Displaying all 3 publications

Abstract:
Sort:
  1. Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica
    Ong SN, Tan BC, Hanada K, Teo CH
    Gene, 2023 Aug 20;878:147579.
    PMID: 37336274 DOI: 10.1016/j.gene.2023.147579
    Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.
  2. Validation of the Subjective Global Nutrition Assessment (SGNA) and Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP) to Identify Malnutrition in Hospitalized Malaysian Children
    Ong SH, Chee WSS, Lapchmanan LM, Ong SN, Lua ZC, Yeo JX
    J Trop Pediatr, 2019 02 01;65(1):39-45.
    PMID: 29514329 DOI: 10.1093/tropej/fmy009
    Background: Early detection of malnutrition in hospitalized children helps reduce length of hospital stay and morbidity. A validated nutrition tool is essential to correctly identify children at risk of malnutrition or who are already malnourished. This study compared the use of the Subjective Global Nutrition Assessment (SGNA, nutrition assessment tool) and Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP, nutrition screening tool) with objective nutritional parameters to identify malnutrition in hospitalized children.

    Methods: A cross-sectional study was carried out in two general paediatric wards in a public hospital. SGNA and STAMP were performed on 82 children (52 boys and 30 girls) of age 1-7 years. The scores from both methods were compared against Academy of Nutrition and Dietetics/American Society of Parental and Enteral Nutrition Consensus Statement for identification of paediatric malnutrition. The objective measurements include anthropometry (weight, height and mid-arm circumference), dietary intake and biochemical markers (C-reactive protein, total lymphocytes and serum albumin). Kappa agreement between methods, sensitivity, specificity and cross-classification were computed.

    Results: SGNA and STAMP identified 45% and 79% of the children to be at risk of malnutrition, respectively. Using a compendium of objective parameters, 46% of the children were confirmed to be malnourished. The agreement between SGNA and objective measurements (k = 0.337) was stronger than between STAMP and objective measurements (k = 0.052) in evaluating the nutritional status of hospitalized children. SGNA also has a 4-fold higher specificity (70.45%) than STAMP (18.18%) in detecting children who are malnourished.

    Conclusion: SGNA is a valid nutrition assessment tool in diagnosing malnutrition status among hospitalized children in Malaysia. The discrepancy in specificity values between the two methods explains the distinguished roles between SGNA and STAMP. The use of STAMP will have to be followed up with a more valid tool such as SGNA to verify the actual nutrition status of the paediatric population.

  3. Effects of alcohol concentration and temperature on the dynamics and stability of mutant Staphylococcal lipase
    Ong SN, Kamarudin NHA, Shariff FM, Noor NDM, Ali MSM, Rahman RNZRA
    J Biomol Struct Dyn, 2023 Nov 15.
    PMID: 37968883 DOI: 10.1080/07391102.2023.2282177
    The stability and activity of lipase in organic media are important parameters in determining how quickly biocatalysis proceeds. This study aimed to examine the effects of two commonly used alcohols in industrial applications, methanol (MtOH) and ethanol (EtOH) on the conformational stability and catalytic activity of G210C lipase, a laboratory-evolved mutant of Staphylococcus epidermidis AT2 lipase. Simulation studies were performed using an open-form predicted structure under 30, 40 and 50% of MtOH and EtOH at 25 °C and 45 °C. The overall enzyme structure becomes more flexible with increasing concentration of MtOH and exhibited the highest flexibility in 40% EtOH. In EtOH, the movement of the lid was found to be temperature-dependent with a noticeable shift in the lid position at 45 °C. Lid opening was evidenced at 50% of MtOH and EtOH which was supported by the increase in SASA of hydrophobic residues of the lid and catalytic triad. The active site remained mostly intact. An open-closed lid transition was observed when the structure was re-simulated in water. Experimental evaluation of the lipase stability showed that the half-life reduced when the enzyme was treated with 40% (v/v) and 50% (v/v) of EtOH and MtOH respectively. The finding implies that a high concentration of alcohol and elevated temperature can induce the lid opening of lipase which could be essential for the activation of the enzyme, provided that the catalytic performance in the active site is not compromised.Communicated by Ramaswamy H. Sarma.
Related Terms
    Try searching for something
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links