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Fulltext SuCComBase: a manually curated repository of plant sulfur-containing compounds

Harun S, Abdullah-Zawawi MR, A-Rahman MRA, Muhammad NAN, Mohamed-Hussein ZA

Database (Oxford), 2019 01 01;2019.
PMID: 30793170 DOI: 10.1093/database/baz021

Plants produce a wide range of secondary metabolites that play important roles in plant defense and immunity, their interaction with the environment and symbiotic associations. Sulfur-containing compounds (SCCs) are a group of important secondary metabolites produced in members of the Brassicales order. SCCs constitute various groups of phytochemicals, but not much is known about them. Findings from previous studies on SCCs were scattered in published literatures, hence SuCComBase was developed to store all molecular information related to the biosynthesis of SCCs. Information that includes genes, proteins and compounds that are involved in the SCC biosynthetic pathway was manually identified from databases and published scientific literatures. Sets of co-expression data was analyzed to search for other possible (previously unknown) genes that might be involved in the biosynthesis of SCC. These genes were named as potential SCC-related encoding genes. A total of 147 known and 92 putative Arabidopsis thaliana SCC-related genes from literatures were used to identify other potential SCC-related encoding genes. We identified 778 potential SCC-related encoding genes, 4026 homologs to the SCC-related encoding genes and 116 SCCs as shown on SuCComBase homepage. Data entries are searchable from the Main page, Search, Browse and Datasets tabs. Users can easily download all data stored in SuCComBase. All publications related to SCCs are also indexed in SuCComBase, which is currently the first and only database dedicated to plant SCCs. SuCComBase aims to become a manually curated and au fait knowledge-based repository for plant SCCs.
Fulltext Biofilm Signaling, Composition and Regulation in Burkholderia pseudomallei

Nyanasegran PK, Nathan S, Firdaus-Raih M, Muhammad NAN, Ng CL

J Microbiol Biotechnol, 2023 Jan 28;33(1):15-27.
PMID: 36451302 DOI: 10.4014/jmb.2207.07032

The incidence of melioidosis cases caused by the gram-negative pathogen Burkholderia pseudomallei (BP) is seeing an increasing trend that has spread beyond its previously known endemic regions. Biofilms produced by BP have been associated with antimicrobial therapy limitation and relapse melioidosis, thus making it urgently necessary to understand the mechanisms of biofilm formation and their role in BP biology. Microbial cells aggregate and enclose within a self-produced matrix of extracellular polymeric substances (EPSs) to form biofilm. The transition mechanism of bacterial cells from planktonic state to initiate biofilm formation, which involves the formation of surface attachment microcolonies and the maturation of the biofilm matrix, is a dynamic and complex process. Despite the emerging findings on the biofilm formation process, systemic knowledge on the molecular mechanisms of biofilm formation in BP remains fractured. This review provides insights into the signaling systems, matrix composition, and the biosynthesis regulation of EPSs (exopolysaccharide, eDNA and proteins) that facilitate the formation of biofilms in order to present an overview of our current knowledge and the questions that remain regarding BP biofilms.
Insights into bacterial community metatranscriptome and metabolome in river water influenced by palm oil mill effluent final discharge

Sharuddin SS, Ramli N, Yusoff MZM, Muhammad NAN, Ho LS, Maeda T

J Appl Microbiol, 2023 Oct 04;134(10).
PMID: 37757470 DOI: 10.1093/jambio/lxad219

AIMS: This study aimed to investigate the effect of palm oil mill effluent (POME) final discharge on the active bacterial composition, gene expression, and metabolite profiles in the receiving rivers to establish a foundation for identifying potential biomarkers for monitoring POME pollution in rivers.
METHODS AND RESULTS: The POME final discharge, upstream (unpolluted by POME), and downstream (effluent receiving point) parts of the rivers from two sites were physicochemically characterized. The taxonomic and gene profiles were then evaluated using de novo metatranscriptomics, while the metabolites were detected using qualitative metabolomics. A similar bacterial community structure in the POME final discharge samples from both sites was recorded, but their composition varied. Redundancy analysis showed that several families, particularly Comamonadaceae and Burkholderiaceae [Pr(>F) = 0.028], were positively correlated with biochemical oxygen demand (BOD5) and chemical oxygen demand (COD). The results also showed significant enrichment of genes regulating various metabolisms in the POME-receiving rivers, with methane, carbon fixation pathway, and amino acids among the predominant metabolisms identified (FDR 4, and PPDE > 0.95). This was further validated through qualitative metabolomics, whereby amino acids were detected as the predominant metabolites.
CONCLUSIONS: The results suggest that genes regulating amino acid metabolism have significant potential for developing effective biomonitoring and bioremediation strategies in river water influenced by POME final discharge, fostering a sustainable palm oil industry.
Fulltext Seamless and orthogonal expression of genetic parts in polyhydroxyalkanoate (PHA)-producing bacterial chassis for plastic bio-upcycling applications

Minggu MM, Naseron NAH, Shaberi HSA, Muhammad NAN, Baharum SN, Ramzi AB

MethodsX, 2023 Dec;11:102434.
PMID: 37846354 DOI: 10.1016/j.mex.2023.102434

Polyhydroxyalkanoate (PHA)-producing bacteria represent a powerful synthetic biology chassis for waste bioconversion and bio-upcycling where PHAs can be produced as the final products. In this study, we present a seamless plasmid construction for orthogonal expression of recombinant PET hydrolase (PETase) in model PHA-producing bacteria P. putida and C. necator. To this end, this study described seamless cloning and expression methods utilizing SureVector (SV) system for generating pSV-Ortho-PHA (pSVOP) expression platform in bioengineered P. putida and C. necator. Genetic parts specifically Trc promoter, pBBR1 origin of replication, anchoring proteins and signal sequences were utilized for the transformation of pSVOP-based plasmid in electrocompetent cells and orthogonal expression of PETase in both P. putida and C. necator. Validation steps in confirming functional expression of PETase activity in corresponding PETase-expressing strains were also described to demonstrate seamless and detailed methods in establishing bioengineered P. putida and C. necator as whole-cell biocatalysts tailored for plastic bio-upcycling.•Seamless plasmid construction for orthogonal expression in PHA-producing bacteria.•Step-by-step guide for high-efficiency generation of electrotransformants of P. putida and C. necator.•Adaptable methods for rapid strain development (Design, Build, Test and Learn) for whole-cell biocatalysis.
Fulltext Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom

Abdullah-Zawawi MR, Govender N, Harun S, Muhammad NAN, Zainal Z, Mohamed-Hussein ZA

Plants (Basel), 2022 Oct 05;11(19).
PMID: 36235479 DOI: 10.3390/plants11192614

In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
Fulltext Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey

Akbar MA, Yusof NYM, Sahrani FK, Usup G, Ahmad A, Baharum SN, et al.

Biology (Basel), 2021 Aug 25;10(9).
PMID: 34571703 DOI: 10.3390/biology10090826

The toxin-producing dinoflagellate Alexandrium minutum is responsible for the outbreaks of harmful algae bloom (HABs). It is a widely distributed species and is responsible for producing paralytic shellfish poisoning toxins. However, the information associated with the environmental adaptation pathway and toxin biosynthesis in this species is still lacking. Therefore, this study focuses on the functional characterization of A. minutum unigenes obtained from transcriptome sequencing using the Illumina Hiseq 4000 sequencing platform. A total of 58,802 (47.05%) unigenes were successfully annotated using public databases such as NCBI-Nr, UniprotKB, EggNOG, KEGG, InterPRO and Gene Ontology (GO). This study has successfully identified key features that enable A. minutum to adapt to the marine environment, including several carbon metabolic pathways, assimilation of various sources of nitrogen and phosphorus. A. minutum was found to encode homologues for several proteins involved in saxitoxin biosynthesis, including the first three proteins in the pathway of saxitoxin biosynthesis, namely sxtA, sxtG and sxtB. The comprehensive transcriptome analysis presented in this study represents a valuable resource for understanding the dinoflagellates molecular metabolic model regarding nutrient acquisition and biosynthesis of saxitoxin.
Randomized clinical trial comparing helmet continuous positive airway pressure (hCPAP) to facemask continuous positive airway pressure (fCPAP) for the treatment of acute respiratory failure in the emergency department

Adi O, Via G, Salleh SH, Chuan TW, Rahman JA, Muhammad NAN, et al.

Am J Emerg Med, 2021 Nov;49:385-392.
PMID: 34271286 DOI: 10.1016/j.ajem.2021.06.031

STUDY OBJECTIVE: To determine whether non-invasive ventilation (NIV) delivered by helmet continuous positive airway pressure (hCPAP) is non-inferior to facemask continuous positive airway pressure (fCPAP) in patients with acute respiratory failure in the emergency department (ED).
METHODS: Non-inferiority randomized, clinical trial involving patients presenting with acute respiratory failure conducted in the ED of a local hospital. Participants were randomly allocated to receive either hCPAP or fCPAP as per the trial protocol. The primary endpoint was respiratory rate reduction. Secondary endpoints included discomfort, improvement in Dyspnea and Likert scales, heart rate reduction, arterial blood oxygenation, partial pressure of carbon dioxide (PaCO2), dryness of mucosa and intubation rate.
RESULTS: 224 patients were included and randomized (113 patients to hCPAP, 111 to fCPAP). Both techniques reduced respiratory rate (hCPAP: from 33.56 ± 3.07 to 25.43 ± 3.11 bpm and fCPAP: from 33.46 ± 3.35 to 27.01 ± 3.19 bpm), heart rate (hCPAP: from 114.76 ± 15.5 to 96.17 ± 16.50 bpm and fCPAP: from 115.07 ± 14.13 to 101.19 ± 16.92 bpm), and improved dyspnea measured by both the Visual Analogue Scale (hCPAP: from 16.36 ± 12.13 to 83.72 ± 12.91 and fCPAP: from 16.01 ± 11.76 to 76.62 ± 13.91) and the Likert scale. Both CPAP techniques improved arterial oxygenation (PaO2 from 67.72 ± 8.06 mmHg to 166.38 ± 30.17 mmHg in hCPAP and 68.99 ± 7.68 mmHg to 184.49 ± 36.38 mmHg in fCPAP) and the PaO2:FiO2 (Partial pressure of arterial oxygen: Fraction of inspired oxygen) ratio from 113.6 ± 13.4 to 273.4 ± 49.5 in hCPAP and 115.0 ± 12.9 to 307.7 ± 60.9 in fCPAP. The intubation rate was lower with hCPAP (4.4% for hCPAP versus 18% for fCPAP, absolute difference -13.6%, p = 0.003). Discomfort and dryness of mucosa were also lower with hCPAP.
CONCLUSION: In patients presenting to the ED with acute cardiogenic pulmonary edema or decompensated COPD, hCPAP was non-inferior to fCPAP and resulted in greater comfort levels and lower intubation rate.