better insight into the feasibility and desirability in implementing a pilot-scale centralised composting plant for a sub-urban community in Malaysia to achieve a low carbon and self-sustainable society, in terms of environment and economic aspects.