Browse publications by year: 2019

  1. Sagadevan S, Chowdhury ZZ, Johan MRB, Aziz FA, Roselin LS, Podder J, et al.
    J Nanosci Nanotechnol, 2019 Nov 01;19(11):7139-7148.
    PMID: 31039868 DOI: 10.1166/jnn.2019.16666
    In this work, a simple, co-precipitation technique was used to prepare un-doped, pure tin oxide (SnO₂). As synthesized SnO₂ nanoparticles were doped with Cu2+ ions. Detailed characterization was carried out to observe the crystalline phase, morphological features and chemical constituents with opto-electrical and magnetic properties of the synthesized nanoparticles (NPs). X-ray diffraction analysis showed the existence of crystalline, tetragonal structure of SnO₂. Both the sample synthesized here showed different crystalline morphology. The band gap energy (Eg) of the synthesized sample was estimated and it was found to decrease from 3.60 to 3.26 eV. The band gap energy reduced due to increase in Cu2+ dopant amount inside the SnO₂ lattice. Optical properties were analyzed using absorption spectra and Photoluminescence (PL) spectra. It was observed that Cu2+ ions incorporated SnO₂ NPs exhibited more degradation efficiencies for Rhodamine B (RhB) dye compared to un-doped sample under UV-Visible irradiation. The dielectric characteristics of un-doped, pure and Cu2+ incorporated SnO₂ nanoparticles were studied at different frequency region under different temperatures. The ac conductivity and impedance analysis of pure and Cu2+ incorporated SnO₂ nanoparticles was also studied. The magnetic properties of the synthesized samples were analysed. Both the sample showed ferromagnetic properties. The research indicated that the Cu2+ ions doping can make the sample a promising candidate for using in the field of optoelectronics, magneto electronics, and microwave devices.
    MeSH terms: Doping in Sports; Electronics; Ions; Microwaves; Rhodamines; Temperature; X-Ray Diffraction; Electric Impedance; Tin Compounds; Nanoparticles; Physical Phenomena
  2. Muthukumaran M, Dhinagaran G, Narayanan V, Raju T, Venkatachalam K, Karthika PC, et al.
    J Nanosci Nanotechnol, 2019 Nov 01;19(11):7215-7220.
    PMID: 31039878 DOI: 10.1166/jnn.2019.16671
    Graphene oxide/Cuprous oxide (GO/Cu₂O) composite is a visible light photocatalyst for the degradation of dyes. A simple and efficient approach for preparing GO/Cu₂O composite adopted in this study involves reducing cuprous oxide precursors in the presence of graphene oxide using an aqueous solution of pulp derived from banana fruit. The GO/Cu₂O composite was characterized by Fourier transform infrared spectroscopy (FT-IR), Diffused reflectance Ultraviolet visible spectroscopy (DRS UV-Vis), Raman spectroscopy and Field Emission Scanning electron microscopy (FE-SEM). Cu₂O particles were distributed randomly on the graphene oxide sheets due to the template effect of GO. The results showed higher photocatalytic activity for the composite (band gap 2.13 eV), for the degradation of the organic dyes (Methylene blue and Rhodamine-B). The enhanced photocatalytic activity is due to effective charge transfer from GO to Cu₂O, and high specific surface area which improves the effective separation of the generated electron-hole pairs. Our present study is inspired by a facile, low cost, green production of (GO/Cu₂O) composite whose photocatalytic activity can be extended to degradation of all other water-born textile dyes.
    MeSH terms: Copper; Coloring Agents; Electrons; Fruit; Graphite; Light; Methylene Blue; Microscopy, Electron, Scanning; Rhodamines; Spectrophotometry, Ultraviolet; Spectrum Analysis, Raman; Textiles; Water; Spectroscopy, Fourier Transform Infrared; Musa
  3. Ng JC, Tan CY, Ong BH, Matsuda A, Basirun WJ, Tan WK, et al.
    J Nanosci Nanotechnol, 2019 Nov 01;19(11):7236-7243.
    PMID: 31039881 DOI: 10.1166/jnn.2019.16717
    Small sized electrocatalysts, which can be obtained by rapid nucleation and high supersaturation are imperative for outstanding methanol oxidation reaction (MOR). Conventional microwave synthesis processes of electrocatalysts include ultrasonication, stirring, pH adjustment, and microwave irradiation of the precursor mixture. Ethylene glycol (EG), which serves as a reductant and solvent was added during the ultrasonication or stirring stage. However, this step and pH adjustment resulted in unintended multi-stage gradual nucleation. In this study, the microwave reduction approach was used to induce rapid nucleation and high supersaturation in order to fabricate small-sized reduced graphene oxide-supported palladium (Pd/rGO) electrocatalysts via the delayed addition of EG, elimination of the pH adjustment step, addition of sodium carbonate (Na₂CO₃), prior microwave irradiation of the EG mixed with Na₂CO₃, and addition of room temperature precursor mixture. Besides its role as a second reducing agent, the addition of Na₂CO₃ was primarily intended to generate an alkaline condition, which is essential for the high-performance of electrocatalysts. Moreover, the microwave irradiation of the EG and Na₂CO₃ mixture generated highly reactive free radicals that facilitate rapid nucleation. Meanwhile, the room temperature precursor mixture increased supersaturation. Results showed improved electrochemically active surface area (78.97 m² g-1, 23.79% larger), MOR (434.49 mA mg-1, 37.96% higher) and stability.
    MeSH terms: Methanol; Carbonates; Free Radicals; Graphite; Hydrogen-Ion Concentration; Microwaves; Oxidation-Reduction; Palladium; Solvents; Temperature; Reducing Agents; Ethylene Glycol
  4. Khoo ACH, Chew GK
    Indian J Nucl Med, 2019 5 2;34(2):162-163.
    PMID: 31040534 DOI: 10.4103/ijnm.IJNM_27_19
    Endometriosis is commonly associated with chronic pelvic pain and its presentation varies between individuals. The only way to confirm the presence of endometriosis is via keyhole or open surgery. In the presence of hematuria, deep endometriotic infiltration needs to be considered. We share an interesting case highlighting the role of 18F-fluorodeoxyglucose positron emission tomography-computed tomography in evaluating a posterior urinary bladder wall lesion and hypodense liver lesions in a middle-aged woman with presenting with frank hematuria in the background of treated cervical intraepithelial neoplasia and adenomyosis.
    MeSH terms: Adult; Urinary Bladder; Uterine Cervical Neoplasms; China/ethnology; Endometriosis; Female; Hematuria; Humans; Liver; Malaysia; Middle Aged; Peritoneal Diseases; Pelvic Pain; Cervical Intraepithelial Neoplasia; Fluorodeoxyglucose F18; Adenomyosis; Positron Emission Tomography Computed Tomography
  5. Nordin ML, Othman AA, Kadir AA, Shaari R, Osman AY, Mohamed M
    Vet World, 2019;12(2):236-242.
    PMID: 31040564 DOI: 10.14202/vetworld.2019.236-242
    Background and Aim: The increasing prevalence of drug resistance eventually leads scientist to discover new drugs that could solve the problem. Since ancient immemorial times, medicinal plants generally known as herbs were widely used in every culture throughout the world. In fact, currently up to 70,000 plant species have been screened for biological activities and about 70% ends up for commercialization. Therefore, this study was aimed to evaluate the potential cytotoxic and antibacterial effect of Syzygium polyanthum leaves which are local Malaysia plants, against 4T1 and MCF-7 mammary carcinoma cells, respectively, and also against bacteria causing mastitis in cows.

    Materials and Methods: The cytotoxic effect of hydromethanolic extract of S. polyanthum against 4T1 and MCF-7 mammary carcinoma cells was evaluated using 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. The cells were treated with the concentration of extracts ranging from 15.63 µg/mL to 1000 µg/ml for 72 h, and the percentage of cell survivability was determined based on minimum concentration that was able to allow at least 50% growth of cancer cells (IC50) after 72 h. The antibacterial activity was tested against common bacteria causing mastitis in cow. The bacteria were isolated from milk samples. The antibacterial activity of the extract was determined by disk diffusion method and susceptibility test based on minimum inhibitory concentration (MIC).

    Results: Staphylococcus aureus, Staphylococcus hyicus, and Staphylococcus intermedius were isolated from the milk samples that positive for mastitis. The MIC values range from 7.12 mm to 13.5 mm. The extract exhibits the widest zone of inhibition (13.5±0.20 mm) at 1000 mg/ml of concentrations. The extract relatively has low cytotoxicity effect against 4T1 and MCF-7 cells with IC50 values ranging from 672.57±59.42 and 126.05±50.89 µg/ml, respectively.

    Conclusion: S. polyanthum exerts weak antibacterial activity and cytotoxic effect to mammary carcinoma cells. The extract does not toxic to cells. However, further study is recommended, especially, this plant should be tested for in vivo.

    MeSH terms: Animals; Anti-Bacterial Agents; Bromides; Cattle; Female; Humans; Malaysia; Mastitis; Microbial Sensitivity Tests; Milk; Plants, Medicinal; Staphylococcal Infections; Staphylococcus aureus; Prevalence; Inhibitory Concentration 50; Syzygium; Staphylococcus hyicus; Staphylococcus intermedius; MCF-7 Cells
  6. Khames A, Khaleel MA, El-Badawy MF, El-Nezhawy AOH
    Int J Nanomedicine, 2019;14:2515-2531.
    PMID: 31040672 DOI: 10.2147/IJN.S190502
    Background: Fungal keratitis (FK) is a serious pathogenic condition usually associated with significant ocular morbidity. Natamycin (NAT) is the first-line and only medication approved by the Food and Drug Administration for the treatment of FK. However, NAT suffers from poor corneal penetration, which limits its efficacy for treating deep keratitis.

    Purpose: The objective of this work was to prepare NAT solid lipid nanoparticles (NAT-SLNs) to achieve sustained drug release and increased corneal penetration.

    Methods: NAT-SLNs were prepared using the emulsification-ultrasonication technique. Box- Behnken experimental design was applied to optimize the effects of independent processing variables (lipid concentration [X1], surfactant concentration [X2], and sonication frequency [X3]) on particle size (R1), zeta potential (ZP; R2), and drug entrapment efficiency (EE%) (R3) as responses. Drug release profile, ex vivo corneal permeation, antifungal susceptibility, and cytotoxicity of the optimized formula were evaluated.

    Results: The optimized formula had a mean particle size of 42 r.nm (radius in nanometers), ZP of 26 mV, and EE% reached ~85%. NAT-SLNs showed an extended drug release profile of 10 hours, with enhanced corneal permeation in which the apparent permeability coefficient (Papp) and steady-state flux (Jss) reached 11.59×10-2 cm h-1 and 3.94 mol h-1, respectively, in comparison with 7.28×10-2 cm h-1 and 2.48 mol h-1 for the unformulated drug, respectively. Antifungal activity was significantly improved, as indicated by increases in the inhibition zone of 8 and 6 mm against Aspergillus fumigatus ATCC 1022 and a Candida albicans clinical isolate, respectively, and minimum inhibitory concentration values that were decreased 2.5-times against both of these pathogenic strains. NAT-SLNs were found to be non-irritating to corneal tissue. NAT-SLNs had a prolonged drug release rate, that improved corneal penetration, and increased antifungal activity without cytotoxic effects on corneal tissues.

    Conclusion: Thus, NAT-SLNs represent a promising ocular delivery system for treatment of deep corneal keratitis.

  7. Reddy G, Gleibs IH
    Front Psychol, 2019;10:792.
    PMID: 31040805 DOI: 10.3389/fpsyg.2019.00792
    Psychological literature on race has discussed in depth how racial identities are dialogically constructed and context dependent. However, racial identity construction is often not compared across different socio-political contexts. By researching racial identity construction in three different multicultural countries, Malaysia, Singapore, and the United Kingdom, we examined how three racial identities, Chinese, Malay, and Indian, are constructed among Malaysians and Singaporeans in this qualitative study comprised of 10 focus group discussions (N = 39). We applied Dialogical Analysis to the data. This paper shows that both racial ingroups and outgroups constructed all three racial identities, with ingroups constructing their identities more heterogeneously compared to outgroups. Participants also engaged with colonial constructions of the three racial identities. The geographical locations, and therefore their perceptual contexts, of the participants differed. Yet, colonial constructions of race endured in contemporary identity construction and were contested in the group settings. We conclude that the socio-political context as understood by the context of colonialism and post-coloniality influenced their racial identity constructions. Participants, regardless of differences in geographical location, used similar colonial constructions of Malay, Chinese, and Indian identities to position themselves as well as Others in their group interactions. These findings show that there is value in conceptualising the context beyond that which individuals are immediately presented with, and that psychologists should consider the inclusion of cultural legacies of colonialism in their conceptualisation of the present context.
    MeSH terms: Humans; Malaysia; Publications; Singapore; Focus Groups; Colonialism; Cultural Diversity; Qualitative Research; Continental Population Groups
  8. Abbott AL, Merican J, Pearce DC, Juric A, Worsnop C, Foster E, et al.
    Front Neurol, 2019;10:322.
    PMID: 31040812 DOI: 10.3389/fneur.2019.00322
    Background and Purpose: Variability in transcranial Doppler (TCD) detection of embolic signals (ES) is important for risk stratification. We tested the effect of time of day on ES associated with 60-99% asymptomatic carotid stenosis. Materials and Methods: Subjects were from the Asymptomatic Carotid Stenosis Embolus Detection (ASED) Study such that half were previously ES-positive and half ES-negative with 6-monthly 60-min TCD monitoring. All underwent bilateral TCD monitoring for two 12-h sessions separated by 24 h. ES detection rates were calculated using 6 and 4-h intervals from midnight and effective TCD monitoring time. Results: Ten subjects (8 male, mean age 79.5 years) were monitored. Over 24 h, 5/10 study arteries with 60-99% asymptomatic carotid stenosis were ES-positive (range 1-28 ES/artery, 56 total ES from 177.9 total effective monitoring hours). The remaining five study arteries and all eight successfully monitored contralateral arteries were ES-negative. Using 6-h intervals the mean ES detection rate peaked at 0600-midday (0.64/h) and was lowest 1800-midnight (0.09/h) with an incidence rate ratio of 7.26 (95% CI 2.52-28.64, P ≤ 0.001). Using 4-h intervals the mean ES detection rate peaked at 0800-midday (0.64/h) and was lowest midnight-0400 (0.12/h) with an incidence rate ratio of 5.51 (95% CI 1.78-22.67, P = 0.001). Conclusions: Embolism associated with asymptomatic carotid stenosis shows circadian variation with highest rates 4-6 h before midday. This corresponds with peak circadian incidence of stroke and other vascular complications. These and ASED Study results show that monitoring frequency, duration, and time of day are important in ES detection.
  9. Anasir MI, Poh CL
    Front Microbiol, 2019;10:738.
    PMID: 31040832 DOI: 10.3389/fmicb.2019.00738
    Although vaccines have proven pivotal against arrays of infectious viral diseases, there are still no effective vaccines against many viruses. New structural insights into the viral envelope, protein conformation, and antigenic epitopes can guide the design of novel vaccines against challenging viruses such as human immunodeficiency virus (HIV), hepatitis C virus, enterovirus A71, and dengue virus. Recent studies demonstrated that applications of this structural information can solve some of the vaccine conundrums. This review focuses on recent advances in structure-based vaccine design, or structural vaccinology, for novel and innovative viral vaccine design.
    MeSH terms: Epitopes; Dengue Virus; Enterovirus Infections; Enterovirus; Humans; Protein Conformation; Viral Vaccines; HIV Infections; Hepacivirus
  10. Lim YK, Keng FS, Phang SM, Sturges WT, Malin G, Abd Rahman N
    PeerJ, 2019;7:e6758.
    PMID: 31041152 DOI: 10.7717/peerj.6758
    Marine algae have been reported as important sources of biogenic volatile halocarbons that are emitted into the atmosphere. These compounds are linked to destruction of the ozone layer, thus contributing to climate change. There may be mutual interactions between the halocarbon emission and the environment. In this study, the effect of irradiance on the emission of halocarbons from selected microalgae was investigated. Using controlled laboratory experiments, three tropical marine microalgae cultures, Synechococcus sp. UMACC 371 (cyanophyte), Parachlorella sp. UMACC 245 (chlorophyte) and Amphora sp. UMACC 370 (diatom) were exposed to irradiance of 0, 40 and 120 µmol photons m-2s-1. Stress in the microalgal cultures was indicated by the photosynthetic performance (Fv/Fm, maximum quantum yield). An increase in halocarbon emissions was observed at 120 µmol photons m-2s-1, together with a decrease in Fv/Fm. This was most evident in the release of CH3I by Amphora sp. Synechococcus sp. was observed to be the most affected by irradiance as shown by the increase in emissions of most halocarbons except for CHBr3 and CHBr2Cl. High positive correlation between Fv/Fm and halocarbon emission rates was observed in Synechococcus sp. for CH2Br2. No clear trends in correlation could be observed for the other halocarbons in the other two microalgal species. This suggests that other mechanisms like mitochondria respiration may contribute to halocarbon production, in addition to photosynthetic performance.
    MeSH terms: Chlorophyta; Atmosphere; Hydrocarbons, Halogenated; Mitochondria; Photosynthesis; Diatoms; Photons; Synechococcus; Climate Change; Microalgae; Stratospheric Ozone
  11. Robins JG, Husson S, Fahroni A, Singleton I, Nowak MG, Fluch G, et al.
    Front Vet Sci, 2019;6:111.
    PMID: 31041315 DOI: 10.3389/fvets.2019.00111
    Designed as a new method to facilitate the reintroduction and post-release monitoring of orangutans and other apes, implanted radio-telemetry (IRT) was developed and first deployed in 2009. Since that time, it has been necessary to collate and review information on its uptake and general efficacy to inform its ongoing development and that of other emerging tracking technologies. We present here technical specifications and the surgical procedure used to implant miniaturized radio transmitters, as well as a formal testing procedure for measuring detectable transmission distances of implanted devices. Feedback from IRT practitioners (veterinarians and field managers) was gathered through questionnaires and is also presented. To date, IRT has been used in at least 250 individual animals (mainly orangutans) from four species of ape in both Asia and Africa. Median surgical and wound healing times were 30 min and 15 days, respectively, with implants needing to be removed on at least 36 separate occasions. Confirmed failures within the first year of operation were 18.1%, while longer distances were reported from positions of higher elevation relative to the focal animal. IRT has been a transformational technology in facilitating the relocation of apes after their release, resulting in much larger amounts of post-release data collection than ever before. It is crucial however, that implant casings are strengthened to prevent the requirement for recapture and removal surgeries, especially for gradually adapting apes. As with all emerging technological solutions, IRT carries with it inherent risk, especially so due to the requirement for subcutaneous implantation. These risks must, however, be balanced with the realities of releasing an animal with no means of relocation, as has historically been, and is still, the case with orangutans and gorillas.
  12. Goh SH, Ismail R, Lau SF, Megat Abdul Rani PA, Mohd Mohidin TB, Daud F, et al.
    PMID: 31035316 DOI: 10.3390/ijerph16091499
    This study determined the potential risk factors that may contribute to seropositivity among dogs and dog handlers from working dog and dog shelter institutions. Data was collected from dogs (n = 266) and dog handlers (n = 161) using a standardised guided questionnaire. Serum obtained from the dogs and dog handlers was tested using the microscopic agglutination test (MAT). A logistic regression analysis was used to predict leptospiral seropositivity of dogs and dog handlers based on potential risk factors. A total of 22.2% of dogs and 21.7% of dog handlers were seropositive. The significant predictors for the dogs' seropositivity were presence of rats (OR = 4.61 (95% CI: 1.05, 20.33), p = 0.043) and shared common area (OR = 5.12 (95% CI: 1.94, 13.46), p = 0.001) within the organisation. Significant predictor for dog handler seropositivity was contact time with the dogs of more than six hours/day (OR = 3.28 (95% CI: 1.28, 8.40), p = 0.013) after controlling for the effect of other risk factors such as small mammal contact, rat infestation at home, flooding at housing area (within three months) and urban locality. The exposure to various disease sources identified poses risk to dogs and dog handlers. Risk could be reduced with adequate application of protection at work while handling dogs and thus limiting contact with these sources and reducing exposure to infection.
    MeSH terms: Animals; Cross-Sectional Studies; Dog Diseases/blood; Dog Diseases/epidemiology*; Dogs; Female; Humans; Leptospirosis/blood; Leptospirosis/epidemiology; Leptospirosis/veterinary*; Malaysia/epidemiology; Male; Risk Factors; Zoonoses/blood; Zoonoses/epidemiology*; Seroepidemiologic Studies; Rats
  13. Yang J, Ching YC, Chuah CH
    Polymers (Basel), 2019 Apr 28;11(5).
    PMID: 31035331 DOI: 10.3390/polym11050751
    Lignocellulosic fibers and lignin are two of the most important natural bioresources in the world. They show tremendous potential to decrease energy utilization/pollution and improve biodegradability by replacing synthetic fibers in bioplastics. The compatibility between the fiber-matrix plays an important part in the properties of the bioplastics. The improvement of lignocellulosic fiber properties by most surface treatments generally removes lignin. Due to the environmental pollution and high cost of cellulose modification, focus has been directed toward the use of lignocellulosic fibers in bioplastics. In addition, lignin-reinforced bioplastics are fabricated with varying success. These applications confirm there is no need to remove lignin from lignocellulosic fibers when preparing the bioplastics from a technical point of view. In this review, characterizations of lignocellulosic fibers and lignin related to their applications in bioplastics are covered. Then, we generalize the developments and problems of lignin-reinforced bioplastics and modification of lignin to improve the interaction of lignin-matrix. As for lignocellulosic fiber-reinforced bioplastics, we place importance on the low compatibility of the lignocellulosic fiber-matrix. The applications of lignin-containing cellulose and lignocellulosic fibers without delignification in the bioplastics are reviewed. A comparison between lignocellulosic fibers and lignin in the bioplastics is given.
  14. Fung FY, Koh YLE, Malhotra R, Ostbye T, Lee PY, Shariff Ghazali S, et al.
    BMC Geriatr, 2019 04 29;19(1):122.
    PMID: 31035928 DOI: 10.1186/s12877-019-1137-8
    BACKGROUND: Sarcopenia is the age-related loss of muscle mass and function, which increases fall risks in older persons. Hyperglycemia relating to Type-2 Diabetes Mellitus (T2DM) is postulated to aggravate sarcopenia. This study aimed to determine the prevalence of sarcopenia among ambulatory community-dwelling older patients, aged 60-89 years, with T2DM in a primary care setting and to identify factors which mitigate sarcopenia.

    METHODS: A total of 387 patients were recruited from a public primary care clinic in Singapore. Data on their socio-demography, clinical and functional status, levels of physical activity (International Physical Activity Questionnaire) and frailty status was collected. The Asian Working Group for Sarcopenia (AWGS) criteria were used to define sarcopenia based on muscle mass, grip strength and gait speed.

    RESULTS: The study population comprised men (53%), Chinese (69%), mean age = 68.3 ± SD5.66 years, lived in public housing (90%), had hypertension (88%) and dyslipidemia (96%). Their mean muscle mass was 6.3 ± SD1.2 kg/m2; mean gait speed was 1.0 ± SD0.2 m/s and mean grip strength was 25.5 ± SD8.1 kg. Overall, 30% had pre-sarcopenia, 24% with sarcopenia and 4% with severe sarcopenia. Age (OR = 1.14; 95%CI = 1.09-1.20;p 

    MeSH terms: Aged; Aged, 80 and over; Diabetes Mellitus, Type 2/diagnosis; Diabetes Mellitus, Type 2/ethnology*; Diabetes Mellitus, Type 2/therapy; Female; Humans; Male; Middle Aged; Primary Health Care/methods*; Singapore/epidemiology; Exercise/physiology; Prevalence; Hand Strength/physiology; Asian Continental Ancestry Group/ethnology*; Sarcopenia/diagnosis; Sarcopenia/ethnology*; Sarcopenia/therapy
  15. Hamilton MG, Mekkawy W, Benzie JAH
    Genet. Sel. Evol., 2019 Apr 29;51(1):17.
    PMID: 31035934 DOI: 10.1186/s12711-019-0454-x
    Catla catla (Hamilton) fertilised spawn was collected from the Halda, Jamuna and Padma rivers in Bangladesh from which approximately 900 individuals were retained as 'candidate founders' of a breeding population. These fish were fin-clipped and genotyped using the DArTseq platform to obtain, 3048 single nucleotide polymorphisms (SNPs) and 4726 silicoDArT markers. Using SNP data, individuals that shared no putative parents were identified using the program COLONY, i.e. 140, 47 and 23 from the Halda, Jamuna and Padma rivers, respectively. Allele frequencies from these individuals were considered as representative of those of the river populations, and genomic relationship matrices were generated. Then, half-sibling and full-sibling relationships between individuals were assigned manually based on the genomic relationship matrices. Many putative half-sibling and full-sibling relationships were found between individuals from the Halda and Jamuna rivers, which suggests that catla sampled from rivers as spawn are not necessarily representative of river populations. This has implications for the interpretation of past population genetics studies, the sampling strategies to be adopted in future studies and the management of broodstock sourced as river spawn in commercial hatcheries. Using data from individuals that shared no putative parents, overall multi-locus pairwise estimates of Wright's fixation index (FST) were low (≤ 0.013) and the optimum number of clusters using unsupervised K-means clustering was equal to 1, which indicates little genetic divergence among the SNPs included in our study within and among river populations.
    MeSH terms: Alleles; Animals; Animal Husbandry; Asia, Southeastern; Breeding/methods; Carps/genetics*; Cyprinidae/genetics; Gene Frequency/genetics; Genetics, Population/methods*; Genotype; Polymorphism, Single Nucleotide/genetics; Genomics; Siblings; Rivers
  16. Ahmed MA, Quan FS
    Malar J, 2019 Apr 29;18(1):150.
    PMID: 31035999 DOI: 10.1186/s12936-019-2782-2
    BACKGROUND: The high proportion of human cases due to the simian malaria parasite Plasmodium knowlesi in Malaysia is a cause of concern, as they can be severe and even fatal. Merozoite surface protein 7 (MSP7) is a multigene family which forms a non-covalent complex with MSP-1 prior to receptor-ligand recognition in Plasmodium falciparum and thus an important antigen for vaccine development. However, no study has been done in any of the ortholog family members in P. knowlesi from clinical samples. This study investigates the level of polymorphism, haplotypes, and natural selection acting at the pkmsp-7D gene in clinical samples from Malaysia.

    METHODS: Thirty-six full-length pkmsp7D gene sequences (along with the reference H-strain: PKNH_1266000) obtained from clinical isolates of Malaysia, which were orthologous to pvmsp7H (PVX_082680) were downloaded from public databases. Population genetic, evolutionary and phylogenetic analyses were performed to determine the level of genetic diversity, polymorphism, recombination and natural selection.

    RESULTS: Analysis of 36 full-length pkmsp7D sequences identified 147 SNPs (91 non-synonymous and 56 synonymous substitutions). Nucleotide diversity across the full-length gene was higher than its ortholog in Plasmodium vivax (msp7H). Region-wise analysis of the gene indicated that the nucleotide diversity at the central region was very high (π = 0.14) compared to the 5' and 3' regions. Most hyper-variable SNPs were detected at the central domain. Multiple test for natural selection indicated the central region was under strong positive natural selection however, the 5' and 3' regions were under negative/purifying selection. Evidence of intragenic recombination were detected at the central region of the gene. Phylogenetic analysis using full-length msp7D genes indicated there was no geographical clustering of parasite population.

    CONCLUSIONS: High genetic diversity with hyper-variable SNPs and strong evidence of positive natural selection at the central region of MSP7D indicated exposure of the region to host immune pressure. Negative selection at the 5' and the 3' regions of MSP7D might be because of functional constraints at the unexposed regions during the merozoite invasion process of P. knowlesi. No evidence of geographical clustering among the clinical isolates from Malaysia indicated uniform selection pressure in all populations. These findings highlight the further evaluation of the regions and functional characterization of the protein as a potential blood stage vaccine candidate for P. knowlesi.

    MeSH terms: Haplotypes; Humans; Malaria/parasitology; Malaysia; Membrane Proteins/genetics*; Phylogeny; Recombination, Genetic; Selection, Genetic*; Genetic Variation*; Protozoan Proteins/genetics*; Plasmodium knowlesi/genetics*; Sequence Analysis, DNA; Polymorphism, Single Nucleotide
  17. Ong AL, Teh CK, Kwong QB, Tangaya P, Appleton DR, Massawe F, et al.
    Sci Rep, 2019 04 29;9(1):6619.
    PMID: 31036825 DOI: 10.1038/s41598-019-42989-y
    Meiotic crossovers in outbred species, such as oil palm (Elaeis guineensis Jacq., 2n = 32) contribute to allelic re-assortment in the genome. Such genetic variation is usually exploited in breeding to combine positive alleles for trait superiority. A good quality reference genome is essential for identifying the genetic factors underlying traits of interest through linkage or association studies. At the moment, an AVROS pisifera genome is publicly available for oil palm. Distribution and frequency of crossovers throughout chromosomes in different origins of oil palm are still unclear. Hence, an ultrahigh-density genomic linkage map of a commercial Deli dura x AVROS pisifera family was constructed using the OP200K SNP array, to evaluate the genetic alignment with the genome assembly. A total of 27,890 linked SNP markers generated a total map length of 1,151.7 cM and an average mapping interval of 0.04 cM. Nineteen linkage groups represented 16 pseudo-chromosomes of oil palm, with 61.7% of the mapped SNPs present in the published genome. Meanwhile, the physical map was also successfully extended from 658 Mb to 969 Mb by assigning unplaced scaffolds to the pseudo-chromosomes. A genic linkage map with major representation of sugar and lipid biosynthesis pathways was subsequently built for future studies on oil related quantitative trait loci (QTL). This study improves the current physical genome of the commercial oil palm, and provides important insights into its recombination landscape, eventually unlocking the full potential genome sequence-enabled biology for oil palm.
    MeSH terms: Alleles; Breeding; Chromosome Mapping; Chromosomes; Industrial Oils; Genetic Linkage; Recombination, Genetic; Polymorphism, Single Nucleotide; Genomics; Arecaceae; Quantitative Trait Loci
  18. Ng WL, Wu W, Zou P, Zhou R
    AoB Plants, 2019 Apr;11(2):plz019.
    PMID: 31037213 DOI: 10.1093/aobpla/plz019
    Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.
  19. Cutiongco-de la Paz EM, Chung BH, Faradz SMH, Thong MK, David-Padilla C, Lai PS, et al.
    Am J Med Genet C Semin Med Genet, 2019 06;181(2):177-186.
    PMID: 31037827 DOI: 10.1002/ajmg.c.31703
    The status of training in clinical genetics and genetic counseling in Asia is at diverse stages of development and maturity. Most of the training programs are in academic training centers where exposure to patients in the clinics or in the hospital is a major component. This setting provides trainees with knowledge and skills to be competent geneticists and genetic counselors in a variety of patient care interactions. Majority of the training programs combine clinical and research training which provide trainees a broad and integrated approach in the diagnosis and management of patients while providing opportunities for research discoveries that can be translated to better patient care. The background on how the training programs in clinical genetics and genetic counseling in Asia evolved to their current status are described. Each of these countries can learn from each other through sharing of best practices and resources.
    MeSH terms: Asia; Patient Care; Genetic Counseling; Hospitals; Humans; Research; Training Support; Counselors
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