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Fulltext The matrix (M) protein of Newcastle disease virus binds to human bax through its BH3 domain

Molouki A, Hsu YT, Jahanshiri F, Abdullah S, Rosli R, Yusoff K

Virol J, 2011;8:385.
PMID: 21810274 DOI: 10.1186/1743-422X-8-385

The underlying mechanisms by which Newcastle disease virus (NDV) kills cancer cells are still unclear. Recent discoveries have shown that many viruses contain Bcl-2 homology-like domains which enabled their interaction with Bcl-2 family members, and thereby accounting for their virulence and pathogenicity. Alignment of the protein sequences of Malaysian strain of NDV, known as AF2240, with those from members of the human Bcl-2 family showed many similar regions; most notably we found that its matrix (AF2240-M) protein, large (AF2240-L) protein and fusion (AF2240-F) protein all contain BH3-like regions. In addition, there are BH1-like domains in these proteins, where AF2240-F and Mcl-1 share 55% identity within this region. To further investigate our hypothesis that the presence of the BH3-like domains in these proteins may convey cytotoxicity, AF2240-M and AF2240-F genes were cloned into pFLAG and pEGFP.N2 vectors and transfected into HeLa cells. The expression of these constructs promoted cell death. As shown by flow cytometry, AF2240-M protein with deleted BH3-like region showed five-fold decrease in apoptosis. Moreover, the construct containing the N-terminal of AF2240-M showed nearly the same cell death rate as to that of the full-length protein, strongly suggesting that the BH3-like domain within this protein participates in promoting cell death. Moreover, AF2240-M transfection promoted Bax redistribution to mitochondria. Therefore, to determine whether there is any direct interaction between NDV viral proteins with some members of the Bcl-2 family, various constructs were co-transfected into HeLa cells. Co-immunoprecipitation trials showed that the AF2240-M indeed directly interacted with Bax protein via its BH3-domain, as the mutant proteins failed to interact with Bax. AF2240-F failed to interact with any of the tested proteins, although Bcl-XL slowed down the rate of cell death caused by this construct by nearly five-fold. In a parallel experiment, the level of expression of endogenous Bax and Bcl-2 after infection of HeLa cells with NDV was assessed by qRT-PCR, but no statistically significant change was observed. Consequently, the Bax/Bcl-2 ratio at the mRNA level did not alter. Overall, our study has shed additional light into the mechanisms by which NDV induces apoptosis.
Newcastle disease virus infection promotes Bax redistribution to mitochondria and cell death in HeLa cells

Molouki A, Hsu YT, Jahanshiri F, Rosli R, Yusoff K

Intervirology, 2010;53(2):87-94.
PMID: 19955813 DOI: 10.1159/000264198

Newcastle disease virus (NDV) is an avian paramyxovirus that has gained a lot of interest in cancer viro-therapeutic applications because of its ability to selectively induce apoptosis in human cancer cells. However, the underlying mechanisms by which NDV induces apoptosis in human cancer cells are still not entirely understood.
Microencapsulation of probiotic bacteria Lactobacillus plantarum 15HN using alginate-psyllium-fenugreek polymeric blends

Haghshenas B, Abdullah N, Nami Y, Radiah D, Rosli R, Yari Khosroushahi A

J Appl Microbiol, 2015 Apr;118(4):1048-57.
PMID: 25619628 DOI: 10.1111/jam.12762

Investigation on the use of herbal-based biopolymers for probiotic-Lactobacillus plantarum 15HN-encapsulation is presented. The objectives are to enhance its oral delivery, colonic release and survival rate of these probiotic cultures in gastrointestinal environment.
A newly isolated probiotic Enterococcus faecalis strain from vagina microbiota enhances apoptosis of human cancer cells

Nami Y, Abdullah N, Haghshenas B, Radiah D, Rosli R, Yari Khosroushahi A

J Appl Microbiol, 2014 Aug;117(2):498-508.
PMID: 24775273 DOI: 10.1111/jam.12531

This study aimed to describe probiotic properties and bio-therapeutic effects of newly isolated Enterococcus faecalis from the human vaginal tract.
In silico identification and characterization of a putative phosphatidylinositol 4-phosphate 5-kinase (PIP5K) gene in Eimeria tenella

Ling KH, Loo SS, Rosli R, Shamsudin MN, Mohamed R, Wan KL

In Silico Biol. (Gedrukt), 2007;7(1):115-21.
PMID: 17688436

Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) play diverse roles in the cellular biology of many organisms, including signal transduction, secretion and vesicular trafficking, and regulation of cytoskeleton assembly. Discovery of the PIP5K gene in Eimeria tenella may shed light on its role in the biology of this avian protozoan, and afford further understanding of the cell-host interaction, particularly during the invasion process. In this study, we report the identification of the PIP5K coding region in the genome sequence of Eimeria tenella using in silico gene prediction approaches. Prediction of the PIP5K coding sequence was confirmed by mapping the full-length cDNA sequence, generated via the Rapid Amplification of cDNA Ends (RACE) method, to the genomic sequence. The putative PIP5K gene of Eimeria tenella is located on the complementary strand of the E1080B12.b1 contig, and comprises 12 exons. Further analysis showed that the coding region spans from exon 1 to exon 7, with all exons obeying the adopted 'gt...ag' splicing rule of intronic sequences. Consensus of the hexameric 5' donor-splice site was deduced as GTRDBB... and the consensus for the 3' acceptor-splice sites as ...BHDYAG. The gene encodes a 252-amino acid residue protein. Domain search and protein fold recognition analyses provide compelling evidences that the deduced protein is a PIP5K.
Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ, Madeira AM, et al.

Genome Res, 2007 Mar;17(3):311-9.
PMID: 17284678

Eimeria tenella is an intracellular protozoan parasite that infects the intestinal tracts of domestic fowl and causes coccidiosis, a serious and sometimes lethal enteritis. Eimeria falls in the same phylum (Apicomplexa) as several human and animal parasites such as Cryptosporidium, Toxoplasma, and the malaria parasite, Plasmodium. Here we report the sequencing and analysis of the first chromosome of E. tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite. The chromosome--which appears to be representative of the genome--is gene-dense and rich in simple-sequence repeats, many of which appear to give rise to repetitive amino acid tracts in the predicted proteins. Most striking is the segmentation of the chromosome into repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions. Predicted genes differ in character between the two types of segment, and the repeat-rich regions appear to be associated with strain-to-strain variation.
Quantitative analysis of fetal DNA in maternal plasma in gestational diabetes mellitus, iron deficiency anemia and gestational hypertension pregnancies

Zamanpoor M, Rosli R, Yazid MN, Husain Z, Nordin N, Thilakavathy K

J Matern Fetal Neonatal Med, 2013 Jul;26(10):960-6.
PMID: 23339569 DOI: 10.3109/14767058.2013.766710

OBJECTIVE: To quantify circulating fetal DNA (fDNA) levels in the second and third trimesters of normal healthy pregnant individuals and pregnant women with the following clinical conditions: gestational diabetes mellitus (GDM), iron deficiency anemia and gestational hypertension (GHT).
METHODS: The SRY gene located on the Y chromosome was used as a unique fetal marker. The fDNA was extracted from maternal plasma and the SRY gene concentrations were measured by quantitative real-time polymerase chain reaction (PCR) amplification using TaqMan dual labeled probe system.
RESULTS: No significant differences were observed in the mean fDNA concentration between normal and GDM pregnancy samples (p > 0.05) and also between normal and anemic pregnancy samples (p > 0.05) in both trimesters, but significant differences were observed between the third trimester normal and GHT pregnancy samples (p = 0.001). GDM and iron deficiency anemia do not affect the levels of fDNA in maternal plasma while GHT significantly elevates the levels of fDNA in maternal plasma.
CONCLUSIONS: Increased amount of circulating fDNA in maternal plasma could be used for early identification of adverse pregnancies. GDM and anemia do not affect the levels of fDNA in maternal plasma while GHT significantly elevates the levels of fDNA in maternal plasma. Hence, the elevated fDNA values could be used as a potential screening marker in pregnancies complicated with GHT but not with GDM and iron deficiency anemia.
Fulltext Genotypic and Phenotypic Detection of AmpC β-lactamases in Enterobacter spp. Isolated from a Teaching Hospital in Malaysia

Mohd Khari FI, Karunakaran R, Rosli R, Tee Tay S

PLoS One, 2016;11(3):e0150643.
PMID: 26963619 DOI: 10.1371/journal.pone.0150643

OBJECTIVES: The objective of this study was to determine the occurrence of chromosomal and plasmid-mediated β-lactamases (AmpC) genes in a collection of Malaysian isolates of Enterobacter species. Several phenotypic tests for detection of AmpC production of Enterobacter spp. were evaluated and the agreements between tests were determined.
METHODS: Antimicrobial susceptibility profiles for 117 Enterobacter clinical isolates obtained from the Medical Microbiology Diagnostic Laboratory, University Malaya Medical Centre, Malaysia, from November 2012-February 2014 were determined in accordance to CLSI guidelines. AmpC genes were detected using a multiplex PCR assay targeting the MIR/ACT gene (closely related to chromosomal EBC family gene) and other plasmid-mediated genes, including DHA, MOX, CMY, ACC, and FOX. The AmpC β-lactamase production of the isolates was assessed using cefoxitin disk screening test, D69C AmpC detection set, cefoxitin-cloxacillin double disk synergy test (CC-DDS) and AmpC induction test.
RESULTS: Among the Enterobacter isolates in this study, 39.3% were resistant to cefotaxime and ceftriaxone and 23.9% were resistant to ceftazidime. Ten (8.5%) of the isolates were resistant to cefepime, and one isolate was resistant to meropenem. Chromosomal EBC family gene was amplified from 36 (47.4%) E. cloacae and three (25%) E. asburiae. A novel blaDHA type plasmid-mediated AmpC gene was identified for the first time from an E. cloacae isolate. AmpC β-lactamase production was detected in 99 (89.2%) of 111 potential AmpC β-lactamase producers (positive in cefoxitin disk screening) using D69C AmpC detection set. The detection rates were lower with CC-DDS (80.2%) and AmpC induction tests (50.5%). There was low agreement between the D69C AmpC detection set and the other two phenotypic tests. Of the 40 isolates with AmpC genes detected in this study, 87.5%, 77.5% and 50.0% of these isolates were positive by the D69C AmpC detection set, CC-DDS and AmpC induction tests, respectively.
CONCLUSIONS: Besides MIR/ACT gene, a novel plasmid-mediated AmpC gene belonging to the DHA-type was identified in this study. Low agreement was noted between the D69C AmpC detection set and two other phenotypic tests for detection of AmpC production in Enterobacter spp. As plasmid-mediated genes may serve as the reservoir for the emergence of antibiotic resistance in a clinical setting, surveillance and infection control measures are necessary to limit the spread of these genes in the hospital.
Fulltext Cytotoxicity and physicochemical characterization of iron-manganese-doped sulfated zirconia nanoparticles

Al-Fahdawi MQ, Rasedee A, Al-Qubaisi MS, Alhassan FH, Rosli R, El Zowalaty ME, et al.

Int J Nanomedicine, 2015;10:5739-50.
PMID: 26425082 DOI: 10.2147/IJN.S82586

Iron-manganese-doped sulfated zirconia nanoparticles with both Lewis and Brønsted acidic sites were prepared by a hydrothermal impregnation method followed by calcination at 650°C for 5 hours, and their cytotoxicity properties against cancer cell lines were determined. The characterization was carried out using X-ray diffraction, thermogravimetric analysis, Fourier transform infrared spectroscopy, Brauner-Emmett-Teller (BET) surface area measurements, X-ray fluorescence, X-ray photoelectron spectroscopy, zeta size potential, and transmission electron microscopy (TEM). The cytotoxicity of iron-manganese-doped sulfated zirconia nanoparticles was determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays against three human cancer cell lines (breast cancer MDA-MB231 cells, colon carcinoma HT29 cells, and hepatocellular carcinoma HepG2 cells) and two normal human cell lines (normal hepatocyte Chang cells and normal human umbilical vein endothelial cells [HUVECs]). The results suggest for the first time that iron-manganese-doped sulfated zirconia nanoparticles are cytotoxic to MDA-MB231 and HepG2 cancer cells but have less toxicity to HT29 and normal cells at concentrations from 7.8 μg/mL to 500 μg/mL. The morphology of the treated cells was also studied, and the results supported those from the cytotoxicity study in that the nanoparticle-treated HepG2 and MDA-MB231 cells had more dramatic changes in cell morphology than the HT29 cells. In this manner, this study provides the first evidence that iron-manganese-doped sulfated zirconia nanoparticles should be further studied for a wide range of cancer applications without detrimental effects on healthy cell functions.
Fulltext Beta thalassaemia mutations in Malays: a simplified cost-effective strategy to identify the mutations

George, E., Teh, L.K., Rosli, R., Lai, M.I., Tan, J.A.M.A.

Malaysian Journal of Medicine and Health Sciences, 2012;8(1):45-53.
MyJurnal

Beta (β)- thalassaemia is a public health problem in Malaysia. The carrier rate is estimated to be 4.5% by micro-mapping studies particularly among Malays who comprise 53.5% of the population in Malaysia. The common diagnostic method in Malaysia for mutation detection is by amplification refractory mutation system (ARMS). It allows single mutation detection in each reaction but is labour intensive and time consuming when many mutations need to be identified. The purpose of this study was to develop a diagnostic tool for effective mutation detection of beta thalassaemia in Malay patients and compare its efficacy with ARMS-PCR, the current method in use. Methods: Reverse dot blot hybridization (RDBH) technique was incorporated in the development of two strip assays [RDBH-Strip M(6) and RDBH-Strip C(6)] to identify common beta thalassaemia mutations in the Malays. The panels of selected mutations were based on the mutation frequencies in Malaysia reported in previous studies. RDBH-Strip M(6) was applied as step 1 and RDBH-Strip C(6) was applied as step 2 for unidentified mutations. The strips were validated with the gold standard method, ARMS- PCR. Results: One hundred and thirty seven Malay patients with 274 alleles were studied. In Step 1 mutation detection, 238 alleles (86.9%) were identified in 119 of patients by RDBH-Strip M(6). Step 2 resulted in a further detection of 20 alleles in another 10 patients by RDBH-Strip C(6). The combination of both strips resulted in the identification of 258 alleles in 129 (94.6%) of 137 Malay patients. The strip assays were 100% sensitive and specific when compared with ARMS-PCR method. Conclusion: Two strip assays utilising the RDBH technique were developed to identify common β-thalassaemia mutations in Malays. The RDBH Strip M(6) identified 86.9% of the mutations and the RDBH-Strip C (6) detected further 7.3% alleles. This two step strategy was found to be rapid and cost effective for the direct diagnosis of β-thalassaemia mutations in the Malays. The remaining unidentified mutations would require DNA sequencing. It can serve as a specific molecular diagnostic tool for effective diagnosis of
β-thalassaemia mutations in this ethnic group.
Fulltext Assessing the efficacy of machine learning algorithms for syncope classification: A systematic review

Goh CH, Ferdowsi M, Gan MH, Kwan BH, Lim WY, Tee YK, et al.

MethodsX, 2024 Jun;12:102508.
PMID: 38162148 DOI: 10.1016/j.mex.2023.102508

Syncope is a transient loss of consciousness with rapid onset. The aims of the study were to systematically evaluate available machine learning (ML) algorithm for supporting syncope diagnosis to determine their performance compared to existing point scoring protocols. We systematically searched IEEE Xplore, Web of Science, and Elsevier for English articles (Jan 2011 - Sep 2021) on individuals aged five and above, employing ML algorithms in syncope detection with Head-up titl table test (HUTT)-monitored hemodynamic parameters and reported metrics. Extracted data encompassed subject count, age range, syncope protocols, ML type, hemodynamic parameters, and performance metrics. Of the 6301 studies initially identified, 10 studies, involving 1205 participants aged 5 to 82 years, met the inclusion criteria, and formed the basis for it. Selected studies must use ML algorithms in syncope detection with hemodynamic parameters recorded throughout HUTT. The overall ML algorithm performance achieved a sensitivity of 88.8% (95% CI: 79.4-96.1%), specificity of 81.5% (95% CI: 69.8-92.8%) and accuracy of 85.8% (95% CI: 78.6-92.8%). Machine learning improves syncope diagnosis compared to traditional scoring, requiring fewer parameters. Future enhancements with larger databases are anticipated. Integrating ML can curb needless admissions, refine diagnostics, and enhance the quality of life for syncope patients.
Fulltext Analyses of hypomethylated oil palm gene space

Low ET, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, et al.

PLoS One, 2014;9(1):e86728.
PMID: 24497974 DOI: 10.1371/journal.pone.0086728

Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
Fulltext Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm

Ting NC, Yaakub Z, Kamaruddin K, Mayes S, Massawe F, Sambanthamurthi R, et al.

BMC Genomics, 2016;17(1):289.
PMID: 27079197 DOI: 10.1186/s12864-016-2607-4

The commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called 'palm oil') with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil.
SSR mining in oil palm EST database: application in oil palm germplasm diversity studies

Ting NC, Zaki NM, Rosli R, Low ET, Ithnin M, Cheah SC, et al.

J Genet, 2010 Aug;89(2):135-45.
PMID: 20861564

This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.
Fulltext Acute toxicity profiling of the ethyl acetate fraction of Swietenia macrophylla seeds and in-vitro neuroprotection studies

Sayyad M, Tiang N, Kumari Y, Goh BH, Jaiswal Y, Rosli R, et al.

Saudi Pharm J, 2017 Feb;25(2):196-205.
PMID: 28344469 DOI: 10.1016/j.jsps.2016.05.002

Swietenia macrophylla (SM) is a medicinally important plant found in tropical and subtropical regions of the world. The ethyl acetate fraction of the seeds of S. macrophylla (SMEAF) is reported to exhibit potent anticancer, antitumor, anti-inflammatory and antifeedant activities. Till date, there have been no studies reported on the acute oral toxicity profile of the ethyl acetate fraction of the seeds of SM. The objective of the present study was to determine the acute toxicity of SMEAF and evaluate the in-vitro neuroprotective activity of SMEAF using primary neuronal cell cultures. In acute oral toxicity study, the SMEAF did not produce any lethal signs of morbidity and mortality. Histo-pathological findings, support the safety of SMEAF, as there were no significant changes observed in any of the parameters studied. Based on the results obtained in MTT assay, we infer that SMEAF has a significant neuroprotective effect, as it increased the cell viability and exhibited protection to the neuronal cells against TBHP induced oxidative stress. Thus, SMEAF can be suggested for use in the development of herbal drug formulations with neuroprotective potential.
Using fuzzy association rule mining in cancer classification

Mahmoodian H, Hamiruce Marhaban M, Abdulrahim R, Rosli R, Saripan I

Australas Phys Eng Sci Med, 2011 Apr;34(1):41-54.
PMID: 21327594 DOI: 10.1007/s13246-011-0054-8

The classification of the cancer tumors based on gene expression profiles has been extensively studied in numbers of studies. A wide variety of cancer datasets have been implemented by the various methods of gene selection and classification to identify the behavior of the genes in tumors and find the relationships between them and outcome of diseases. Interpretability of the model, which is developed by fuzzy rules and linguistic variables in this study, has been rarely considered. In addition, creating a fuzzy classifier with high performance in classification that uses a subset of significant genes which have been selected by different types of gene selection methods is another goal of this study. A new algorithm has been developed to identify the fuzzy rules and significant genes based on fuzzy association rule mining. At first, different subset of genes which have been selected by different methods, were used to generate primary fuzzy classifiers separately and then proposed algorithm was implemented to mix the genes which have been associated in the primary classifiers and generate a new classifier. The results show that fuzzy classifier can classify the tumors with high performance while presenting the relationships between the genes by linguistic variables.
Fulltext The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB

Singh R, Low ET, Ooi LC, Ong-Abdullah M, Nookiah R, Ting NC, et al.

Nat Commun, 2014 Jun 30;5:4106.
PMID: 24978855 DOI: 10.1038/ncomms5106

Oil palm, a plantation crop of major economic importance in Southeast Asia, is the predominant source of edible oil worldwide. We report the identification of the virescens (VIR) gene, which controls fruit exocarp colour and is an indicator of ripeness. VIR is a R2R3-MYB transcription factor with homology to Lilium LhMYB12 and similarity to Arabidopsis production of anthocyanin pigment1 (PAP1). We identify five independent mutant alleles of VIR in over 400 accessions from sub-Saharan Africa that account for the dominant-negative virescens phenotype. Each mutation results in premature termination of the carboxy-terminal domain of VIR, resembling McClintock's C1-I allele in maize. The abundance of alleles likely reflects cultural practices, by which fruits were venerated for magical and medicinal properties. The identification of VIR will allow selection of the trait at the seed or early-nursery stage, 3-6 years before fruits are produced, greatly advancing introgression into elite breeding material.
Fulltext Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, et al.

Nature, 2013 Aug 15;500(7462):335-9.
PMID: 23883927 DOI: 10.1038/nature12309

Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
Fulltext Investigation of Surface Plasmon Resonance (SPR) in MoS2- and WS2-Protected Titanium Side-Polished Optical Fiber as a Humidity Sensor

Zakaria R, Zainuddin NAM, Leong TC, Rosli R, Rusdi MF, Harun SW, et al.

Micromachines (Basel), 2019 Jul 11;10(7).
PMID: 31336745 DOI: 10.3390/mi10070465

In this paper, we report the effects of a side-polished fiber (SPF) coated with titanium (Ti) films in different thicknesses, namely 5 nm, 13 nm, and 36 nm, protected by a thin layer of transition metal dichalcogenides (TMDCs) such as molybdenum disulfide (MoS2) and tungsten disulfide (WS2), which provide ultra-sensitive sensor-based surface plasmon resonance (SPR) covering from the visible to mid-infrared region. The SPF deposited with Ti exhibits strong evanescent field interaction with the MoS2 and WS2, and good optical absorption, hence resulting in high-sensitivity performance. Incremental increases in the thickness of the Ti layer contribute to the enhancement of the intensity of transmission with redshift and broad spectra. The findings show that the optimum thickness of Ti with 36 nm combined with MoS2 causes weak redshifts of the longitudinal localized surface plasmon resonance (LSPR) mode, while the same thickness of Ti with WS2 causes large blueshifts. The redshifts are possibly due to a reduced plasmon-coupling effect with the excitonic region of MoS2. The observed blueshifts of the LSPR peak position are possibly due to surface modification between WS2 and Ti. Changing the relative humidity from 58% to 88% only elicited a response in Ti/MoS2. Thus, MoS2 shows more sensitivity on 36-nm thickness of Ti compared with WS2. Therefore, the proposed fiber-optic sensor with integration of 2D materials is capable of measuring humidity in any environment.
Preliminary observation on the effect of baking soda volume on controlling odour from discarded organic waste

Qamaruz-Zaman N, Kun Y, Rosli RN

Waste Manag, 2015 Jan;35:187-90.
PMID: 25445259 DOI: 10.1016/j.wasman.2014.09.017

Food wastes with high moisture and organic matter content are likely to emit odours as a result of the decomposition process. The management of odour from decomposing wastes is needed to sustain the interest of residents and local councils in the source separation of kitchen wastes. This study investigated the potential of baking soda (at 50 g, 75 g and 100g per kg food waste) to control odour from seven days stored food waste. It was found that 50 g of baking soda, spread at the bottom of 8l food wastes bin, can reduce the odour by about 70%. A higher amount (above 100g) is not advised as a pH higher than 9.0 may be induced leading to the volatilization of odorous ammonia. This research finding is expected to benefit the waste management sector, food processing industries as well as the local authorities where malodour from waste storage is a pressing issue.

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