Systemic biology of Geobacillus thermocatenulatus upon thermal stress induced by high temperature / Mohd Nur Fakhruzzaman Noorizhab

Thermophile is a group of microorganisms that are capable of growing at high temperature and the ability that allowed them to do so is termed as thermophily. Geobacilli is an example of thermophile which predominately lives in soils and hot springs. It is a well-known source of thermostable enzymes but very little is understood so far in term of the mechanisms that regulate or produce these enzymes. And there may be more hidden biological features of Geobacillus that contribute to better bioresources. This project aimed to investigate the genomic structures of Geobacillus thermocatenulatus A8 and the biological features associated with living in high temperatures. G. thermocatenulatus A8 was sequenced and gene sequences was annotated to biological properties like DNA repair genomics islands (GIs) and CRISPR repeats, preferences for hydrophobic and certain amino acids; and overpresentation of genetic features that are shared with other thermophilic bacilli were investigated. To investigate its thermophily trait, the bacteria were grown in two different temperatures (60 and 70°C) and the differential protein and metabolome profiles expressed were studied using SDS-PAGE and LCMS-QTOF. Through genomic analysis, the bacterial capabilities in producing protease and AMP were determined and the phenotypes were demonstrated on culture plates. Proteome profiles of G. thermocatenulatus A8 grown at optimum growth temperature (OGT) and under thermal stress were compared and different set of proteins were expressed from the bacteria to maintain regular cellular functions. The proteins which were expressed under thermal stress were found to pertubate the lipids and energy metabolisms of thermophile and signalling pathways for motility, membrane transport and amino acid tRNA. The metabolomics study identified 19 differentially expressed compounds which were involved in 5 pathways that were classified into lipids, energy, amino acid and secondary metabolite biosynthesis pathways. The biological properties of G. thermocatenulatus identified in this study highlighted its potential application as source of AMP in addition to other enzymes that were produced. Combination of omics platforms are useful to provide insights on bacteria characteristic to discover untapped biological resources

Signatory metabolomics biomarkers of stress, anxiety, and depression: a proof of concept for precision health among university students: A cross-sectional study

Purpose The highly competitive nature of tertiary education and the pressure to perform academically have increased psychological morbidity like emotional distress. Untargeted metabolomics was used to analyze serum samples of university students for biomarkers and perturbated metabolism due to stress, anxiety, and depression (SAD). Methods Depression, Anxiety, Stress Scale 21 (DASS-21) was used to assess the severity of SAD in university students. The metabolite fingerprint of each subject was obtained using liquid chromatography-mass spectrometry quadrupole time-of-flight (LC/MS QTOF). The signature metabolites for each trait were determined by projections to latent structures discriminant analysis (PLS-DA) with variable importance for the projection (VIP) score > 1.0 (P<0.05) and subjected to analysis using the area under the receiver operating characteristic curve (AUROC). Potential biomarkers with an area under the curve (AUC) value exceeding 0.65 were identified. Results Various groups of glycerophospholipids were upregulated in the studied traits. On the other hand, metabolites such as glycocholic acid was upregulated in depression, while hypoxanthine was upregulated in anxiety, and PE-Cer(d14:1(4E)/22:1(13Z)) was upregulated in stress. Conclusion To our knowledge, this is the first study to assess the relationship of the differentially expressed metabolites in university students of different categories of SAD using the DASS-21 screening tool in Malaysia as we move forward with precision health

Relative proteome quantification of alpha, beta, gamma and delta globin chains in early eluting peaks of Bio-Rad variant II® CE-HPLC of hemoglobin from healthy and beta-thalassemia subjects in Malaysia

This is the first report of QQQ-mass spectrometric identification and quantification of the Hb subunits, alpha, beta, delta and gamma globin peptides, derived from enzymatic-digestion of proteins in the early unknown peaks of the Bio-Rad cation-exchange chromatography of haemoglobin. The objectives were to assess the relationship of the quantity of the free alpha, beta, delta and gamma globin chains with the phenotypic diversity of beta-thalassaemias (β-thal). The results demonstrate that the pools of free globin chains in red blood cells were correlating with the severity of the disease in patients with different phenotypes of β-thal. The mechanism and the regulation of synthesis of free globin chains pool in a normal individual and in patients with different β-thal phenotypes could arise from several mechanisms which will require further investigation. The role of the free globin pool in patients with β-thal for development of novel therapeutic approaches based on these potential targets requires further investigation. Pertinent biomarkers improves the diagnosis of the β-thal, especially in low-income countries where they are most common and allows more effective therapeutic intervention leading to more successful therapeutic outcome. Keywords: Anaemia, Thalassemia, Mass spectrometry, Globin chain, Quantification, HPLC, Unknown peak

SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave

Objectives This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program. Methods COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle threshold values <30 were obtained throughout Malaysia. Sequencing of SARS-CoV-2 complete genomes was performed using Illumina, Oxford Nanopore, or Ion Torrent platforms. A total of 6163 SARS-CoV-2 complete genome sequences were generated over the surveillance period. All sequences were submitted to the Global Initiative on Sharing All Influenza Data database. Results From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern, including the original B.1.617.2 lineage and descendant AY lineages. The B.1.617.2 lineage was identified as the early dominant circulating strain throughout the country but over time, was displaced by AY.59 and AY.79 lineages in Peninsular (west) Malaysia, and the AY.23 lineage in east Malaysia. In December 2021, pilgrims returning from Saudi Arabia facilitated the introduction and spread of the BA.1 lineage (Omicron variant of concern) in the country. Conclusion The changing trends of circulating SARS-CoV-2 lineages were identified, with differences observed between west and east Malaysia. This initiative highlighted the importance of leveraging research expertise in the country to facilitate pandemic response and preparedness

SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave

Objectives: This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program. Methods: COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle threshold values <30 were obtained throughout Malaysia. Sequencing of SARS-CoV-2 complete genomes was performed using Illumina, Oxford Nanopore, or Ion Torrent platforms. A total of 6163 SARS-CoV-2 complete genome sequences were generated over the surveillance period. All sequences were submitted to the Global Initiative on Sharing All Influenza Data database. Results: From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern, including the original B.1.617.2 lineage and descendant AY lineages. The B.1.617.2 lineage was identified as the early dominant circulating strain throughout the country but over time, was displaced by AY.59 and AY.79 lineages in Peninsular (west) Malaysia, and the AY.23 lineage in east Malaysia. In December 2021, pilgrims returning from Saudi Arabia facilitated the introduction and spread of the BA.1 lineage (Omicron variant of concern) in the country. Conclusion: The changing trends of circulating SARS-CoV-2 lineages were identified, with differences observed between west and east Malaysia. This initiative highlighted the importance of leveraging research expertise in the country to facilitate pandemic response and preparedness