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Quantification and characterisation of Trichoderma spp. from different ecosystems

Sariah M, Choo CW, Zakaria H, Norihan MS

Mycopathologia, 2005 Jan;159(1):113-7.
PMID: 15750742

Basal stem rot of oil palm caused by Ganoderma boninense is of major economic importance. Observations of the low incidence of disease due to Ganoderma species in natural stands, suggest that the disease is kept under control by some biological means. Trichoderma spp. are saprophytic fungi with high antagonistic activities against soil-borne pathogens. However, their abundance and distribution are soil and crop specific. Trichoderma species have been found to be concentrated in the A1 (0-30 cm) and Be soil horizons (30-60 cm), although the abundance of Trichoderma was not significantly different between the oil palm and non-oil palm ecosystems. Characterisation of Trichoderma isolates based on cultural, morphological and DNA polymorphism showed that T. harzianum, T. virens, T. koningii and T. longibrachiatum made up 72, 14, 10 and 4% of the total Trichoderma isolates isolated. As Trichoderma species are present in the oil palm ecosystem, but at lower numbers and in locations different from those desired, soil augmentation with antagonistic Trichoderma spp. can be developed as a strategy towards integrated management of basal stem rot of oil palm.
Molecular alterations of Ras-Raf-mitogen-activated protein kinase and phosphatidylinositol 3-kinase-Akt signaling pathways in colorectal cancers from a tertiary hospital at Kuala Lumpur, Malaysia

Yip WK, Choo CW, Leong VC, Leong PP, Jabar MF, Seow HF

APMIS, 2013 Oct;121(10):954-66.
PMID: 23992303 DOI: 10.1111/apm.12152

Molecular alterations in KRAS, BRAF, PIK3CA, and PTEN have been implicated in designing targeted therapy for colorectal cancer (CRC). The present study aimed to determine the status of these molecular alterations in Malaysian CRCs as such data are not available in the literature. We investigated the mutations of KRAS, BRAF, and PTEN, the gene amplification of PIK3CA, and the protein expression of PTEN and phosphatidylinositol 3-kinase (PI3K) catalytic subunit (p110α) by direct DNA sequencing, quantitative real-time PCR, and immunohistochemistry, respectively, in 49 CRC samples. The frequency of KRAS (codons 12, 13, and 61), BRAF (V600E), and PTEN mutations, and PIK3CA amplification was 25.0% (11/44), 2.3% (1/43), 0.0% (0/43), and 76.7% (33/43), respectively. Immunohistochemical staining demonstrated loss of PTEN protein in 54.5% (24/44) of CRCs and no significant difference in PI3K p110α expression between CRCs and the adjacent normal colonic mucosa (p = 0.380). PIK3CA amplification was not associated with PI3K p110α expression level, but associated with male cases (100% of male cases vs 56% of female cases harbored amplified PIK3CA, p = 0.002). PI3K p110α expression was significantly higher (p = 0.041) in poorly/moderately differentiated carcinoma compared with well-differentiated carcinoma. KRAS mutation, PIK3CA amplification, PTEN loss, and PI3K p110α expression did not correlate with Akt phosphorylation or Ki-67 expression. KRAS mutation, PIK3CA amplification, and PTEN loss were not mutually exclusive. This is the first report on CRC in Malaysia showing comparable frequency of KRAS mutation and PTEN loss, lower BRAF mutation rate, higher PIK3CA amplification frequency, and rare PTEN mutation, as compared with published reports.
Evaluation of air quality in Sunway City, Selangor, Malaysia from a mobile monitoring campaign using air pollution micro-sensors

Lee CC, Tran MV, Choo CW, Tan CP, Chiew YS

Environ Pollut, 2020 Oct;265(Pt A):115058.
PMID: 32806396 DOI: 10.1016/j.envpol.2020.115058

Due to the increase of the human population and the rapid industrial growth in the past few decades, air quality monitoring is essential to assess the pollutant levels of an area. However, monitoring air quality in a high-density area like Sunway City, Selangor, Malaysia is challenging due to the limitation of the local monitoring network. To establish a comprehensive data for air pollution in Sunway City, a mobile monitoring campaign was employed around the city area with a duration of approximately 6 months, from September 2018 to March 2019. Measurements of air pollutants such as carbon dioxide (CO2) and nitrogen dioxide (NO2) were performed by using mobile air pollution sensors facilitated with a GPS device. In order to acquire a more in-depth understanding on traffic-related air pollution, the measurement period was divided into two different time blocks, which were morning hours (8 a.m.-12 p.m.) and afternoon hours (3 p.m.-7 p.m.). The data set was analysed by splitting Sunway City into different zones and routes to differentiate the conditions of each region. Meteorological variables such as ambient temperature, relative humidity, and wind speed were studied in line with the pollutant concentrations. The air quality in Sunway City was then compared with various air quality standards such as Malaysian Air Quality Standards and World Health Organisation (WHO) guidelines to understand the risk of exposure to air pollution by the residence in Sunway City.
ADAMTSL5 and CDH11: putative epigenetic markers for therapeutic resistance in acute lymphoblastic leukemia

Abdullah M, Choo CW, Alias H, Abdul Rahman EJ, Mohd Ibrahim H, Jamal R, et al.

Hematology, 2017 Aug;22(7):386-391.
PMID: 28292214 DOI: 10.1080/10245332.2017.1299417

BACKGROUND AND OBJECTIVES: DNA hypermethylation has been linked to poor treatment outcome in childhood acute lymphoblastic leukemia (ALL). Genes differentially methylated in the chemoresponsive pre-B-ALL compared to chemoresistant pre-B-ALL cases provide potential prognostic markers.
METHODS: DNA methylation profiles of five B-ALL childhood patients who achieved morphological complete remission (chemoresponsive) and five B-ALL patients who did not (chemoresistant) after induction treatments as well as four normal controls were compared on 27 000 CpG sites microarray chips. Subsequently, methylation-specific polymerase chain reaction (MSP) on selected hypermethylated genes was conducted on an additional 37 chemoresponsive and 9 chemoresistant B-ALL samples and 2 normal controls.
RESULTS: Both methods were found to be highly correlated. Unsupervised principal component analysis showed that the chemotherapy-responsive and -resistant B-ALL patients could be segregated from one another. Selection of segregated genes at high stringency identified two potential genes (CDH11 and ADAMTSL5). MSP analysis on the larger cohort of samples (42 chemoresponsive, 14 chemoresistant B-ALL samples and 6 normal controls) revealed significantly higher rates of hypermethylation in chemoresistant samples for ADAMTSL5 (93 vs. 38%; p = 0.0001) and CDH11 (79% vs. 40%, p
Fulltext Effect of Dabigatran on Clotting Time in the Clotpro Ecarin Clotting Assay: A Prospective, Single-Arm, Open-Label Study

Fong AYY, Tiong LL, Tan SSN, Geruka D, Apil GG, Choo CW, et al.

Clin Appl Thromb Hemost, 2020 12 8;26:1076029620972473.
PMID: 33284050 DOI: 10.1177/1076029620972473

Routine coagulation tests do not enable rapid, accurate determination of direct oral anticoagulant (DOAC) therapy. The ecarin clotting assay (ECA), performed on the ClotPro viscoelastic testing device, may enable sensitive and specific detection of dabigatran. We assessed the association between trough plasma dabigatran concentration and clotting time (CT) in the ClotPro ECA, in patients with non-valvular atrial fibrillation (NVAF). Each patient provided a single venous blood sample, ∼1 hour before dabigatran dosing. The study included 118 patients, of whom 64 were receiving dabigatran 110 mg twice daily and 54 were receiving 150 mg twice daily. ECA CT was moderately correlated with trough plasma dabigatran concentration (r = 0.80, p < 0.001). Slight trends toward increased plasma dabigatran concentration and prolonged ECA CT were apparent with 150 mg versus the 110 mg dose (differences not statistically significant). Individuals with creatinine clearance below 50 mL/minute had significantly higher plasma dabigatran concentrations and significantly prolonged ECA CT versus those with creatinine clearance ≥50 mL/minute. In conclusion, this preliminary study has demonstrated that CT in the ClotPro ECA reflects the plasma concentration of dabigatran in patients with NVAF. The ECA could potentially be used to assess the impact of dabigatran on a patient's coagulation status.