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Fulltext Insights into the genome structure and copy-number variation of Eimeria tenella

Lim LS, Tay YL, Alias H, Wan KL, Dear PH

BMC Genomics, 2012;13:389.
PMID: 22889016 DOI: 10.1186/1471-2164-13-389

Eimeria is a genus of parasites in the same phylum (Apicomplexa) as human parasites such as Toxoplasma, Cryptosporidium and the malaria parasite Plasmodium. As an apicomplexan whose life-cycle involves a single host, Eimeria is a convenient model for understanding this group of organisms. Although the genomes of the Apicomplexa are diverse, that of Eimeria is unique in being composed of large alternating blocks of sequence with very different characteristics - an arrangement seen in no other organism. This arrangement has impeded efforts to fully sequence the genome of Eimeria, which remains the last of the major apicomplexans to be fully analyzed. In order to increase the value of the genome sequence data and aid in the effort to gain a better understanding of the Eimeria tenella genome, we constructed a whole genome map for the parasite.
Fulltext Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

Chan CS, Chan KG, Tay YL, Chua YH, Goh KM

Front Microbiol, 2015;6:177.
PMID: 25798135 DOI: 10.3389/fmicb.2015.00177

The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.
Fulltext Mitragynine, an euphoric compound inhibits hERG1a/1b channel current and upregulates the complexation of hERG1a-Hsp90 in HEK293-hERG1a/1b cells

Tay YL, Amanah A, Adenan MI, Wahab HA, Tan ML

Sci Rep, 2019 12 24;9(1):19757.
PMID: 31874991 DOI: 10.1038/s41598-019-56106-6

Mitragyna speciosa Korth (M. speciosa) has been widely used as a recreational product, however, there are growing concerns on the abuse potentials and toxicity of the plant. Several poisoning and fatal cases involving kratom and mitragynine have been reported but the underlying causes remain unclear. The human ether-a-go-go-related gene 1 (hERG1) encodes the pore-forming subunit underlying cardiac rapidly delayed rectifier potassium current (IKr). Pharmacological blockade of the IKr can cause acquired long QT syndrome, leading to lethal cardiac arrhythmias. This study aims to elucidate the mechanisms of mitragynine-induced inhibition on hERG1a/1b current. Electrophysiology experiments were carried out using Port-a-Patch system. Quantitative RT-PCR, Western blot analysis, immunofluorescence and co-immunoprecipitation methods were used to determine the effects of mitragynine on hERG1a/1b expression and hERG1-cytosolic chaperones interaction. Mitragynine was found to inhibit the IKr current with an IC50 value of 332.70 nM. It causes a significant reduction of the fully-glycosylated (fg) hERG1a protein expression but upregulates both core-glycosylated (cg) expression and hERG1a-Hsp90 complexes, suggesting possible impaired hERG1a trafficking. In conclusion, mitragynine inhibits hERG1a/1b current through direct channel blockade at lower concentration, but at higher concentration, it upregulates the complexation of hERG1a-Hsp90 which may be inhibitory towards channel trafficking.
Fulltext Genome sequence of Hydrogenophaga sp. strain PBC, a 4-aminobenzenesulfonate-degrading bacterium

Gan HM, Chew TH, Tay YL, Lye SF, Yahya A

J Bacteriol, 2012 Sep;194(17):4759-60.
PMID: 22887664 DOI: 10.1128/JB.00990-12

Hydrogenophaga sp. strain PBC is an effective degrader of 4-aminobenzenesulfonate isolated from textile wastewater. Here we present the assembly and annotation of its genome, which may provide further insights into its metabolic potential. This is the first announcement of the draft genome sequence of a strain from the genus Hydrogenophaga.
Fulltext Genome sequence of Ralstonia sp. strain PBA, a bacterium involved in the biodegradation of 4-aminobenzenesulfonate

Gan HM, Chew TH, Tay YL, Lye SF, Yahya A

J Bacteriol, 2012 Sep;194(18):5139-40.
PMID: 22933765 DOI: 10.1128/JB.01165-12

Ralstonia sp. strain PBA was isolated from textile wastewater in a coculture with Hydrogenophaga sp. strain PBC. Here we present the assembly and annotation of its genome, which may provide further insights into the mechanism of its interaction with strain PBC during 4-aminobenzenesulfonate degradation.
Fulltext Perception of the Movement Control Order during the COVID-19 Pandemic: A Qualitative Study in Malaysia

Tay YL, Abdullah Z, Chelladorai K, Low LL, Tong SF

Int J Environ Res Public Health, 2021 08 20;18(16).
PMID: 34444527 DOI: 10.3390/ijerph18168778

Malaysia implemented its first Movement Control Order (MCO) during the early phase of the COVID-19 pandemic to slow the transmission of the virus. This study aimed to explore the public perception of the MCO implementation and people's experiences during this period. The study employed qualitative explorative in-depth interviews conducted with 23 Malaysian adults from various demographic backgrounds. Thematic analysis was performed using NVivo 12. Three main themes were identified: a period of information surge, heterogeneous emotional response, and attempts to adapt. During the MCO, the participants obtained information from multiple platforms. They suggested the need for clear and repeated instructions to avoid confusion and misinformation. They also acknowledged the importance of the MCO in breaking the chain of transmission and safeguarding high-risk groups; however, they also expressed that stricter enforcement from the authorities was warranted. The changes in the participants' work-life routines, lack of physical interaction, and uncertainty about their health and the economy due to the MCO negatively impacted their psychological states. Despite these challenges, the participants attempted to adapt to life under the MCO in different ways. The findings imply that during a crisis, the public tends to seek clear and reliable information, experience emotional turmoil, and adapt to changes. The MCO implementation can be improved through an effective communication strategy and efforts to battle misinformation.
Determination of CYP3A4 Inducing Properties of Compounds Using a Laboratory-Developed Cell-Based Assay

Seah TC, Tay YL, Tan HK, Muhammad TS, Wahab HA, Tan ML

Int J Toxicol, 2015 08 12;34(5):454-68.
PMID: 26268769 DOI: 10.1177/1091581815599335

A cell-based assay to measure cytochrome P450 3A4 (CYP3A4) induction was developed to screen for potential CYP3A4 inducers. This 96-well format assay utilizes HepG2 cells transfected with a gene construct of CYP3A4 proximal promoter linked to green fluorescence protein (GFP) gene, and the expression of the GFP is then measured quantitatively. Bergamottin at 5 to 25 µmol/L produced low induction relative to the positive control. Both curcumin and lycopene were not found to affect the expression of GFP, suggesting no induction properties toward CYP3A4. Interestingly, resveratrol produced significant induction from 25 µmol/L onward, which was similar to omeprazole and may warrant further studies. In conclusion, the present study demonstrated that this cell-based assay can be used as a tool to evaluate the potential CYP3A4 induction properties of compounds. However, molecular docking data have not provided satisfactory pointers to differentiate between CYP3A4 inducers from noninducers or from inhibitors, more comprehensive molecular screening may be indicated.
Fulltext Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome

Amiruddin N, Lee XW, Blake DP, Suzuki Y, Tay YL, Lim LS, et al.

BMC Genomics, 2012 Jan 13;13:21.
PMID: 22244352 DOI: 10.1186/1471-2164-13-21

BACKGROUND: Eimeria tenella is an apicomplexan parasite that causes coccidiosis in the domestic fowl. Infection with this parasite is diagnosed frequently in intensively reared poultry and its control is usually accorded a high priority, especially in chickens raised for meat. Prophylactic chemotherapy has been the primary method used for the control of coccidiosis. However, drug efficacy can be compromised by drug-resistant parasites and the lack of new drugs highlights demands for alternative control strategies including vaccination. In the long term, sustainable control of coccidiosis will most likely be achieved through integrated drug and vaccination programmes. Characterisation of the E. tenella transcriptome may provide a better understanding of the biology of the parasite and aid in the development of a more effective control for coccidiosis.
RESULTS: More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an E. tenella second generation merozoite full-length cDNA library. Clustering of these sequences produced 1,529 unique transcripts (UTs). Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated. These sequences varied in length, ranging from 441 bp to 3,083 bp, with an average size of 1,647 bp. Simple sequence repeat (SSR) analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in E. tenella are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. Subsequent analysis of the E. tenella complete coding sequences identified 25 putative secretory and 60 putative surface proteins, all of which are now rational candidates for development as recombinant vaccines or drug targets in the effort to control avian coccidiosis.
CONCLUSIONS: This paper describes the generation and characterisation of full-length cDNA sequences from E. tenella second generation merozoites and provides new insights into the E. tenella transcriptome. The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the E. tenella genome sequence.
Fulltext Effects of home visits on quality of life among older adults: a systematic review protocol

Tay YL, Abu Bakar NS, Tumiran R, Ab Rahman NH, Mohd Ma'amor NAA, Yau WK, et al.

Syst Rev, 2021 Dec 06;10(1):307.
PMID: 34872589 DOI: 10.1186/s13643-021-01862-8

BACKGROUND: Home visiting services for older adults have been offered for decades to maintain and promote health and independent functioning, thus enhancing quality of life. Previous systematic reviews have provided a mixed picture of the benefits of home visiting programmes in older adults, primarily because of heterogeneity in study designs, targeted populations, and intervention strategies. These reviews may also become out of date; thus, an updated synthesis of relevant studies is warranted. Our objective is to perform a systematic review of recently published primary studies on the effectiveness of multi-professional home visits on quality of life among older adults.
METHODS: We will perform a comprehensive search for studies investigating the effect of a multi-professional home visit approach on quality of life among older adults. We will conduct the literature search in selected electronic databases and relevant research websites from January 2010 onwards. We will include randomised controlled trials (RCTs), cluster randomised controlled trials (cluster RCTs), and observational studies that enrolled older adults without dementia over 60 years old, along with studies involving multi-professional preventive-promotive home visit approaches not related to recent hospital discharge. We will report our planned review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We will retrieve and record relevant data in a standardised data extraction form and evaluate the quality of the included articles using the Cochrane risk of bias tool and the quality assessment tool for studies with diverse designs (QATSDD). Where appropriate, outcomes will be pooled for meta-analysis using a random-effects model. The main outcomes include quality of life, incidence of falls, depression, dementia, and emergency department admissions.
DISCUSSION: This review may provide evidence for the effectiveness of home visits in improving older adults' quality of life. It will potentially benefit health care professionals, policymakers, and researchers by facilitating the design and delivery of interventions related to older generations and improve service delivery in future.
SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42021234531 .
Mitragynine and its potential blocking effects on specific cardiac potassium channels

Tay YL, Teah YF, Chong YM, Jamil MFA, Kollert S, Adenan MI, et al.

Toxicol Appl Pharmacol, 2016 08 15;305:22-39.
PMID: 27260674 DOI: 10.1016/j.taap.2016.05.022

Mitragyna speciosa Korth is known for its euphoric properties and is frequently used for recreational purposes. Several poisoning and fatal cases involving mitragynine have been reported but the underlying causes remain unclear. Human ether-a-go-go-related gene (hERG) encodes the cardiac IKr current which is a determinant of the duration of ventricular action potentials and QT interval. On the other hand, IK1, a Kir current mediated by Kir2.1 channel and IKACh, a receptor-activated Kir current mediated by GIRK channel are also known to be important in maintaining the cardiac function. This study investigated the effects of mitragynine on the current, mRNA and protein expression of hERG channel in hERG-transfected HEK293 cells and Xenopus oocytes. The effects on Kir2.1 and GIRK channels currents were also determined in the oocytes. The hERG tail currents following depolarization pulses were inhibited by mitragynine with an IC50 value of 1.62μM and 1.15μM in the transfected cell line and Xenopus oocytes, respectively. The S6 point mutations of Y652A and F656A attenuated the inhibitor effects of mitragynine, indicating that mitragynine interacts with these high affinity drug-binding sites in the hERG channel pore cavity which was consistent with the molecular docking simulation. Interestingly, mitragynine does not affect the hERG expression at the transcriptional level but inhibits the protein expression. Mitragynine is also found to inhibit IKACh current with an IC50 value of 3.32μM but has no significant effects on IK1. Blocking of both hERG and GIRK channels may cause additive cardiotoxicity risks.
Fulltext Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel

Alim FZD, Romanova EV, Tay YL, Rahman AYBA, Chan KG, Hong KW, et al.

PLoS One, 2019;14(6):e0216679.
PMID: 31211771 DOI: 10.1371/journal.pone.0216679

The "ship" of the Arabian and North African deserts, the one-humped dromedary camel (Camelus dromedarius) has a remarkable capacity to survive in conditions of extreme heat without needing to drink water. One of the ways that this is achieved is through the actions of the antidiuretic hormone arginine vasopressin (AVP), which is made in a specialised part of the brain called the hypothalamo-neurohypophyseal system (HNS), but exerts its effects at the level of the kidney to provoke water conservation. Interestingly, our electron microscopy studies have shown that the ultrastructure of the dromedary HNS changes according to season, suggesting that in the arid conditions of summer the HNS is in an activated state, in preparation for the likely prospect of water deprivation. Based on our dromedary genome sequence, we have carried out an RNAseq analysis of the dromedary HNS in summer and winter. Amongst the 171 transcripts found to be significantly differentially regulated (>2 fold change, p value <0.05) there is a significant over-representation of neuropeptide encoding genes, including that encoding AVP, the expression of which appeared to increase in summer. Identification of neuropeptides in the HNS and analysis of neuropeptide profiles in extracts from individual camels using mass spectrometry indicates that overall AVP peptide levels decreased in the HNS during summer compared to winter, perhaps due to increased release during periods of dehydration in the dry season.
Fulltext Genomic analysis of the causative agents of coccidiosis in domestic chickens

Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, et al.

Genome Res, 2014 Oct;24(10):1676-85.
PMID: 25015382 DOI: 10.1101/gr.168955.113

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

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