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An antibody binding-based fluorescent assay for the rapid quantification of globotriaosylceramide levels in human Fabry cells

Ng AWR, Narayanan K

Anal Biochem, 2021 09 01;628:114287.
PMID: 34119486 DOI: 10.1016/j.ab.2021.114287

Fabry disease is caused by reduced α-GAL A activity and accumulation of globotriaosylceramide (Gb3). Here, we describe a microplate Gb3 assay using fluorophore-tagged antibody and crude cellular lipid extracts. The assay is able to detect higher Gb3 concentrations in human Fabry cells compared to non-diseased cells. This result was verified by immunofluorescence staining that revealed large amounts of Gb3 deposits in Fabry cell lines, demonstrating the accuracy of this method. This assay may provide the basis for detecting Fabry disease by quantifying Gb3 deposits from human biological samples, for example, from urine and blood.
Visualization of Bacteria-Mediated Gene Delivery Using High-Resolution Electron and Confocal Microscopy

Osahor AN, Ng AWR, Narayanan K

Methods Mol Biol, 2021;2211:29-40.
PMID: 33336268 DOI: 10.1007/978-1-0716-0943-9_3

Visual analysis of the gene delivery process when using invasive bacteria as a vector has been conventionally performed using standard light and fluorescence microscopy. These microscopes can provide basic information on the invasiveness of the bacterial vector including the ability of the vector to successfully adhere to the cell membrane. Standard microscopy techniques however fall short when finer details including membrane attachment as well as internalization into the cytoplasm are desired. High-resolution visual analysis of bacteria-mediated gene delivery can allow accurate measurement of the adherence and internalization capabilities of engineered vectors. Here, we describe the use of scanning electron microscopy (SEM) to directly quantify vectors when they are external to the cell wall, and confocal microscopy to evaluate the vectors when they have internalized into the cytoplasm. By performing the invasion procedure on microscope coverslips, cells can be easily prepared for analysis using electron or confocal microscopes. Imaging the invasion complexes in high resolution can provide important insights into the behavior of bacterial vectors including E. coli, Listeria, and Salmonella when invading their target cells to deliver DNA and other molecules.
Fulltext Partial purification and characterization of polyphenol oxidase from Chinese parsley (Coriandrum sativum)

Lin H, Ng AWR, Wong CW

Food Sci Biotechnol, 2016;25(Suppl 1):91-96.
PMID: 30263491 DOI: 10.1007/s10068-016-0103-x

Purification and characterization of polyphenol oxidase (PPO) from Chinese parsley (Coriandrum sativum) were achieved. Crude PPO exhibited an enzyme activity of 1,952.24 EU/mL. PPO was partially purified up to 6.52x with a 10.89% yield using gel filtration chromatography. Maximal PPO activity was found at 35°C, pH 8.0 for 4-methylcatechol and at 40°C, pH 7.0 for catechol. PPO showed a higher affinity towards 4-methylcatechol, but a higher thermal stability when reacting with catechol. LCysteine was a better inhibitor than citric acid for reducing PPO activity at concentrations of 1 and 3mM in the presence of either substrate. Two 46 kDa isoenzymes were identified using SDS-PAGE. Isolation and characterization of Chinese parsley serves as a guideline for prediction of enzyme behavior leading to effective prevention of enzymatic browning during processing and storage, including inhibition and inactivation of PPO.
A polyol-stevia blended sugar replacer exhibits low glycemic response among human subjects

Ng AWR, Loh KK, Gupta N, Narayanan K

Clin Nutr ESPEN, 2019 10;33:39-41.
PMID: 31451273 DOI: 10.1016/j.clnesp.2019.07.014

BACKGROUND & AIMS: Consumption of sugars in food and beverages has increased at an alarming rate. While excessive daily sugar intake has been well-associated as the onset of medical complications, additional sugars are still used in manufactured food products just to satisfy the consumers' needs. Hence, there is a need to develop sugar replacers that have low glycemic response without compromising the organoleptic characteristics of food products. This study aimed to determine if SUITENA™, a novel sweetener containing erythritol, xylitol, and Stevia, has low glycemic response upon consumption by human subjects.
METHODS: Six human subjects were randomly chosen and were healthy at the point of experimentation. Capillary blood was collected via finger-prick method to monitor the glycemic response of every individual for 90 min after ingestion of sugar solution.
RESULTS: It was found that the mean area under the curve (AUC) of the dextrose standard was 11.8-fold higher (p
Fulltext Customizable BAC-based DNA markers for pulsed-field gel electrophoresis

Wong YC, Ng AWR, Osahor A, Narayanan K

Anal Biochem, 2024 Oct;693:115596.
PMID: 38936495 DOI: 10.1016/j.ab.2024.115596

DNA markers are used as a size reference and sample loading control during gel electrophoresis. Most markers are designed for conventional gel electrophoresis to separate DNA smaller than 20 kb. For larger molecules, pulsed-field gel electrophoresis (PFGE) marker is required. Limited PFGE markers are available because large DNA are prone to nicking and degradation, causing smeary bands. Here, we developed a robust marker based on bacterial artificial chromosomes (BACs) with bands up to 184 kb. This marker could consistently confer intense and distinct bands for accurate gel analysis in molecular biology studies, laboratory validations or clinical diagnosis.
Phage N15-Based Vectors for Gene Cloning and Expression in Bacteria and Mammalian Cells

Wong YC, Ng AWR, Chen Q, Liew PS, Lee CW, Sim EUH, et al.

ACS Synth Biol, 2023 Apr 21;12(4):909-921.
PMID: 37026178 DOI: 10.1021/acssynbio.2c00580

Bacteriophage N15 is the first virus known to deliver linear prophage into Escherichia coli. During its lysogenic cycle, N15 protelomerase (TelN) resolves its telomerase occupancy site (tos) into hairpin telomeres. This protects the N15 prophage from bacterial exonuclease degradation, enabling it to stably replicate as a linear plasmid in E. coli. Interestingly, purely proteinaceous TelN can retain phage DNA linearization and hairpin formation without involving host- or phage-derived intermediates or cofactors in the heterologous environment. This unique feature has led to the advent of synthetic linear DNA vector systems derived from the TelN-tos module for the genetic engineering of bacterial and mammalian cells. This review will focus on the development and advantages of N15-based novel cloning and expression vectors in the bacterial and mammalian environments. To date, N15 is the most widely exploited molecular tool for the development of linear vector systems, especially the production of therapeutically useful miniDNA vectors without a bacterial backbone. Compared to typical circular plasmids, linear N15-based plasmids display remarkable cloning fidelity in propagating unstable repetitive DNA sequences and large genomic fragments. Additionally, TelN-linearized vectors with the relevant origin of replication can replicate extrachromosomally and retain transgenes functionality in bacterial and mammalian cells without compromising host cell viability. Currently, this DNA linearization system has shown robust results in the development of gene delivery vehicles, DNA vaccines and engineering mammalian cells against infectious diseases or cancers, highlighting its multifaceted importance in genetic studies and gene medicine.
Phage N15 protelomerase resolves its tos recognition site into hairpin telomeres within mammalian cells

Liew PS, Chen Q, Ng AWR, Chew YC, Ravin NV, Sim EUH, et al.

Anal Biochem, 2019 10 15;583:113361.
PMID: 31306622 DOI: 10.1016/j.ab.2019.113361

Phage N15 protelomerase (TelN) cleaves double-stranded circular DNA containing a telomerase-occupancy-site (tos) and rejoins the resulting linear-ends to form closed-hairpin-telomeres in Escherichia coli (E. coli). Continued TelN expression is essential to support resolution of the linear structure. In mammalian cells, no enzyme with TelN-like activities has been found. In this work, we show that phage TelN, expressed transiently and stably in human and mouse cells, recapitulates its native activities in these exogenous environments. We found TelN to accurately resolve tos-DNA in vitro and in vivo within human and mouse cells into linear DNA-containing terminal telomeres that are resistant to RecBCD degradation, a hallmark of protelomerase processing. In stable cells, TelN activity was detectable for at least 60 days, which suggests the possibility of limited silencing of its expression. Correspondingly, linear plasmid containing a 100 kb human β-globin gene expressed for at least 120 h in non-β-globin-expressing mouse cells with TelN presence. Our results demonstrate TelN is able to cut and heal DNA as hairpin-telomeres within mammalian cells, providing a tool for creating novel structures by DNA resolution in these hosts. The TelN protelomerase may be useful for exploring novel technologies for genome interrogation and chromosome engineering.
Fulltext In silico-guided sequence modifications of K-ras epitopes improve immunological outcome against G12V and G13D mutant KRAS antigens

Ng AWR, Tan PJ, Hoo WPY, Liew DS, Teo MYM, Siak PY, et al.

PeerJ, 2018;6:e5056.
PMID: 30042874 DOI: 10.7717/peerj.5056

Background: Somatic point substitution mutations in the KRAS proto-oncogene primarily affect codons 12/13 where glycine is converted into other amino acids, and are highly prevalent in pancreatic, colorectal, and non-small cell lung cancers. These cohorts are non-responsive to anti-EGFR treatments, and are left with non-specific chemotherapy regimens as their sole treatment options. In the past, the development of peptide vaccines for cancer treatment was reported to have poor AT properties when inducing immune responses. Utilization of bioinformatics tools have since become an interesting approach in improving the design of peptide vaccines based on T- and B-cell epitope predictions.
Methods: In this study, the region spanning exon 2 from the 4th to 18th codon within the peptide sequence of wtKRAS was chosen for sequence manipulation. Mutated G12V and G13D K-ras controls were generated in silico, along with additional single amino acid substitutions flanking the original codon 12/13 mutations. IEDB was used for assessing human and mouse MHC class I/II epitope predictions, as well as linear B-cell epitopes predictions, while RNA secondary structure prediction was performed via CENTROIDFOLD. A scoring and ranking system was established in order to shortlist top mimotopes whereby normalized and reducing weighted scores were assigned to peptide sequences based on seven immunological parameters. Among the top 20 ranked peptide sequences, peptides of three mimotopes were synthesized and subjected to in vitro and in vivo immunoassays. Mice PBMCs were treated in vitro and subjected to cytokine assessment using CBA assay. Thereafter, mice were immunized and sera were subjected to IgG-based ELISA.
Results: In silico immunogenicity prediction using IEDB tools shortlisted one G12V mimotope (68-V) and two G13D mimotopes (164-D, 224-D) from a total of 1,680 candidates. Shortlisted mimotopes were predicted to promote high MHC-II and -I affinities with optimized B-cell epitopes. CBA assay indicated that: 224-D induced secretions of IL-4, IL-5, IL-10, IL-12p70, and IL-21; 164-D triggered IL-10 and TNF-α; while 68-V showed no immunological responses. Specific-IgG sera titers against mutated K-ras antigens from 164-D immunized Balb/c mice were also elevated post first and second boosters compared to wild-type and G12/G13 controls.
Discussion: In silico-guided predictions of mutated K-ras T- and B-cell epitopes were successful in identifying two immunogens with high predictive scores, Th-bias cytokine induction and IgG-specific stimulation. Developments of such immunogens are potentially useful for future immunotherapeutic and diagnostic applications against KRAS(+) malignancies, monoclonal antibody production, and various other research and development initiatives.