Displaying publications 61 - 80 of 92 in total

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  1. Identification of curcumin as a potential α-glucosidase and dipeptidyl-peptidase 4 inhibitor: Molecular docking study, in vitro and in vivo biological evaluation
    Cao W, Chen X, Chin Y, Zheng J, Lim PE, Xue C, et al.
    J Food Biochem, 2021 Apr 04.
    PMID: 33817806 DOI: 10.1111/jfbc.13686
    Natural compounds have tremendous potential to regulate glucose metabolism, but conventional methods for studying their bioactivities are usually labor intensive. Here, hypoglycemic properties in 22 selected food-derived compounds were examined using molecular docking. The results indicated that curcumin is an inhibitor of both α-glucosidase and dipeptidyl-peptidase 4 (DPP-4), which are important for glycemic control. These effects of curcumin were also confirmed by enzymatic determination in vitro. Furthermore, curcumin significantly improved diet-induced hyperglycemia (e.g., fasting plasma glucose levels and glycogen storage in muscle or liver) in mice. This might be attributed to its inhibitory effects on the activities of α-glucosidase and DPP-4 in vivo. Curcumin also upregulated the expression of genes (e.g., glucagon-like peptide 1) related to DPP-4 activity in the small intestine. In conclusion, curcumin is a potential ingredient of functional foods used for diet-induced hyperglycemia management. PRACTICAL APPLICATIONS: Curcumin has been widely used as a colorant in the food industry. Moreover, a growing number of studies have described its diverse biological functions, such as anti-inflammatory, anti-oxidant, and anti-angiogenic activities. Thus, curcumin is regarded as a potential ingredient in functional foods. Our results highlighted the hyperglycemic effect of curcumin, suggesting that curcumin may be included in food products for hyperglycemic patients.
  2. Differential abundance and core members of the bacterial community associated with wild male Zeugodacus cucurbitae fruit flies (Insecta: Tephritidae) from three geographical regions of Southeast Asia
    Yong HS, Song SL, Eamsobhana P, Pasartvit A, Lim PE
    Mol Biol Rep, 2019 Aug;46(4):3765-3776.
    PMID: 31012029 DOI: 10.1007/s11033-019-04818-3
    Zeugodacus cucurbitae (Coquillet) is one of the most significant and widespread tephritid pest species of agricultural crops. This study reports the bacterial communities associated with Z. cucurbitae from three geographical regions in Southeast Asia (Thailand, Peninsular Malaysia, and Sarawak). The bacterial microbiota were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina Mi-Seq platform. At 97% similarity and filtering at 0.001%, there were seven bacterial phyla and unassigned bacteria, comprising 11 classes, 23 orders, 39 families and 67 genera. The bacterial diversity and richness varied within and among the samples from the three geographical regions. Five phyla were detected for the Sarawak sample, and six each for the Thailand and Peninsular Malaysia samples. Four phyla-Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria-were represented in all the fruit fly specimens, forming the core members of the bacterial community. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Fifty-three genera were represented in the Thailand sample, 56 in the Peninsular Malaysia sample, and 55 in the Sarawak sample. Forty-two genera were present in all the three geographical regions. The predominant core members were order Enterobacteriales (Proeteobacteria), and family Enterobacteriaceae (Enterobacteriales). Klebsiella (Enterobacteriaceae) was the predominant genus and K. oxytoca the predominant species with all specimens having > 10% relative abundance. The results indicate the presence of a great diversity as well as core members of the bacterial community associated with different populations of Z. cucurbitae.
  3. Operational factors affecting the bioregeneration of mono-amine modified silica loaded with Acid Orange 7
    Al-Amrani WA, Lim PE, Seng CE, Ngah WS
    Water Res, 2012 Dec 1;46(19):6419-29.
    PMID: 23062787 DOI: 10.1016/j.watres.2012.09.014
    In this study, the operational factors affecting the bioregeneration of AO7-loaded MAMS particles in batch system, namely redox condition, initial acclimated biomass concentration, shaking speed and type of acclimated biomass were investigated. The results revealed that with the use of mixed culture acclimated to AO7 under anoxic/aerobic conditions, enhancement of the bioregeneration efficiency of AO7-loaded MAMS and the total removal efficiency of COD could be achieved when the bio-decolorization and bio-mineralization stages were fully aerated with dissolved oxygen above 7 mg/L. Shorter duration of bioregeneration was achieved by using relatively higher initial biomass concentration and lower shaking speed, respectively, whereas variations of biomass concentration and shaking speed did not have a pronounced effect on the bioregeneration efficiency. The duration and efficiency of bioregeneration process were greatly affected by the chemical structures of mono-azo dyes to which the biomasses were acclimated.
  4. Sun-Dried and Air-Dried Kappaphycus alvarezii Attenuates 5-Fluorouracil-Induced Intestinal Mucositis in Mice
    Zhang Q, Yang R, Lim PE, Chin Y, Zhou S, Gao Y, et al.
    Nutr Cancer, 2021 Sep 23.
    PMID: 34555987 DOI: 10.1080/01635581.2021.1981403
    5-fluorouracil (5-FU)-induced intestinal mucositis (IM) often makes chemotherapy patients suffer from physical and psychological suffering. Kappaphycus alvarezii (KA) is known for its potent multiple biological activities from decades. In the current study, we explored the effect of sun-dried and air-dried Kappaphycus alvarezii as a whole food supplement on 5-FU-induced IM. Diets supplemented with sun-dried Kappaphycus alvarezii (SKA, 3%), air-dried Kappaphycus alvarezii (AKA, 3%), and 5-aminosalicylic acid (0.005%) for consecutive14 days. While intraperitoneal injection of 5-FU (50 mg/kg) induced IM for last three consecutive days, and IM was assessed by the disease activity index (DAI) and inflammatory cytokine levels. Pretreatment of KA could alleviate phenotypic index, inhibit the increase of DAI, and reverse villus/crypt ratio. On the 14th day, AKA significantly increased the weight growth rate of the mice. The intervention of SKA significantly reduced the level of TNF-α and IL-1β (P 
  5. Differentiating sibling species of Zeugodacus caudatus (Insecta: Tephritidae) by complete mitochondrial genome
    Yong HS, Song SL, Lim PE, Eamsobhana P, Suana IW
    Genetica, 2016 Oct;144(5):513-521.
    PMID: 27502829
    Zeugodacus caudatus is a pest of pumpkin flowers. It has a Palearctic and Oriental distribution. We report here the complete mitochondrial genome of the Malaysian and Indonesian samples of Z. caudatus determined by next-generation sequencing of genomic DNA and determine their taxonomic status as sibling species and phylogeny with other taxa of the genus Zeugodacus. The whole mitogenome of both samples possessed 37 genes (13 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region. The mitogenome of the Indonesian sample (15,885 bp) was longer than that of the Malaysian sample (15,866 bp). In both samples, TΨC-loop was absent in trnF and DHU-loop was absent in trnS1. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes), with the two samples of Z. caudatus forming a sister group and the genus Zeugodacus was monophyletic. The Malaysian and Indonesian samples of Z. caudatus have a genetic distance of p = 7.8 % based on 13 PCGs and p = 7.0 % based on 15 mitochondrial genes, indicating status of sibling species. They are proposed to be accorded specific status as members of a species complex.
  6. Native κ-carrageenan induced-colitis is related to host intestinal microecology
    Mi Y, Chin YX, Cao WX, Chang YG, Lim PE, Xue CH, et al.
    Int J Biol Macromol, 2020 Mar 15;147:284-294.
    PMID: 31926226 DOI: 10.1016/j.ijbiomac.2020.01.072
    Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, has gradually emerged as a public health challenge worldwide. Carrageenan is a popular food additive that has been in use for decades. However, controversy exists regarding to the safety of carrageenan due to its exacerbation of colitis in experimental models. In this study, we studied the effects of vehicle and host intestinal microflora on carrageenan inflammatory properties in C57BL/6 J mice. We found that in high-fat diet model, native carrageenan in drinking water increased the disease activity index (DAI), myeloperoxidase (MPO) activity and the mRNA expression of TLR4 in colon, whereas carrageenan-supplemented diet has no visible effects. However, no signs of colitis were observed under low-fat diet regardless of the mode of vehicle used. Moreover, we discovered that carrageenan-induced colitis in high-fat diet model was robustly correlated with changes in the composition of gut microbiota, specifically Alistipes finegoldii and Bacteroides acidifaciens. Hence, we propose that the inflammatory property of carrageenan is influenced greatly by its intake form via modification of host intestinal microecology.
  7. Data set on the diversity and core members of bacterial community associated with two specialist fruit flies Bactrocera melastomatos and B. umbrosa (Insecta, Tephritidae)
    Song SL, Yong HS, Chua KO, Lim PE, Eamsobhana P
    Data Brief, 2022 Dec;45:108727.
    PMID: 36425974 DOI: 10.1016/j.dib.2022.108727
    Bactrocera melastomatos Drew & Hancock and Bactrocera umbrosa (Fabricius) are fruit flies of the subfamily Dacinae under the family Tephritidae [1]. B. melastomatos occurs in India (Andaman Island), Thailand, Peninsular Malaysia, Singapore, and Indonesia (Sumatra, Kalimantan, Java) [1] while B. umbrosa is distributed from southern Thailand and Malaysia to New Guinea and New Caledonia [2]. The adult male flies of B. melastomatos are attracted to Cue lure while the adult male flies of B. umbrosa are attracted to methyl eugenol [3]. Fruit flies of Bactrocera melastomatos infest Melastomataceae while those of B. umbrosa infest Moraceae. We compare the diversity of microbiota associated with the wild adult males of these two specialist fruit flies infesting different families of host plants. Targeted 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform. Six bacterial phyla (Actinobacteria, Armatimonadetes, Bacteroidetes, Cyanobacteria/Melainabacteria group, Firmicutes, Proteobacteria) were detected at 97% similarity clustering and 0.001% abundance filtering. Four phyla (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria) were present in all the specimens studied. Proteobacteria was the predominant phylum in both B. melastomatos and B. umbrosa. Enterobacteriaceae was the predominant family in UM B. melastomatos and B. umbrosa, and Orbaceae was the predominant family in Awana B. melastomatos. Klebsiella was the predominant genus in B. umbrosa, Citrobacter in UM B. melastomatos, and Orbus in Awana B. melastomatos. Double Wolbachia infections were present in UM B. melastomatos. In general, the bacterial diversity and richness varied within and between the samples of B. melastomatos and B. umbrosa.
  8. A metabolomic approach to investigate effects of ocean acidification on a polar microalga Chlorella sp
    Tan YH, Lim PE, Beardall J, Poong SW, Phang SM
    Aquat Toxicol, 2019 Dec;217:105349.
    PMID: 31734626 DOI: 10.1016/j.aquatox.2019.105349
    Ocean acidification, due to increased levels of anthropogenic carbon dioxide, is known to affect the physiology and growth of marine phytoplankton, especially in polar regions. However, the effect of acidification or carbonation on cellular metabolism in polar marine phytoplankton still remains an open question. There is some evidence that small chlorophytes may benefit more than other taxa of phytoplankton. To understand further how green polar picoplankton could acclimate to high oceanic CO2, studies were conducted on an Antarctic Chlorella sp. Chlorella sp. maintained its growth rate (∼0.180 d-1), photosynthetic quantum yield (Fv/Fm = ∼0.69) and chlorophyll a (0.145 fg cell-1) and carotenoid (0.06 fg cell-1) contents under high CO2, while maximum rates of electron transport decreased and non-photochemical quenching increased under elevated CO2. GCMS-based metabolomic analysis reveal that this polar Chlorella strain modulated the levels of metabolites associated with energy, amino acid, fatty acid and carbohydrate production, which could favour its survival in an increasingly acidified ocean.
  9. Core members and differential abundance of chrysomelid microbiota in the life stages of Podontiaaffinis (Galerucinae) and adult Silanafarinosa(Cassidinae, Coleoptera)
    Song SL, Yong HS, Chua KO, Eamsobhana P, Lim PE, Chan KG
    Biodivers Data J, 2022;10:e87459.
    PMID: 36761655 DOI: 10.3897/BDJ.10.e87459
    The chrysomelid beetlesPodontiaaffinis and Silanafarinosa are members of the subfamilies Galerucinae and Cassidinae, respectively. This study, based on 16S rRNA gene-targeted metagenomics sequencing, reports the core members and differential abundance of bacterial communities in the larvae and adult beetles of P.affinis and the adult S.farinosa. Cyanobacteria/Melainabacteria group was the predominant phylum in the larvae of P.affinis, while Proteobacteria was the predominant phylum in adult P.affinis and S.farinosa. The number of Order, Family, Genus and Species OTUs in the adult stage of P.affinis was higher than that in the larval stage. The bacterial species richness of adult P.affinis was significantly higher than that of adult S.farinosa. Betaproteobacteria was the predominant class in adult P.affinis, Cyanobacteria in the larvae of P.affinis and Gammaproteobacteria in S.farinosa. The larvae and adult beetles of P.affinis and adult S.farinosahad a low number of unique and shared bacterial OTUs (> 5% relative abundance). The differences in the microbiota indicate possible differences in nutrient assimilation, host taxonomy and other stochastic processes. These findings provide new information to our understanding of the bacteria associated with specialist phytophagous chrysomelid beetles and beetles in general.
  10. Effect of operational factors on bioregeneration of binary phenol and 4-chlorophenol-loaded granular activated carbon using PVA-immobilized biomass cryogels
    Leong KY, Adnan R, Lim PE, Ng SL, Seng CE
    Environ Sci Pollut Res Int, 2017 Sep;24(26):20959-20971.
    PMID: 28726220 DOI: 10.1007/s11356-017-9636-7
    The effects of dry biomass density in cryogel beads, shaking speed and initial concentration ratio of phenol to 4-chlorophenol (4-CP) on the bioregeneration efficiencies of binary phenol and 4-CP-loaded granular activated carbon (GAC) for phenol and 4-CP, respectively, were investigated under the simultaneous adsorption and biodegradation approach. The results revealed higher bioregeneration efficiencies of binary-loaded GAC for phenol and 4-CP at higher dry biomass density but moderate shaking speed. The optimum dry biomass density in cryogel beads and shaking speed for use in bioregeneration were found to be 0.01 g/mL and 250 rpm, respectively. With respect to the initial phenol to 4-CP concentration ratio, the bioregeneration efficiencies were lower under increasing phenol and 4-CP initial concentrations, respectively, with the effect being more conspicuous under increasing 4-CP concentration. Higher bioregeneration efficiencies were achieved with the use of immobilized rather than suspended biomasses.
  11. Fulltext A Pilot Study on Anti-Obesity Mechanisms of KappaphycusAlvarezii: The Role of Native κ-Carrageenan and the Leftover Sans-Carrageenan Fraction
    Chin YX, Mi Y, Cao WX, Lim PE, Xue CH, Tang QJ
    Nutrients, 2019 May 21;11(5).
    PMID: 31117266 DOI: 10.3390/nu11051133
    Kappaphycus is a commercially important edible red alga widely cultivated for carrageenan production. Here, we aimed to investigate the anti-obesity mechanism of Kappaphycusalvarezii by comparing the effects of whole seaweed (T), extracted native κ-carrageenan (CGN), and the leftover fraction sans-carrageenan (SCGN) supplementations (5%, w/w) on diet-induced obese C57BL/6J mice. A high-fat diet induced both a raised body fat percentage and serum cholesterol level, increased adipocytes size, abnormal levels of adipocytokines, and promoted gut dysbiosis. Our results showed that, overall, both CGN and SCGN were more effective in reversing obesity and related metabolic syndromes to normal levels than T. Furthermore, these findings suggested that CGN- and SCGN-modulated gut dysbiosis induced by a high-fat diet, which may play an influencing role in adiponectin dysregulation. Our data also showed some evidence that CGN and SCGN have distinct effects on selected genes involved in lipid metabolism. In conclusion, both κ-carrageenan and SCGN have novel anti-obesity potential with possible different mechanisms of action.
  12. Transcriptomic analysis reveals distinct mechanisms of adaptation of a polar picophytoplankter under ocean acidification conditions
    Tan YH, Poong SW, Yang CH, Lim PE, John B, Pai TW, et al.
    Mar Environ Res, 2022 Dec;182:105782.
    PMID: 36308800 DOI: 10.1016/j.marenvres.2022.105782
    Human emissions of carbon dioxide are causing irreversible changes in our oceans and impacting marine phytoplankton, including a group of small green algae known as picochlorophytes. Picochlorophytes grown in natural phytoplankton communities under future predicted levels of carbon dioxide have been demonstrated to thrive, along with redistribution of the cellular metabolome that enhances growth rate and photosynthesis. Here, using next-generation sequencing technology, we measured levels of transcripts in a picochlorophyte Chlorella, isolated from the sub-Antarctic and acclimated under high and current ambient CO2 levels, to better understand the molecular mechanisms involved with its ability to acclimate to elevated CO2. Compared to other phytoplankton taxa that induce broad transcriptomic responses involving multiple parts of their cellular metabolism, the changes observed in Chlorella focused on activating gene regulation involved in different sets of pathways such as light harvesting complex binding proteins, amino acid synthesis and RNA modification, while carbon metabolism was largely unaffected. Triggering a specific set of genes could be a unique strategy of small green phytoplankton under high CO2 in polar oceans.
  13. Fulltext Genetic and morphological analyses of Gracilaria firma and G. changii (Gracilariaceae, Rhodophyta), the commercially important agarophytes in western Pacific
    Ng PK, Lin SM, Lim PE, Hurtado AQ, Phang SM, Yow YY, et al.
    PLoS One, 2017;12(7):e0182176.
    PMID: 28759629 DOI: 10.1371/journal.pone.0182176
    Many studies classifying Gracilaria species for the exploitation of agarophytes and the development of the agar industry were conducted before the prevalence of molecular tools, resulting in the description of many species based solely on their morphology. Gracilaria firma and G. changii are among the commercially important agarophytes from the western Pacific; both feature branches with basal constrictions that taper toward acute apices. In this study, we contrasted the morpho-anatomical circumscriptions of the two traditionally described species with molecular data from samples that included representatives of G. changii collected from its type locality. Concerted molecular analyses using the rbcL and cox1 gene sequences, coupled with morphological observations of the collections from the western Pacific, revealed no inherent differences to support the treatment of the two entities as distinct taxa. We propose merging G. changii (a later synonym) into G. firma and recognize G. firma based on thallus branches with abrupt basal constrictions that gradually taper toward acute (or sometimes broken) apices, cystocarps consisting of small gonimoblast cells and inconspicuous multinucleate tubular nutritive cells issuing from gonimoblasts extending into the inner pericarp at the cystocarp floor, as well as deep spermatangial conceptacles of the verrucosa-type. The validation of specimens under different names as a single genetic species is useful to allow communication and knowledge transfer among groups from different fields. This study also revealed considerably low number of haplotypes and nucleotide diversity with apparent phylogeographic patterns for G. firma in the region. Populations from the Philippines and Taiwan were divergent from each other as well as from the populations from Malaysia, Thailand, Singapore and Vietnam. Establishment of baseline data on the genetic diversity of this commercially important agarophyte is relevant in the context of cultivation, as limited genetic diversity may jeopardize the potential for its genetic improvement over time.
  14. Fulltext Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta)
    Tan J, Lim PE, Phang SM, Hong DD, Sunarpi H, Hurtado AQ
    PLoS One, 2012;7(12):e52905.
    PMID: 23285223 DOI: 10.1371/journal.pone.0052905
    DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.
  15. Fulltext Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae
    Ng PK, Lin SM, Lim PE, Liu LC, Chen CM, Pai TW
    BMC Genomics, 2017 Jan 06;18(1):40.
    PMID: 28061748 DOI: 10.1186/s12864-016-3453-0
    BACKGROUND: The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined.

    RESULTS: The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support.

    CONCLUSIONS: Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of Gracilaria sensu lato complex and recognition of Hydropuntia as a genus distinct from Gracilaria sensu stricto.

  16. Fulltext Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice
    Mohd Hanafiah N, Cheng A, Lim PE, Sethuraman G, Mohd Zain NA, Baisakh N, et al.
    Life (Basel), 2022 Oct 04;12(10).
    PMID: 36294977 DOI: 10.3390/life12101542
    While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (Oryza sativa) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources.
  17. Abundance of microplastics and its ecological risk assessment in coral reef regions of Peninsular Malaysia
    Lim KP, Sun C, Yusoff S, Ding J, Loh KH, Li J, et al.
    Mar Pollut Bull, 2024 Dec;209(Pt A):117112.
    PMID: 39406069 DOI: 10.1016/j.marpolbul.2024.117112
    Microplastic contamination is an emerging concern in marine ecosystems, with limited knowledge on its impact on coral reefs, particularly in Malaysia. Surface waters were collected from several coral reef regions in Peninsular Malaysia by towing a plankton net behind the boat. Microplastics were detected at all sites, with a mean abundance of 0.344 ± 0.457 MP/m3. Perhentian Islands (0.683 ± 0.647 MP/m3) had significantly higher microplastic levels than Tioman Island (0.108 ± 0.063 MP/m3), likely due to oceanographic differences. Over half of the microplastics (55.7 %) were small microplastics (<1 mm), with the 0.05-0.5 mm size class being most abundant (29.2 %). Fragments and fibres dominated, and black, blue, and green were the prevalent colours. Polyethylene (PE), rayon (RY), chlorinated polyethylene (CPE), and polypropylene (PP) were the most common polymers. This study reveals the abundance and characteristics of microplastics, provides important data for further research on microplastics in coral reef ecosystem.
  18. Metabolomic and physiological analyses of two picochlorophytes from distinct oceanic latitudes under future ocean acidification and warming
    Tan YH, Poong SW, Beardall J, Phang SM, Lim PE
    Mar Environ Res, 2025 Mar 21;208:107095.
    PMID: 40163968 DOI: 10.1016/j.marenvres.2025.107095
    Phytoplankton are cosmopolitan marine photosynthetic organisms that are vital to biogeochemical cycles and marine ecosystems. The current rise in atmospheric CO2 and surface ocean temperatures are poised to disrupt the ecological niches of phytoplankton. Picochlorophytes, a broad taxon of small green eukaryotic phytoplankton, have been shown to perform well under future rising oceanic CO2 and temperature scenarios. This study investigates the acclimation responses of cosmopolitan picochlorophytes from the Chlorella-lineage under high CO2 (1000 p.p.m.) and a rise of 4 °C (8 °C - polar picochlorophyte; 32 °C, tropical picochlorophyte). In order to determine how the future ocean warming and acidification might affect picochlorophytes, a polar strain of Chlorella and a tropical Parachlorella were selected, and their physiology and GCMS-based metabolomics were investigated. Growth rate and cellular dimensions (diameter, volume, and surface area) of Chlorella significantly increased in all environmental future scenarios compared to Parachlorella. Photosynthetic parameters of the picochlorophytes studied showed acclimation, with high temperature and high CO2 triggering the adaptation of Fv/Fm, NPQmax, and Ek of Chlorella and Parachlorella, respectively. High CO2 induced the most changes in the Chlorella metabolome, altering the levels of metabolites related to amino acids and their derivatives, glutathione production, carbohydrates, and photochemical quenching. Combined high CO2/temperature altered Parachlorella's metabolome, though with a small number of biomarkers detected. This study provided evidence to support the hypothesis that picochlorophytes could thrive in a more acidified and warmer ocean.
  19. A re-assessment of the infra-generic classification of the genus Caulerpa (Caulerpaceae, Chlorophyta) inferred from a time-calibrated molecular phylogeny
    Draisma SG, van Reine WF, Sauvage T, Belton GS, Gurgel CF, Lim PE, et al.
    J Phycol, 2014 Dec;50(6):1020-34.
    PMID: 26988784 DOI: 10.1111/jpy.12231
    The siphonous green algal family Caulerpaceae includes the monotypic genus Caulerpella and the species-rich genus Caulerpa. A molecular phylogeny was inferred from chloroplast tufA and rbcL DNA sequences analyzed together with a five marker dataset of non-caulerpacean siphonous green algae. Six Caulerpaceae lineages were revealed, but relationships between them remained largely unresolved. A Caulerpella clade representing multiple cryptic species was nested within the genus Caulerpa. Therefore, that genus is subsumed and Caulerpa ambigua Okamura is reinstated. Caulerpa subgenus status is proposed for the six lineages substantiated by morphological characters, viz., three monotypic subgenera Cliftonii, Hedleyi, and Caulerpella, subgenus Araucarioideae exhibiting stolons covered with scale-like appendages, subgenus Charoideae characterized by a verticillate branching mode, and subgenus Caulerpa for a clade regarded as the Caulerpa core clade. The latter subgenus is subdivided in two sections, i.e., Sedoideae for species with pyrenoids and a species-rich section Caulerpa. A single section with the same name is proposed for each of the other five subgenera. In addition, species status is proposed for Caulerpa filicoides var. andamanensis (W.R. Taylor). All Caulerpa species without sequence data were examined (or data were taken from species descriptions) and classified in the new classification scheme. A temporal framework of Caulerpa diversification is provided by calibrating the phylogeny in geological time. The chronogram suggests that Caulerpa diversified into subgenera and sections after the Triassic-Jurassic mass extinction and that infra-section species radiation happened after the Cretaceous-Tertiary mass extinction.
  20. Fulltext Mitochondrial Genome Supports Sibling Species of Angiostrongylus costaricensis (Nematoda: Angiostrongylidae)
    Yong HS, Song SL, Eamsobhana P, Goh SY, Lim PE, Chow WL, et al.
    PLoS One, 2015;10(7):e0134581.
    PMID: 26230642 DOI: 10.1371/journal.pone.0134581
    Angiostrongylus costaricensis is a zoonotic parasitic nematode that causes abdominal or intestinal angiostrongyliasis in humans. It is endemic to the Americas. Although the mitochondrial genome of the Brazil taxon has been published, there is no available mitochondrial genome data on the Costa Rica taxon. We report here the complete mitochondrial genome of the Costa Rica taxon and its genetic differentiation from the Brazil taxon. The whole mitochondrial genome was obtained from next-generation sequencing of genomic DNA. It had a total length of 13,652 bp, comprising 36 genes (12 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region (A + T rich non-coding region). It is longer than that of the Brazil taxon (13,585 bp). The larger mitogenome size of the Costa Rica taxon is due to the size of the control region as the Brazil taxon has a shorter length (265 bp) than the Costa Rica taxon (318 bp). The size of 6 PCGs and the start codon for ATP6, CYTB and NAD5 genes are different between the Costa Rica and Brazil taxa. Additionally, the two taxa differ in the stop codon of 6 PCGs. Molecular phylogeny based on 12 PCGs was concordant with two rRNA, 22 tRNA and 36 mitochondrial genes. The two taxa have a genetic distance of p = 16.2% based on 12 PCGs, p = 15.3% based on 36 mitochondrial genes, p = 13.1% based on 2 rRNA genes and p = 10.7% based on 22 tRNA genes, indicating status of sibling species. The Costa Rica and Brazil taxa of A. costaricensis are proposed to be accorded specific status as members of a species complex.
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