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Malays with thalassaemia in West Malaysia

George E, Khuziah R

Trop Geogr Med, 1984 Jun;36(2):123-5.
PMID: 6332395

Hereditary haemolytic anaemias have been found to be a significant cause of haemolytic disease in West Malaysia. This paper reports a micromapping study of 916 healthy Malay males from June to August 1983 to determine the distribution of the relevant thalassaemia genes in West Malaysia. Beta thalassaemia trait was found in 2.18%, HbE 3.49% and alpha thal2 (alpha+) trait in 26%. Of the sixteen transfusion dependant Malay thalassaemic patients at the Paediatric Unit, National University of Malaysia, eight patients had HbE beta thalassaemia and the rest are beta thalassaemia major; these patients who are transfusion dependant receive inadequate treatment. Prevention is the only resort.

Matched MeSH terms: Hemoglobin A2/genetics; Hemoglobin E/genetics; Thalassemia/genetics*
Glucose-6-phosphate dehydrogenase enzyme activity in normal, hemizygote and heterozygote Kelantanese Malays

Normah J, Choo KE, Oppenheimer SJ, Selamah G

J Paediatr Child Health, 1991 Dec;27(6):376-9.
PMID: 1756082

This prospective study was performed to quantify glucose-6-phosphate dehydrogenase (G6PD) enzyme activity in deficient males and female heterozygotes. The methods used in the study were the fluorescent spot test, G6PD enzyme electrophoresis on cellulose acetate and quantitative assays. Forty-seven children who had been detected as spot screen deficient at birth were rescreened. Their first degree relatives were also included in the study. The mean enzyme activity of deficient males was 0.74 iu/g Hb (s.d. +/- 0.8), of female heterozygotes was 6.5 iu/g Hb (s.d. +/- 3.2) and of normal males was 12.1 iu/g Hb (s.d. +/- 3.5). The mean activity in deficient males was 6.1% of normal males. Most (35 of 47) of these fell into class 2 in Beutler's classification of G6PD variants. This indicates a population which may be susceptible to favism. Female heterozygotes had an intermediate enzyme activity with a wide scatter. Using a cut off point of enzyme activity of below 9.0 iu/g Hb gave sensitivity and specificity of 87% and 84% in detecting female heterozygotes. This group could be defined more accurately by combining quantitative assays with family studies.

Matched MeSH terms: Favism/genetics; Glucosephosphate Dehydrogenase/genetics; Glucosephosphate Dehydrogenase Deficiency/genetics*
Regions on nucleocapsid protein of Newcastle disease virus that interact with its phosphoprotein

Kho CL, Tan WS, Tey BT, Yusoff K

Arch Virol, 2004 May;149(5):997-1005.
PMID: 15098113 DOI: 10.1007/s00705-003-0273-8

The nucleocapsid (NP) and phospho-(P) proteins of paramyxoviruses are involved in transcription and replication of the viral genome. An in vitro protein binding assay was used to investigate the regions on NP protein that interact with the P protein of Newcastle disease virus (NDV). Truncated NP mutants were first immobilised on a solid phase and then interacted with radio-labelled [(35)S]-P protein synthesised in rabbit reticulocyte. The interaction affinity was quantitated by measuring the radioactivity that was retained on the solid phase. Using this approach, a highly interactive region was identified to be resided at the first 25 amino acids of NP N-terminus. The interaction between these two proteins remained strong even with the removal of 114 amino acids from the C-terminal end of NP. However, it is possible that the 49 amino acids at the C-terminal end might have another contact region for P protein, which is not as critical as the N-terminal end. The interaction regions mapped in this study are significantly different from the other two paramyxoviruses: Sendai and measles viruses in which the C-termini of their NP proteins play an important role in binding to the P.

Matched MeSH terms: Nucleoproteins/genetics; Viral Proteins/genetics; Nucleocapsid Proteins/genetics
STR Data for the AmpFlSTR Identifiler loci in three ethnic groups (Malay, Chinese, Indian) of the Malaysian population

Seah LH, Jeevan NH, Othman MI, Jaya P, Ooi YS, Wong PC, et al.

Forensic Sci Int, 2003 Dec 17;138(1-3):134-7.
PMID: 14642733

Allele frequencies for the 15 STR loci in the AmpFlSTR Identifiler kit were determined and compared for the three main ethnic groups of the Malaysian population comprising 210 Malays, 219 Chinese and 209 Indians. Blood was placed on FTA paper and DNA was purified in-situ.

Matched MeSH terms: Ethnic Groups/genetics*; Genetics, Population*
Fulltext Inherited mutations in BRCA1 and BRCA2 in an unselected multiethnic cohort of Asian patients with breast cancer and healthy controls from Malaysia

Wen WX, Allen J, Lai KN, Mariapun S, Hasan SN, Ng PS, et al.

J Med Genet, 2018 02;55(2):97-103.
PMID: 28993434 DOI: 10.1136/jmedgenet-2017-104947

BACKGROUND: Genetic testing for BRCA1 and BRCA2 is offered typically to selected women based on age of onset and family history of cancer. However, current internationally accepted genetic testing referral guidelines are built mostly on data from cancer genetics clinics in women of European descent. To evaluate the appropriateness of such guidelines in Asians, we have determined the prevalence of germ line variants in an unselected cohort of Asian patients with breast cancer and healthy controls.
METHODS: Germ line DNA from a hospital-based study of 2575 unselected patients with breast cancer and 2809 healthy controls were subjected to amplicon-based targeted sequencing of exonic and proximal splice site junction regions of BRCA1 and BRCA2 using the Fluidigm Access Array system, with sequencing conducted on a Illumina HiSeq2500 platform. Variant calling was performed with GATK UnifiedGenotyper and were validated by Sanger sequencing.
RESULTS: Fifty-five (2.1%) BRCA1 and 66 (2.6%) BRCA2 deleterious mutations were identified among patients with breast cancer and five (0.18%) BRCA1 and six (0.21%) BRCA2 mutations among controls. One thousand one hundred and eighty-six (46%) patients and 97 (80%) carriers fulfilled the National Comprehensive Cancer Network guidelines for genetic testing.
CONCLUSION: Five per cent of unselected Asian patients with breast cancer carry deleterious variants in BRCA1 or BRCA2. While current referral guidelines identified the majority of carriers, one in two patients would be referred for genetic services. Given that such services are largely unavailable in majority of low-resource settings in Asia, our study highlights the need for more efficient guidelines to identify at-risk individuals in Asia.

Matched MeSH terms: Breast Neoplasms/genetics*; BRCA1 Protein/genetics*; BRCA2 Protein/genetics*
Fulltext Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides)

Tan CK, Natrah I, Suyub IB, Edward MJ, Kaman N, Samsudin AA

Microbiologyopen, 2019 05;8(5):e00734.
PMID: 30353678 DOI: 10.1002/mbo3.734

AIMS: The aim of this study was to identify and compare the gut microbial community of wild and captive Tor tambroides through 16S rDNA metagenetic sequencing followed by functions prediction.
METHODS AND RESULTS: The library of 16S rDNA V3-V4 hypervariable regions of gut microbiota was amplified and sequenced using Illumina MiSeq. The sequencing data were analyzed using Quantitative Insights into Microbial Ecology (QIIME) pipeline and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The most abundant bacterial phyla in both wild and captive T. tambroides were Firmicutes, Proteobacteria, Fusobacteria and Bacteroidetes. Cetobacterium spp., Peptostreptococcaceae family, Bacteroides spp., Phosphate solubilizing bacteria PSB-M-3, and Vibrio spp. were five most abundant OTU in wild T. tambroides as compared to Cetobacterium spp., Citrobacter spp., Aeromonadaceae family, Peptostreptococcaceae family and Turicibacter spp. in captive T. tambroides.
CONCLUSION: In this study, the specimens of the wild T. tambroides contain more diverse gut microbiota than of the captive ones. The results suggested that Cetobacterium spp. is one of the core microbiota in guts of T. tambroides. Besides, high abundant Bacteroides spp., Citrobacter spp., Turicibacter spp., and Bacillus spp. may provide important functions in T. tambroides guts.
SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study provide significant information of T. tambroides gut microbiota for further understanding of their physiological functions including growth and disease resistance.

Matched MeSH terms: Bacteria/genetics*; DNA, Ribosomal/genetics; RNA, Ribosomal, 16S/genetics
The current state of diagnostic genetics for conditions affecting sex development

Alhomaidah D, McGowan R, Ahmed SF

Clin Genet, 2017 02;91(2):157-162.
PMID: 28127758 DOI: 10.1111/cge.12912

Disorders of sex development (DSD), are a group of rare congenital conditions. Unlike 46, XX DSD where the cause is usually clear, identification of a cause of XY DSD is often unclear and may be attributed to a disorder of gonadal development, androgen synthesis or androgen action. Reaching a firm diagnosis is challenging and requires expertise within a framework that abides by the highest standards of clinical care. Whilst conditions associated with altered sex development have improved our fundamental understanding of sex and gonadal development, it is debatable whether this improvement in our understanding has improved the lives of people with DSD. Thus, there is a need for more emphasis on showing that a firm diagnosis for conditions associated with DSD is associated with a change in clinical practice that benefits the patient. With the rapid advances in diagnostic technology, there is also a need for clearer guidance on the relative merits of biochemical vs genetic evaluation. The standardization and harmonization of complex genetic and biochemical analyses for rare conditions are issues that require further guidance and it is probably that international networks and registries for rare conditions will facilitate the development of this framework.

Matched MeSH terms: Androgens/genetics; Disorders of Sex Development/genetics*; Sexual Development/genetics*
Effects of different mycotoxins on humans, cell genome and their involvement in cancer (Review)

Ahmed Adam MA, Tabana YM, Musa KB, Sandai DA

Oncol Rep, 2017 Mar;37(3):1321-1336.
PMID: 28184933 DOI: 10.3892/or.2017.5424

The chemical nature of most of the mycotoxins makes them highly liposoluble compounds that can be absorbed from the site of exposure such as from the gastrointestinal and respiratory tract to the blood stream where it can be dissimilated throughout the body and reach different organs such as the liver and kidneys. Mycotoxins have a strong tendency and ability to penetrate the human and animal cells and reach the cellular genome where it causes a major mutagenic change in the nucleotide sequence which leads to strong and permanent defects in the genome. This defect will eventually be transcribed, translated and lead to the development of cancer. In this review, the chemical and physical nature of mycotoxins, the action of mycotoxins on the cellular genome and its effect on humans, mycotoxins and their carcinogenicity and mycotoxins research gaps are discussed, and new research areas are suggested. The research review posed various questions. What are the different mycotoxins that can cause cancer, what is the role of mycotoxins in causing cancer and what types of cancers can be caused by mycotoxins? These questions have been selected due to the significant increase in the mycotoxin contamination and the cancer incidence rate in the contemporary world. By revealing and understanding the role of mycotoxins in developing cancer, measures to reduce the risks and incidents of cancer could be taken.

Matched MeSH terms: Cell Transformation, Neoplastic/genetics; Neoplasms/genetics*; Genome, Human/genetics
Complete Genome Sequence of a Novel Polyhydroxyalkanoate (PHA) Producer, Jeongeupia sp. USM3 (JCM 19920) and Characterization of Its PHA Synthases

Zain NA, Ng LM, Foong CP, Tai YT, Nanthini J, Sudesh K

Curr Microbiol, 2020 Mar;77(3):500-508.
PMID: 31893298 DOI: 10.1007/s00284-019-01852-z

A novel polyhydroxyalkanoate (PHA)-producing bacterium, Jeongeupia sp. USM3 (JCM 19920) was isolated from the limestone soil at Gua Tempurung, Perak, Malaysia. This is the first report on the complete genome sequence for the genus Jeongeupia. This genome consists of a circular chromosome with a size of 3,788,814 bp and contains 3557 genes. Two PHA synthase (phaC) genes encoding for the key enzyme in the polymerization of PHA monomers and other PHA-associated genes were identified from the genome. Phylogenetic analysis of the PhaC protein sequences has revealed that both PhaC1 and PhaC2 of Jeongeupia sp. USM3 are categorized as Class I PHA synthases with 56% similarity to each other. Both of the PHA synthase genes of this isolate were cloned and heterologously expressed in a PHA mutant strain Cupriavidus necator PHB-4. The ability of the transformants to accumulate PHA showed that both PhaC1 and PhaC2 were functional.

Matched MeSH terms: Acyltransferases/genetics; Cupriavidus necator/genetics; Betaproteobacteria/genetics*
Understanding thermostability factors of Aspergillus niger PhyA phytase: a molecular dynamics study

Noorbatcha IA, Sultan AM, Salleh HM, Amid A

Protein J, 2013 Apr;32(4):309-16.
PMID: 23636517 DOI: 10.1007/s10930-013-9489-y

Molecular dynamics simulation was used to study the dynamic differences between native Aspergillus niger PhyA phytase and a mutant with 20 % greater thermostability. Atomic root mean square deviation, radius of gyration, and number of hydrogen bonds and salt bridges are examined to determine thermostability factors. The results suggest that, among secondary structure elements, loops have the most impact on the thermal stability of A. niger phytase. In addition, the location rather than the number of hydrogen bonds is found to have an important contribution to thermostability. The results also show that salt bridges may have stabilizing or destabilizing effect on the enzyme and influence its thermostability accordingly.

Matched MeSH terms: Aspergillus niger/genetics; Fungal Proteins/genetics; 6-Phytase/genetics
Fulltext The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns

Pucker B, Pandey A, Weisshaar B, Stracke R

PLoS One, 2020;15(10):e0239275.
PMID: 33021974 DOI: 10.1371/journal.pone.0239275

The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-Seq data. For 280 M. acuminata MYB genes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. The M. acuminata R2R3-MYB genes were functionally categorised, leading to the identification of seven clades containing only M. acuminata R2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded in Musa during genome evolution. This functional classification and expression analysis of the MYB gene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.

Matched MeSH terms: Plant Proteins/genetics*; Transcription Factors/genetics*; Musa/genetics
Fulltext Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4

Zhang L, Cenci A, Rouard M, Zhang D, Wang Y, Tang W, et al.

Sci Rep, 2019 06 03;9(1):8199.
PMID: 31160634 DOI: 10.1038/s41598-019-44637-x

Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cubense, especially by tropical race 4 (Foc TR4), is threatening the global banana industry. Musa acuminata Pahang, a wild diploid banana that displays strong resistance to Foc TR4, holds great potential to understand the underlying resistance mechanisms. Microscopic examination reports that, in a wounding inoculation system, the Foc TR4 infection processes in roots of Pahang (resistant) and a triploid cultivar Brazilian (susceptible) were similar by 7 days post inoculation (dpi), but significant differences were observed in corms of both genotypes at 14 dpi. We compare transcriptomic responses in the corms of Pahang and Brazilian, and show that Pahang exhibited constitutive defense responses before Foc TR4 infection and inducible defense responses prior to Brazilian at the initial Foc TR4 infection stage. Most key enzymatic genes in the phenylalanine metabolism pathway were up-regulated in Brazilian, suggesting that lignin and phytotoxin may be triggered during later stages of Foc TR4 infection. This study unravels a few potential resistance candidate genes whose expression patterns were assessed by RT-qPCR assay and improves our understanding the defense mechanisms of Pahang response to Foc TR4.

Matched MeSH terms: Plant Diseases/genetics*; Musa/genetics*; Disease Resistance/genetics
Fulltext Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis

Loh SC, Othman AS, Veera Singham G

Sci Rep, 2019 10 04;9(1):14296.
PMID: 31586098 DOI: 10.1038/s41598-019-50800-1

Hevea brasiliensis remains the primary crop commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. Here, we described the transcriptional events related to jasmonic acid (JA)- and linolenic acid (LA)-induced secondary laticifer differentiation (SLD) in H. brasiliensis clone RRIM 600 based on RNA-seq approach. Histochemical approach proved that JA- and LA-treated samples resulted in SLD in H. brasiliensis when compared to ethephon and untreated control. RNA-seq data resulted in 86,614 unigenes, of which 2,664 genes were differentially expressed in JA and LA-induced secondary laticifer harvested from H. brasiliensis bark samples. Among these, 450 genes were unique to JA and LA as they were not differentially expressed in ethephon-treated samples compared with the untreated samples. Most transcription factors from the JA- and LA-specific dataset were classified under MYB, APETALA2/ethylene response factor (AP2/ERF), and basic-helix-loop-helix (bHLH) gene families that were involved in tissue developmental pathways, and we proposed that Bel5-GA2 oxidase 1-KNOTTED-like homeobox complex are likely involved in JA- and LA-induced SLD in H. brasiliensis. We also discovered alternative spliced transcripts, putative novel transcripts, and cis-natural antisense transcript pairs related to SLD event. This study has advanced understanding on the transcriptional regulatory network of SLD in H. brasiliensis.

Matched MeSH terms: Plant Proteins/genetics; Transcription Factors/genetics; Hevea/genetics
A 12-residue epitope displayed on phage T7 reacts strongly with antibodies against foot-and-mouth disease virus

Wong CL, Yong CY, Muhamad A, Syahir A, Omar AR, Sieo CC, et al.

Appl Microbiol Biotechnol, 2018 May;102(9):4131-4142.
PMID: 29564523 DOI: 10.1007/s00253-018-8921-9

Foot-and-mouth disease (FMD) is a major threat to the livestock industry worldwide. Despite constant surveillance and effective vaccination, the perpetual mutations of the foot-and-mouth disease virus (FMDV) pose a huge challenge to FMD diagnosis. The immunodominant region of the FMDV VP1 protein (residues 131-170) displayed on phage T7 has been used to detect anti-FMDV in bovine sera. In the present study, the functional epitope was further delineated using amino acid sequence alignment, homology modelling and phage display. Two highly conserved regions (VP1145-152 and VP1159-170) were identified among different FMDV serotypes. The coding regions of these two epitopes were fused separately to the T7 genome and displayed on the phage particles. Interestingly, chimeric phage displaying the VP1159-170 epitope demonstrated a higher antigenicity than that displaying the VP1131-170 epitope. By contrast, phage T7 displaying the VP1145-152 epitope did not react significantly with the anti-FMDV antibodies in vaccinated bovine sera. This study has successfully identified a smaller functional epitope, VP1159-170, located at the C-terminal end of the structural VP1 protein. The phage T7 displaying this shorter epitope is a promising diagnostic reagent to detect anti-FMDV antibodies in vaccinated animals.

Matched MeSH terms: Epitopes/genetics; Bacteriophage T7/genetics; Capsid Proteins/genetics
Cell surface display system for Lactococcus lactis: a novel development for oral vaccine

Raha AR, Varma NR, Yusoff K, Ross E, Foo HL

Appl Microbiol Biotechnol, 2005 Jul;68(1):75-81.
PMID: 15635459

The food-grade Lactococcus lactis is a potential vector to be used as a live vehicle for the delivery of heterologous proteins for vaccine and pharmaceutical purposes. We constructed a plasmid vector pSVac that harbors a 255-bp single-repeat sequence of the cell wall-binding protein region of the AcmA protein. The recombinant plasmid was transformed into Escherichia coli and expression of the gene fragment was driven by the T7 promoter of the plasmid. SDS-PAGE showed the presence of the putative AcmA' fragment and this was confirmed by Western blot analysis. The protein was isolated and purified using a His-tag affinity column. When mixed with a culture of L. lactis MG1363, ELISA and immunofluorescence assays showed that the cell wall-binding fragment was anchored onto the outer surface of the bacteria. This indicated that the AcmA' repeat unit retained the active site for binding onto the cell wall surface of the L. lactis cells. Stability assays showed that the fusion proteins (AcmA/A1, AcmA/A3) were stably docked onto the surface for at least 5 days. The AcmA' fragment was also shown to be able to strongly bind onto the cell surface of naturally occurring lactococcal strains and Lactobacillus and, with less strength, the cell surface of Bacillus sphericus. The new system designed for cell surface display of recombinant proteins on L. lactis was evaluated for the expression and display of A1 and A3 regions of the VP1 protein of enterovirus 71 (EV71). The A1 and A3 regions of the VP1 protein of EV71 were cloned upstream to the cell wall-binding domains of AcmA protein and successfully expressed as AcmA/A1 and AcmA/A3. Whole-cell ELISA showed the successful display of VP1 protein epitopes of EV71 on the surface of L. lactis. The success of the anchoring system developed in this study for docking the A1 and A3 epitopes of VP1 onto the surface of L. lactis cells opens up the possibilities of peptide and protein display for not only Lactococcus but also for other gram-positive bacteria. This novel way of displaying epitopes on the cell surface of L. lactis and other related organisms should be very useful in the delivery of vaccines and other useful proteins.

Matched MeSH terms: Escherichia coli/genetics; Muramidase/genetics; Lactococcus lactis/genetics*
Optimisation of signal peptide for recombinant protein secretion in bacterial hosts

Low KO, Muhammad Mahadi N, Md Illias R

Appl Microbiol Biotechnol, 2013 May;97(9):3811-26.
PMID: 23529680 DOI: 10.1007/s00253-013-4831-z

Escherichia coli-the powerhouse for recombinant protein production-is rapidly gaining status as a reliable and efficient host for secretory expression. An improved understanding of protein translocation processes and its mechanisms has inspired and accelerated the development of new tools and applications in this field and, in particular, a more efficient secretion signal. Several important characteristics and requirements are summarised for the design of a more efficient signal peptide for the production of recombinant proteins in E. coli. General approaches and strategies to optimise the signal peptide, including the selection and modification of the signal peptide components, are included. Several challenges in the secretory production of recombinant proteins are discussed, and research approaches designed to meet these challenges are proposed.

Matched MeSH terms: Bacterial Proteins/genetics; Escherichia coli/genetics; Recombinant Proteins/genetics
Preimplantation genetic diagnosis for beta-thalassemia using single-cell DNA analysis for codons 17 and 26 of beta-globin gene

Nasri NW, Jamal AR, Abdullah NC, Razi ZR, Mokhtar NM

Arch Med Res, 2009 Jan;40(1):1-9.
PMID: 19064120 DOI: 10.1016/j.arcmed.2008.10.008

Preimplantation genetic diagnosis (PGD) of monogenic autosomal hereditary disorders following assisted conception usually involves the removal of one or two blastomeres from preimplantation embryos. However, the amount of DNA from a single blastomere is insufficient to amplify the region of interest. Hence, the whole genome amplification (WGA) method is performed prior to amplifying the genes of interest before analysis of DNA material through polymerase chain reaction (PCR).

Matched MeSH terms: DNA/genetics*; beta-Thalassemia/genetics; beta-Globins/genetics*
Plasmodium inui is not closely related to other quartan Plasmodium species

Kissinger JC, Collins WE, Li J, McCutchan TF

J Parasitol, 1998 Apr;84(2):278-82.
PMID: 9576499

Plasmodium inui (Halberstaedter and von Prowazek, 1907), a malarial parasite of Old World monkeys that occurs in isolated pockets throughout the Celebes, Indonesia, Malaysia, and the Philippines, has traditionally been considered to be related more closely to Plasmodium malariae of humans (and its primate counterpart Plasmodium brasilianum), than to other primate Plasmodium species. This inference was made in part because of the similarities in the periodicities or duration of the asexual cycle in the blood, the extended sporogonic cycle, and the longer period of time for development of the pre-erythrocytic stages in the liver. Both P. inui and P. malariae have quartan (72 hr) periodicities associated with their asexual cycle, whereas other primate malarias, such as Plasmodium fragile and Plasmodium cynomolgi, are associated with tertian periodicities (48 hr), and Plasmodiumn knowlesi, with a quotidian (24 hr) periodicity. Phylogenetic analyses of portions of orthologous small subunit ribosomal genes reveal that P. inui is actually more closely related to the Plasmodium species of the "vivax-type" lineage than to P. malariae. Ribosomal sequence analysis of many different, geographically isolated, antigenically distinct P. inui isolates reveals that the isolates are nearly identical in sequence and thus members of the same species.

Matched MeSH terms: Plasmodium/genetics; RNA, Ribosomal/genetics; RNA, Protozoan/genetics
Fulltext Phylogeographical pattern and evolutionary history of an important Peninsular Malaysian timber species, Neobalanocarpus heimii (Dipterocarpaceae)

Tnah LH, Lee SL, Ng KK, Lee CT, Bhassu S, Othman RY

J Hered, 2013 Jan-Feb;104(1):115-26.
PMID: 23132907 DOI: 10.1093/jhered/ess076

Tectonic movements, climatic oscillations, and marine transgressions during the Cenozoic have had a dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber species, Neobalanocarpus heimii (Dipterocarpaceae). A total of 32 natural populations of N. heimii, with 8 samples from each population were investigated. Fifteen haplotypes were identified from five noncoding chloroplast DNA (cpDNA) regions. Overall, two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to have survived in multiple refugia during climatic oscillations: the northwestern region (R1), the northeastern region (R2), and the southern region (R3). These putative glacial refugia exhibited higher levels of genetic diversity, population differentiation, and the presence of unique haplotypes. Recolonization of refugia R1 and R2 could have first expanded into the northern region and migrated both northeastwards and northwestwards. Meanwhile, recolonization of N. heimii throughout the southern region could have commenced from refugia R3 and migrated toward the northeast and northwest, respectively. The populations of Tersang, Pasir Raja, and Rotan Tunggal exhibited remarkably high haplotype diversity, which could have been the contact zones that have received an admixture of gene pools from the northerly and also southerly regions. As a whole, the populations of N. heimii derived from glacial refugia and contact zones should be considered in the conservation strategies in order to safeguard the long-term survival of the species.

Matched MeSH terms: Haplotypes/genetics; DNA, Chloroplast/genetics; Dipterocarpaceae/genetics*
Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation

Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Diway B, et al.

J Hered, 2019 12 17;110(7):844-856.
PMID: 31554011 DOI: 10.1093/jhered/esz052

Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.

Matched MeSH terms: Genetics, Population*; Dipterocarpaceae/genetics*

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