MyMedR

Fulltext Virological investigation of four outbreaks of influenza B reassortants in the northern region of Taiwan from October 2006 to February 2007

Lee YM, Wang SF, Lee CM, Chen KH, Chan YJ, Liu WT, et al.

BMC Res Notes, 2009;2:86.

PMID: 19426542 DOI: 10.1186/1756-0500-2-86

From October 2006 to February 2007, clinical specimens from 452 patients with symptoms related to respiratory tract infection in the northern region of Taiwan were collected. Real-time PCR and direct immunofluorescent antibody tests showed that 145 (32%) patients had influenza B virus infections. Subsequently, nucleotide sequence analyses of both hemagglutinin (HA) and neuraminidase (NA) genes of 39 isolates were performed. Isolated viruses were antigenically characterized using hemagglutinin inhibition (HI) test.

Fulltext Colostrum supplementation protects against exercise-induced oxidative stress in skeletal muscle in mice

Appukutty M, Radhakrishnan AK, Ramasamy K, Ramasamy R, Abdul Majeed AB, Noor MI, et al.

BMC Res Notes, 2012;5:649.

PMID: 23173926 DOI: 10.1186/1756-0500-5-649

This study examined the effects of bovine colostrum on exercise -induced modulation of antioxidant parameters in skeletal muscle in mice. Adult male BALB/c mice were randomly divided into four groups (control, colostrum alone, exercise and exercise with colostrum) and each group had three subgroups (day 0, 21 and 42). Colostrum groups of mice were given a daily oral supplement of 50 mg/kg body weight of bovine colostrum and the exercise group of mice were made to exercise on the treadmill for 30 minutes per day. Total antioxidants, lipid hydroperoxides, xanthine oxidase and super oxide dismutase level was assayed from the homogenate of hind limb skeletal muscle.

Fulltext Antioxidant and tyrosinase inhibition activity of the fertile fronds and rhizomes of three different Drynaria species

Tan JB, Lim YY

BMC Res Notes, 2015;8:468.

PMID: 26395256 DOI: 10.1186/s13104-015-1414-3

For generations, the rhizomes of Drynaria ferns have been used as traditional medicine in Asia. Despite this, the bioactivities of Drynaria rhizomes and leaves have rarely been studied scientifically.

Fulltext Development of repeatable arrays of proteins using immobilized DNA microplate (RAPID-M) technology

Ashaari NS, Ramarad S, Khairuddin D, Akhir NA, Hara Y, Mahadi NM, et al.

BMC Res Notes, 2015;8:669.

PMID: 26563904 DOI: 10.1186/s13104-015-1637-3

Protein microarrays have enormous potential as in vitro diagnostic tools stemming from the ability to miniaturize whilst generating maximum evaluation of diagnostically relevant information from minute amounts of sample. In this report, we present a method known as repeatable arrays of proteins using immobilized DNA microplates (RAPID-M) for high-throughput in situ protein microarray fabrication. The RAPID-M technology comprises of cell-free expression using immobilized DNA templates and in situ protein purification onto standard microarray slides.

Fulltext Systemic and coronary levels of CRP, MPO, sCD40L and PlGF in patients with coronary artery disease

Fong SW, Few LL, See Too WC, Khoo BY, Nik Ibrahim NN, Yahaya SA, et al.

BMC Res Notes, 2015;8:679.

PMID: 26576922 DOI: 10.1186/s13104-015-1677-8

Biomarkers play a pivotal role in the diagnosis and management of patients with acute coronary syndrome. This study aimed to investigate the differences in level of several biomarkers, i.e. C-reactive protein, myeloperoxidase, soluble CD40 ligand and placental growth factor, between acute coronary syndrome and chronic stable angina patients. The relationship between these biomarkers in the coronary circulation and systemic circulation was also investigated.

Fulltext Neonatal preintubation sedation: a national survey in Malaysia

Hss AS, Linus-Lojikip S, Ismail Z, Ishahar NH, Yusof SS

BMC Res Notes, 2015;8:660.

PMID: 26553069 DOI: 10.1186/s13104-015-1653-3

There is a shift of practice towards administering sedation in neonates around the world. At the present moment, there is no available data or literature on the practice of sedation before intubation of neonates in Malaysia thus, evaluation of these practice was not possible. This study was conducted to evaluate neonatal preintubation sedation practice and the availability of neonatal preintubation sedation policy in government, university and private Malaysian Neonatal Intensive Care Units (NICUs) in 2007.

Fulltext Exploring the intentions of pharmacy students towards pharmacy ownership by using theory of planned behaviour

Khan MU, Ahmad A, Fayyaz M, Ashraf N, Bhagavathula A

BMC Res Notes, 2016;9(1):183.

PMID: 27005815 DOI: 10.1186/s13104-016-1996-4

The objective of this study was to assess the association of the constructs of theory of planned behaviour (behavioural beliefs, normative beliefs, control beliefs) and demographic variables with the intentions of pharmacy students to become pharmacy owner.

Fulltext Harmonizing the interpretation of genetic variants across the world: the Malaysian experience

Hassan NN, Plazzer JP, Smith TD, Halim-Fikri H, Macrae F, Zubaidi AA, et al.

BMC Res Notes, 2016;9:125.

PMID: 26915360 DOI: 10.1186/s13104-015-1798-0

Databases for gene variants are very useful for sharing genetic data and to facilitate the understanding of the genetic basis of diseases. This report summarises the issues surrounding the development of the Malaysian Human Variome Project Country Node. The focus is on human germline variants. Somatic variants, mitochondrial variants and other types of genetic variation have corresponding databases which are not covered here, as they have specific issues that do not necessarily apply to germline variations.

Fulltext Prevalence of stress among medical students: a comparative study between public and private medical schools in Bangladesh

Eva EO, Islam MZ, Mosaddek AS, Rahman MF, Rozario RJ, Iftekhar AF, et al.

BMC Res Notes, 2015;8:327.

PMID: 26223786 DOI: 10.1186/s13104-015-1295-5

Throughout the world all health professionals face stress because of time-pressures, workload, multiple roles and emotional issues. Stress does not only exist among the health professionals but also in medical students. Bangladesh has currently 77 medical colleges 54 of which are private. This study was designed to collect baseline data of stress-level among Bangladeshi students, which we believe will form the basis for further in depth studies.

Fulltext The first Malay database toward the ethnic-specific target molecular variation

Halim-Fikri H, Etemad A, Abdul Latif AZ, Merican AF, Baig AA, Annuar AA, et al.

BMC Res Notes, 2015;8:176.

PMID: 25925844 DOI: 10.1186/s13104-015-1123-y

The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human Variome Project (HVP) country-specific nodes. Since its inception in 9(th) October 2010, MyHVP has attracted the significant number of Malaysian clinicians and researchers to participate and contribute their data to this project. MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian population. A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called the Malaysian Node of the Human Variome Project database (MyHVPDb).

Fulltext Pharmacophore modelling of vanillin derivatives, favipiravir, chloroquine, hydroxychloroquine, monolaurin and tetrodotoxin as MPro inhibitors of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)

Law WY, Asaruddin MR, Bhawani SA, Mohamad S

BMC Res Notes, 2020 Nov 11;13(1):527.

PMID: 33176880 DOI: 10.1186/s13104-020-05379-6

OBJECTIVES: The aim of this study was to use Ligand-based pharmacophore modelling approach for four established antiviral drugs, namely remdesivir, lopinavir, ritonavir and hydroxychloroquine for COVID-19 inhibitors as training sets. In this study Twenty vanillin derivatives together with monolaurin and tetrodotoxin were used as test sets to evaluate as potential SARS-CoV-2 inhibitors. The Structure-based pharmacophore modelling approach was also performed using 5RE6, 5REX and 5RFZ in order to analyse the binding site and ligand-protein complex interactions.

RESULTS: The pharmacophore modelling mode of 5RE6 displayed two Hydrogen Bond Acceptors (HBA) and one Hydrophobic (HY) interaction. Besides, the pharmacophore model of 5REX showed two HBA and two HY interactions. Finally, the pharmacophore model of 5RFZ showed three HBA and one HY interaction. Based on ligand-based approach, 20 Schiff-based vanillin derivatives, showed strong MPro inhibition activity. This was due to their good alignment and common features to PDB-5RE6. Similarly, monolaurin and tetrodotoxin displayed some significant activity against SARS-CoV-2. From structure-based approach, vanillin derivatives (1) to (12) displayed some potent MPro inhibition against SARS-CoV-2. Favipiravir, chloroquine and hydroxychloroquine also showed some significant MPro inhibition.

Fulltext RNA sequencing of kidney and liver transcriptome obtained from wild cynomolgus macaque (Macaca fascicularis) originating from Peninsular Malaysia

Ee Uli J, Yong CS, Yeap SK, Alitheen NB, Rovie-Ryan JJ, Mat Isa N, et al.

BMC Res Notes, 2018 Dec 22;11(1):923.

PMID: 30577850 DOI: 10.1186/s13104-018-4014-1

OBJECTIVE: Using high-throughput RNA sequencing technology, this study aimed to sequence the transcriptome of kidney and liver tissues harvested from Peninsular Malaysia cynomolgus macaque (Macaca fascicularis). M. fascicularis are significant nonhuman primate models in the biomedical field, owing to the macaque's biological similarities with humans. The additional transcriptomic dataset will supplement the previously described Peninsular Malaysia M. fascicularis transcriptomes obtained in a past endeavour.

RESULTS: A total of 75,350,240 sequence reads were obtained via Hi-seq 2500 sequencing technology. A total of 5473 significant differentially expressed genes were called. Gene ontology functional categorisation showed that cellular process, catalytic activity, and cell part categories had the highest number of expressed genes, while the metabolic pathways category possessed the highest number of expressed genes in the KEGG pathway analysis. The additional sequence dataset will further enrich existing M. fascicularis transcriptome assemblies, and provide a dataset for further downstream studies.

Fulltext RNA-seq data of Ganoderma boninense at axenic culture condition and under in planta pathogen-oil palm (Elaeis guineensis Jacq.) interaction

Wong MY, Govender NT, Ong CS

BMC Res Notes, 2019 Sep 24;12(1):631.

PMID: 31551084 DOI: 10.1186/s13104-019-4652-y

OBJECTIVE: Basal stem rot disease causes severe economic losses to oil palm production in South-east Asia and little is known on the pathogenicity of the pathogen, the basidiomyceteous Ganoderma boninense. Our data presented here aims to identify both the house-keeping and pathogenicity genes of G. boninense using Illumina sequencing reads.

DESCRIPTION: The hemibiotroph G. boninense establishes via root contact during early stage of colonization and subsequently kills the host tissue as the disease progresses. Information on the pathogenicity factors/genes that causes BSR remain poorly understood. In addition, the molecular expressions corresponding to G. boninense growth and pathogenicity are not reported. Here, six transcriptome datasets of G. boninense from two contrasting conditions (three biological replicates per condition) are presented. The first datasets, collected from a 7-day-old axenic condition provide an insight onto genes responsible for sustenance, growth and development of G. boninense while datasets of the infecting G. boninense collected from oil palm-G. boninense pathosystem (in planta condition) at 1 month post-inoculation offer a comprehensive avenue to understand G. boninense pathogenesis and infection especially in regard to molecular mechanisms and pathways. Raw sequences deposited in Sequence Read Archive (SRA) are available at NCBI SRA portal with PRJNA514399, bioproject ID.

Fulltext Use of headspace-gas chromatography-ion mobility spectrometry to detect volatile fingerprints of palm fibre oil and sludge palm oil in samples of crude palm oil

Othman A, Goggin KA, Tahir NI, Brodrick E, Singh R, Sambanthamurthi R, et al.

BMC Res Notes, 2019 Apr 16;12(1):229.

PMID: 30992056 DOI: 10.1186/s13104-019-4263-7

OBJECTIVE: The addition of residual oils such as palm fibre oil (PFO) and sludge palm oil (SPO) to crude palm oil (CPO) can be problematic within supply chains. PFO is thought to aggravate the accumulation of monochloropropanediols (MCPDs) in CPO, whilst SPO is an acidic by-product of CPO milling and is not fit for human consumption. Traditional targeted techniques to detect such additives are costly, time-consuming and require highly trained operators. Therefore, we seek to assess the use of gas chromatography-ion mobility spectrometry (GC-IMS) for rapid, cost-effective screening of CPO for the presence of characteristic PFO and SPO volatile organic compound (VOC) fingerprints.

RESULTS: Lab-pressed CPO and commercial dispatch tank (DT) CPO were spiked with PFO and SPO, respectively. Both additives were detectable at concentrations of 1% and 10% (w/w) in spiked lab-pressed CPO, via seven PFO-associated VOCs and 21 SPO-associated VOCs. DT controls could not be distinguished from PFO-spiked DT CPO, suggesting these samples may have already contained low levels of PFO. DT controls were free of SPO. SPO was detected in all SPO-spiked dispatch tank samples by all 21 of the previously distinguished VOCs and had a significant fingerprint consisting of four spectral regions.

Fulltext Nutritional assessment and factors associated with malnutrition among the elderly population of Nepal: a cross-sectional study

Tamang MK, Yadav UN, Hosseinzadeh H, Kafle B, Paudel G, Khatiwada S, et al.

BMC Res Notes, 2019 Apr 30;12(1):246.

PMID: 31039794 DOI: 10.1186/s13104-019-4282-4

OBJECTIVES: This study aimed at assessing the nutritional status among the elderly population and factors associated with malnutrition in the community setting in rural Nepal.

RESULTS: Out of 339 participants, 24.8% (95% CI 20.21-29.30) fell into the normal nutritional status range; 49.6% (95% CI 44.29-54.91) were at risk for malnutrition while 24.8% (95% CI 20.21-29.30) were in the malnourished range, based on Mini Nutritional Assessment scores. Our findings revealed that belonging to a Dalit community, being unemployed, having experience of any form of mistreatment, lack of physical exercise, experiencing problems with concentration in past 30 days and taking medication for more than one co-morbidity was significantly associated with the malnutrition status of the elderly.

Fulltext Rapid spheroid assays in a 3-dimensional cell culture chip

Teh JL, Abdul Rahman SF, Domnic G, Satiyasilan L, Chear NJY, Singh D, et al.

BMC Res Notes, 2021 Aug 13;14(1):310.

PMID: 34389056 DOI: 10.1186/s13104-021-05727-0

OBJECTIVE: The spheroid model provides a physiological platform to study cancer cell biology and drug sensitivity. Usage of bovine collagen I for spheroid assays is costly especially when experiments are conducted in 24-well plates, as high volume of bovine collagen I is needed. The aim of the study was to downsize spheroid assays to a microfluidic 3D cell culture chip and compare the growth, invasion and response to drug/compound of spheroids embedded in the 3D chip to spheroids embedded in 24-well plates.

RESULTS: Spheroids generated from nasopharyngeal carcinoma cell line HK-1 continuously grew and invaded into collagen matrix in a 24-well plate. Similar observations were noticed with spheroids embedded in the 3D chip. Large spheroids in both 24-well plate and the 3D chip disintegrated and invaded into the collagen matrix. Preliminary drug sensitivity assays showed that the growth and invasion of spheroids were inhibited when spheroids were treated with combination of cisplatin and paynantheine at high concentrations, in a 24-well plate. Comparable findings were obtained when spheroids were treated with the same drug combination in the 3D chip. Moving forward, spheroid assays could be performed in the 3D chip in a more high-throughput manner with minimal time and cost.

Fulltext Blood glucose response to a calamansi drink in healthy adults: a non-randomised study

Siner A, Sevanesan MS, Ambomai T, Abd Wahab Z, Lasem L

BMC Res Notes, 2020 Aug 28;13(1):404.

PMID: 32859257 DOI: 10.1186/s13104-020-05250-8

OBJECTIVE: Glycaemic Index (GI) ranks the body's response to carbohydrate content in food such that high GI food increases postprandial blood glucose levels. One of the popular drinks at food and beverage outlets is a drink made from calamansi, a citrus that is believed not to induce an increase in blood glucose levels. In this non-randomised single-blind (participants) study, capillary blood from 10 healthy males were sampled following consumption of either glucose or the calamansi drink. The blood glucose measurements were then used to calculate the GI for the drink.

RESULTS: The GI of the calamansi drink tested was calculated as 37, a value within the range of low GI foods. Trial registration Clinical Trials identifier NCT04462016; Retrospectively registered on July 1, 2020.

Fulltext Transcriptome of Aquilaria malaccensis containing agarwood formed naturally and induced artificially

Abdul Kadir FA, Azizan KA, Othman R

BMC Res Notes, 2021 Mar 25;14(1):117.

PMID: 33766087 DOI: 10.1186/s13104-021-05532-9

OBJECTIVES: Agarwood is the aromatic heartwood formed upon wounding of Aquilaria trees either naturally formed due to physical wound sustained from natural phenomena followed by microbial infection, or artificially induced using different inoculation methods. Different induction methods produce agarwoods with different aromas which have impacts on their commercial values. In lieu of elucidating the molecular mechanisms of agarwood formation under different treatment conditions, the transcriptome profiles of trunk tissues from healthy A. malaccensis tree, and naturally and artificially induced trees were obtained.

DATA DESCRIPTION: The transcriptome of trunk tissues from healthy A. malaccensis, and naturally and artificially induced trees were sequenced using Illumina HiSeq™ 4000 platform which resulted in a total of 38.4 Gb clean reads with Q30 rate of at least 91%. The transcriptome consists of 85,986 unigenes containing 1305 bases on average which were annotated against several databases. From this, 44,654 unigenes were mapped to 290 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. These transcriptome data represent considerable contribution towards Aquilaria transcriptome data and enhance current knowledge in comprehending the molecular mechanisms underlying agarwood formation in Aquilaria spp.

Fulltext Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing

Ten KE, Md Zoqratt MZH, Ayub Q, Tan HS

BMC Res Notes, 2021 Mar 04;14(1):83.

PMID: 33663564 DOI: 10.1186/s13104-021-05493-z

OBJECTIVE: The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen.

RESULTS: One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.

Fulltext Genomic characterization of bacteria from the ultra-oligotrophic Madison aquifer: insight into the archetypical LuxI/LuxR and identification of novel LuxR solos

Wengert PC, Wong NH, Barton HA, Gan HM, Hudson AO, Savka MA

BMC Res Notes, 2021 May 08;14(1):175.

PMID: 33964980 DOI: 10.1186/s13104-021-05589-6

OBJECTIVES: To characterize the bacterial community of Wind Cave's Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems.

RESULTS: Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes, luxI and luxR. Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three luxR orphans (solos). Strain SD129, besides possessing an archetypical AHL QS luxI-luxR pair, also contained two luxR solos, while strain SD316 contained three LuxR solos and no luxI-luxR pairs. The ligand-binding domain of two LuxR solos, one each from strains SD129 and SD316, were found to contain novel substitutions not previously reported, thus may represent two LuxR orphans that detection and response to unknown self-produced signal(s), or to signal(s) produced by other organisms.

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