Displaying publications 1 - 20 of 29 in total

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  1. Cloning and sequencing of its region of two isolates of Phellinus spp obtained from diseased roots of setang (Azadirachta excelsa [Jack] Jacobs)
    Mohd Rosli Haron, Mohd Farid Ahmad, Lee, Su See, Norwati Muhammad
    Buletin Persatuan Genetik Malaysia, 2005;11(1):0-0.
    MyJurnal
    Two isolates of brown root disease fungi were obtained from diseased roots of sentang (Azadirachta excelsa). Morphological characters from macroscopic and microscopic studies suggested that both isolates were from the same genus namely Phellinus noxius and Phellinus sp. Cloning and sequencing of ITS region were conducted to investigate further the variation between the two species at
    molecular level. PCR-amplified ITS regions were cloned in pCR2.1 and sequenced. DNA sequences sized 723bp and 710bp were obtained for Phellinus noxius and Phellinus sp respectively. Comparison between the two sequences showed 98% similarity where three nucleotide substitutions and three insertion/deletion regions were found sized 8bp, 2bp and 3bp respectively.
  2. Non-protein coding RNA-based genosensor with quantum dots as electrochemical labels for attomolar detection of multiple pathogens
    Vijian D, Chinni SV, Yin LS, Lertanantawong B, Surareungchai W
    Biosens Bioelectron, 2016 Mar 15;77:805-11.
    PMID: 26513287 DOI: 10.1016/j.bios.2015.10.057
    The ability of a diagnostic test to detect multiple pathogens simultaneously is useful to obtain meaningful information for clinical treatment and preventive measures. We report a highly sensitive and specific electrochemical biosensor assay for simultaneous detection of three gene targets using quantum dots (QDs). The targets are novel non-protein coding RNA (npcRNA) sequences of Vibrio cholerae, Salmonella sp. and Shigella sp., which cause diarrheal diseases. QDs (PbS, CdS, ZnS) were synthesized and functionalized with DNA probes that were specific to each pathogen. Electrochemical detection of QDs was performed using square wave anodic stripping voltammetry (SWASV). The QDs gave distinct peaks at 0.5 V (PbS), 0.75 V (CdS) and 1.1 V (ZnS). There was no interference in signal response when all three QDs were mixed and detected simultaneously. The detection limits of single and multiplex assays with linear targets and PCR products were in the attomolar ranges. The high assay sensitivity, in combination with specific npcRNA sequences as novel diagnostic targets, makes it a viable tool for detecting pathogens from food, environment and clinical samples.
  3. Electrochemical DNA detection of hepatitis E virus genotype 3 using PbS quantum dot labelling
    Ngo DB, Chaibun T, Yin LS, Lertanantawong B, Surareungchai W
    Anal Bioanal Chem, 2021 Feb;413(4):1027-1037.
    PMID: 33236225 DOI: 10.1007/s00216-020-03061-1
    The aim of this study was to develop a highly specific electrochemical DNA sensor using functionalized lead sulphide (PbS) quantum dots for hepatitis E virus genotype 3 (HEV3) DNA target detection. Functionalized-PbS quantum dots (QDs) were used as an electrochemical label for the detection of HEV3-DNA target by the technique of square wave anodic stripping voltammetry (SWASV). The functionalized-PbS quantum dots were characterized by UV-vis, FTIR, XRD, TEM and zeta potential techniques. As-prepared, functionalized-PbS quantum dots have an average size of 4.15 ± 1.35 nm. The detection platform exhibited LOD and LOQ values of 1.23 fM and 2.11 fM, respectively. HEV3-DNA target spiked serum is also reported.Graphical abstract.
  4. A nanoplex PCR assay for the rapid detection of vancomycin and bifunctional aminoglycoside resistance genes in Enterococcus species
    Yean CY, Yin LS, Lalitha P, Ravichandran M
    BMC Microbiol, 2007 Dec 11;7:112.
    PMID: 18070365
    BACKGROUND: Enterococci have emerged as a significant cause of nosocomial infections in many parts of the world over the last decade. The most common enterococci strains present in clinical isolates are E. faecalis and E. faecium which have acquired resistant to either gentamicin or vancomycin. The conventional culture test takes 2-5 days to yield complete information of the organism and its antibiotic sensitivity pattern. Hence our present study was focused on developing a nanoplex PCR assay for the rapid detection of vancomycin and bifunctional aminoglycoside resistant enterococci (V-BiA-RE). This assay simultaneously detects 8 genes namely 16S rRNA of Enterococcus genus, ddl of E. faecalis and E. faecium, aacA-aphD that encodes high level gentamicin resistance (HLGR), multilevel vancomycin resistant genotypes such as vanA, vanB, vanC and vanD and one internal control gene.

    RESULTS: Unique and specific primer pairs were designed to amplify the 8 genes. The specificity of the primers was confirmed by DNA sequencing of the nanoplex PCR products and BLAST analysis. The sensitivity and specificity of V-BiA-RE nanoplex PCR assay was evaluated against the conventional culture method. The analytical sensitivity of the assay was found to be 1 ng at the DNA level while the analytical specificity was evaluated with 43 reference enterococci and non-enterococcal strains and was found to be 100%. The diagnostic accuracy was determined using 159 clinical specimens, which showed that 97% of the clinical isolates belonged to E. faecalis, of which 26% showed the HLGR genotype, but none were vancomycin resistant. The presence of an internal control in the V-BiA-RE nanoplex PCR assay helped us to rule out false negative cases.

    CONCLUSION: The nanoplex PCR assay is robust and can give results within 4 hours about the 8 genes that are essential for the identification of the most common Enterococcus spp. and their antibiotic sensitivity pattern. The PCR assay developed in this study can be used as an effective surveillance tool to study the prevalence of enterococci and their antibiotic resistance pattern in hospitals and farm animals.

  5. Fulltext Demystifying the life domain in work-life balance: A Malaysian perspective
    Jayasingam S, Lee ST, Mohd Zain KN
    Curr Psychol, 2023;42(1):1-12.
    PMID: 33519148 DOI: 10.1007/s12144-021-01403-5
    Traditionally, the word 'life' in the concept of work-life balance focuses on family obligations. This conceptual paper sets out to present the notion that "life" goes beyond family responsibilities and is unique to employees of different demographics. Given the impending difference in how "life" is viewed by different groups of employees, this study reviews the literature and argues for the need to distinguish between different dimensions of the non-work domain. The discussion is centered on the transformation taking place within the Malaysian workforce. Recent trends indicate that "life" and "family" are indeed distinct domains. There is a need for organizations to acknowledge this distinction and provide relevant support to attain a balance between work, life, and family. The paper will help strengthen the knowledge about the "life" in the concept of work-life balance and employers better understand the conceptualization of "life" in work-life balance so that they can strategize and enhance employee well-being and eventually gain competitive advantage. Currently, the terms work-life balance and work-family balance are used interchangeably to represent a balance between the family and work domain. This is especially evident in collectivist countries such as Malaysia. However, the emphasis on family without due consideration to the needs of employees with different demographic configurations may result in work-life backlash. Hence, this study argues that the non-work domain is not limited to family obligations and should encompass both family obligations and personal activities. The emphasis on striking a balance between work and family domain should not be done at the expense of the well-being of employees with lesser or no family obligations.
  6. Fulltext Addressing the COVID-19 Shock: The Potential Job Creation in China by the RCEP
    Wu X, Yong CC, Lee ST
    Int J Environ Res Public Health, 2022 Nov 25;19(23).
    PMID: 36497744 DOI: 10.3390/ijerph192315669
    In 2020, coronavirus disease (COVID-19) left around 81% of the global workforce, nearly 2.7 billion workers, affected. Employment in China was the first to be hit by COVID-19. The Regional Comprehensive Economic Partnership (RCEP) is expected to bring dynamism to China's employment market in an era of long COVID-19. This study aims to examine the number of sectoral jobs that the RCEP will create in China, with the number of skilled or unskilled labour employed in each sector. The exogenous shocks to the RCEP can be reflected in the number of jobs created through multipliers based on a social accounting matrix compiled from China's input-output tables in 2017, combined with the employment satellite accounts compiled. The results show that the RCEP is expected to create over 17 million potential jobs in China, with unskilled labour accounting for 10.44 million and skilled labour for 6.77 million. It is even expected that there will be job losses in the metalworking machinery sector. The contribution of this paper can serve as a reference for policies to protect vulnerable sectors, further open up trade markets and strengthen cooperation among RCEP members as important measures to address the employment impact of long COVID-19.
  7. Fulltext Efficient extraction of small and large RNAs in bacteria for excellent total RNA sequencing and comprehensive transcriptome analysis
    Heera R, Sivachandran P, Chinni SV, Mason J, Croft L, Ravichandran M, et al.
    BMC Res Notes, 2015;8(1):754.
    PMID: 26645211 DOI: 10.1186/s13104-015-1726-3
    Next-generation transcriptome sequencing (RNA-Seq) has become the standard practice for studying gene splicing, mutations and changes in gene expression to obtain valuable, accurate biological conclusions. However, obtaining good sequencing coverage and depth to study these is impeded by the difficulties of obtaining high quality total RNA with minimal genomic DNA contamination. With this in mind, we evaluated the performance of Phenol-free total RNA purification kit (Amresco) in comparison with TRI Reagent (MRC) and RNeasy Mini (Qiagen) for the extraction of total RNA of Pseudomonas aeruginosa which was grown in glucose-supplemented (control) and polyethylene-supplemented (growth-limiting condition) minimal medium. All three extraction methods were coupled with an in-house DNase I treatment before the yield, integrity and size distribution of the purified RNA were assessed. RNA samples extracted with the best extraction kit were then sequenced using the Illumina HiSeq 2000 platform.
  8. Gold-nanoparticle based electrochemical DNA sensor for the detection of fish pathogen Aphanomyces invadans
    Kuan GC, Sheng LP, Rijiravanich P, Marimuthu K, Ravichandran M, Yin LS, et al.
    Talanta, 2013 Dec 15;117:312-7.
    PMID: 24209346 DOI: 10.1016/j.talanta.2013.09.016
    Epizootic ulcerative syndrome (EUS) is a devastating fish disease caused by the fungus, Aphanomyces invadans. Rapid diagnosis of EUS is needed to control and treat this highly invasive disease. The current diagnostic methods for EUS are labor intensive. We have developed a highly sensitive and specific electrochemical genosensor towards the 18S rRNA and internal transcribed spacer regions of A. invadans. Multiple layers of latex were synthesized with the help of polyelectrolytes, and labeled with gold nanoparticles to enhance sensitivity. The gold-latex spheres were functionalized with specific DNA probes. We describe here the novel application of this improved platform for detection of PCR product from real sample of A. invadans using a premix sandwich hybridization assay. The premix assay was easier, more specific and gave higher sensitivity of one log unit when compared to the conventional method of step-by-step hybridization. The limit of detection was 0.5 fM (4.99 zmol) of linear target DNA and 1 fM (10 amol) of PCR product. The binding positions of the probes to the PCR amplicons were optimized for efficient hybridization. Probes that hybridized close to the 5' or 3' terminus of the PCR amplicons gave the highest signal due to minimal steric hindrance for hybridization. The genosensor is highly suitable as a surveillance and diagnostic tool for EUS in the aquaculture industry.
  9. Enzyme-linked amperometric electrochemical genosensor assay for the detection of PCR amplicons on a streptavidin-treated screen-printed carbon electrode
    Yean CY, Kamarudin B, Ozkan DA, Yin LS, Lalitha P, Ismail A, et al.
    Anal Chem, 2008 Apr 15;80(8):2774-9.
    PMID: 18311943 DOI: 10.1021/ac702333x
    A general purpose enzyme-based amperometric electrochemical genosensor assay was developed wherein polymerase chain reaction (PCR) amplicons labeled with both biotin and fluorescein were detected with peroxidase-conjugated antifluorescein antibody on a screen-printed carbon electrode (SPCE). As a proof of principle, the response selectivity of the genosensor was evaluated using PCR amplicons derived from lolB gene of Vibrio cholerae. Factors affecting immobilization, hybridization, and nonspecific binding were optimized to maximize sensitivity and reduce assay time. On the basis of the background amperometry signals obtained from nonspecific organisms and positive signals obtained from known V. cholerae, a threshold point of 4.20 microA signal was determined as positive. Under the optimum conditions, the limit of detection (LOD) of the assay was 10 CFU/mL of V. cholerae. The overall precision of this assay was good, with the coefficient of variation (CV) being 3.7% using SPCE and intermittent pulse amperometry (IPA) as an electrochemical technique. The assay is sensitive, safe, and cost-effective when compared to conventional agarose gel electrophoresis, real-time PCR, and other enzyme-linked assays for the detection of PCR amplicons. Furthermore, the use of a hand-held portable reader makes it suitable for use in the field.
  10. Target Induced-DNA strand displacement reaction using gold nanoparticle labeling for hepatitis E virus detection
    Ngamdee T, Yin LS, Vongpunsawad S, Poovorawan Y, Surareungchai W, Lertanantawong B
    Anal Chim Acta, 2020 Oct 16;1134:10-17.
    PMID: 33059855 DOI: 10.1016/j.aca.2020.08.018
    DNA strand displacement is an attractive, enzyme-free target hybridization strategy for nano-biosensing. The target DNA induces a strand displacement reaction by replacing the pre-hybridized strand that is labeled with gold nanoparticles (AuNPs). Thus, the amount of displaced-AuNP-labeled strand is proportional to the amount of target DNA in the sample. The use of a magnetogenosensing technique to isolate the target DNA allows for a simple, one-pot detection approach, which minimizes possible carry-over contamination and pipetting errors. We sought a proof-of-concept for this technology in its ability to detect DNA-equivalent of hepatitis E virus (HEV), which causes acute viral hepatitis for which rapid and simple diagnostic methods remain limited. Signal detection was done via visual observation, spectrophotometry, and electrochemistry. The sensor demonstrated good sensitivity with detection limits of 10 pM (visual), 10 pM (spectrophotometry) and 1 fM (electrochemical). This sensor also exhibited high specificity for real target amplicons and could discriminate between perfect and mismatched sequences. Lyophilized biosensor reagents stored at 4 °C, 25 °C, and outdoor ambient temperature, were stable for up to 90, 50, and 40 days, respectively. The integration of magnetic separation and target DNA-induced strand displacement reaction in a dry reagent form makes the sensing platform easy-to-use and suitable for field settings.
  11. Hebeloma in the Malay Peninsula: Masquerading within Psathyrella
    Eberhardt U, Schütz N, Beker HJ, Lee SS, Horak E
    MycoKeys, 2021;77:117-141.
    PMID: 33551660 DOI: 10.3897/mycokeys.77.57394
    In 1994 Corner published five new species within the genus Psathyrella, all having been collected on the Malay Peninsula between 1929 and 1930. Three of these species belong to the genus Hebeloma and with their vinaceous colored lamellae and spore print, when fresh, they belong to H. sect. Porphyrospora. Of these three species, only one, P. flavidifolia, was validly published and thus we herewith recombine it as H. flavidifolium. The other two species, P. splendens and P. verrucispora, are synonyms of H. parvisporum and H. lactariolens, respectively. We also describe a new Malayan species, H. radicans, which also belongs to H. sect. Porphyrospora. These findings confirm the western Pacific Rim as a diversity hotspot for H. sect. Porphyrospora. The records described within this paper, represent the first recognition that the genus Hebeloma, and indeed that members of the ectomycorrhizal Hymenogastraceae, are present on the Malay Peninsula.
  12. Fulltext Nutritional, Medicinal and Toxicological Attributes of Star-Fruits (Averrhoa carambola L.): A Review
    Muthu N, Lee SY, Phua KK, Bhore SJ
    Bioinformation, 2016;12(12):420-424.
    PMID: 28405126 DOI: 10.6026/97320630012420
    Plants are very complex organisms that produce medicinally important natural products. The Star-fruit producing plant (Averrhoa carambola L.) is a species of woody plant in the family Oxalidaceae native to the Philippines, Indonesia, Malaysia, Vietnam, India, Bangladesh and Sri Lanka; but, cultivated in many parts of the world. Star-fruits are popular tropical fruits and used commonly in Ayurvedic and Traditional Chinese Medicines (TCM) in India, China, and Brazil to relieve ailments such as chronic headache, fever, cough, gastro-enteritis, diarrhoea, ringworm infections, and skin inflammations. However, this fruit contains high amount of oxalate, which is hazardous for uremic patients, and caramboxin (CBX), which is neurotoxic. The aim of this review is to highlight the nutritional, medicinal and toxicological traits of the star-fruits.
  13. Electrochemical genosensor assay using lyophilized gold nanoparticles/latex microsphere label for detection of Vibrio cholerae
    Liew PS, Lertanantawong B, Lee SY, Manickam R, Lee YH, Surareungchai W
    Talanta, 2015 Jul 1;139:167-73.
    PMID: 25882423 DOI: 10.1016/j.talanta.2015.02.054
    Vibrio cholerae is a Gram-negative bacterium that causes cholera, a diarrheal disease. Cholera is widespread in poor, under-developed or disaster-hit countries that have poor water sanitation. Hence, a rapid detection method for V. cholerae in the field under these resource-limited settings is required. In this paper, we describe the development of an electrochemical genosensor assay using lyophilized gold nanoparticles/latex microsphere (AuNPs-PSA) reporter label. The reporter label mixture was prepared by lyophilization of AuNPs-PSA-avidin conjugate with different types of stabilizers. The best stabilizer was 5% sorbitol, which was able to preserve the dried conjugate for up to 30 days. Three methods of DNA hybridization were compared and the one-step sandwich hybridization method was chosen as it was fastest and highly specific. The performance of the assay using the lyophilized reagents was comparable to the wet form for detection of 1aM to 1fM of linear target DNA. The assay was highly specific for V. cholerae, with a detection limit of 1fM of PCR products. The ability of the sensor is to detect LAMP products as low as 50ngµl(-1). The novel lyophilized AuNPs-PSA-avidin reporter label with electrochemical genosensor detection could facilitate the rapid on-site detection of V. cholerae.
  14. Notes on Amanita section Caesareae from Malaysia
    Tang LP, Lee SS, Zeng NK, Cai Q, Zhang P, Yang ZL
    Mycologia, 2017 12 04;109(4):557-567.
    PMID: 29200380 DOI: 10.1080/00275514.2017.1394789
    Some Amanita specimens collected from Malaysia are critically investigated by morphological examination and molecular analysis of two gene fragments, the nuc rDNA partial 28S (28S) gene and the internal transcriber spacer (ITS1-5.8S-ITS2 = ITS) regions. Six phylogenetic species of Amanita section Caesareae are recognized among the studied collections. One of them is described as new, A. malayensis. Four of the phylogenetic species correspond with existing morphology-based taxa: A. aporema, A. javanica, A. princeps, and A. similis. The remaining species is not described because of the paucity of material. Detailed descriptions and the distribution of these southeastern Asian species are provided, along with a key to the species of section Caesareae from Malaysia.
  15. Job satisfaction of foreign-educated nurses in Malaysia: A cross-sectional study
    Lee SY, Soh KL, Japar S, Ong SL, Soh KG, Tsujita Y
    Belitung Nurs J, 2021;7(5):361-369.
    PMID: 37496510 DOI: 10.33546/bnj.1682
    BACKGROUND: The transition process of migration to work abroad can be challenging and, depending on how it is handled, can impact the job satisfaction level of these foreign-educated nurses. A clear understanding of migrant nurses' job satisfaction is critical for effective translation of nursing practice across the health systems and cultures.

    OBJECTIVE: This study examined the job satisfaction of the foreign-educated nurses in Malaysia, which includes the job satisfaction dimensions and the significant difference between sociodemographic status and job satisfaction.

    METHODS: A cross-sectional survey of 102 foreign-educated nurses working in private hospitals, clinics, hemodialysis centers, nursing homes, and private homes in Malaysia was conducted from September 2017 to March 2018. Data were collected using a structured questionnaire. Descriptive statistics, Mann-Whitney U, and Kruskal Wallis tests were used to analyze the data.

    RESULTS: The study revealed that the participants had a median satisfaction score of 22 (IQR = 19 to 24). Serving the sick and needy and participants' self-respect were the highest satisfaction dimensions among the participants (Median = 3, IQR = 3 to 3). Moreover, the job satisfaction was significantly higher for registered foreign-educated nurses (mean rank = 62.5) than for unregistered foreign-educated nurses (mean rank = 48.65) when working in other countries (p = 0.02). Indian nurses (mean rank = 60.36) also expressed higher satisfaction in terms of working in other countries than Filipino nurses (mean rank = 46.88; p = 0.02). In addition, positive relationships with colleagues and superiors led to higher satisfaction among Indian nurses (mean rank = 61.02) than among Filipino nurses (mean rank = 47.24; p = 0.04). The job satisfaction of male foreign-educated nurses was significantly higher than their female counterparts in terms of self-respect, relationship with fellow nurses and superiors, working in other countries, career development, and ease of finding employment (p < 0.05).

    CONCLUSION: The overall job satisfaction among the foreign-educated nurses in Malaysia is high, mainly when serving the sick and needy, and their degree of self-respect. Understanding job satisfaction among foreign-educated nurses in Malaysia enables the management team to develop effective strategies for addressing nursing shortages and improving the quality of patient care.

  16. Fulltext An Ultrasensitive Voltammetric Genosensor for the Detection of Bacteria Vibrio cholerae in Vegetable and Environmental Water Samples
    Futra D, Tan LL, Lee SY, Lertanantawong B, Heng LY
    Biosensors (Basel), 2023 Jun 04;13(6).
    PMID: 37366981 DOI: 10.3390/bios13060616
    In view of the presence of pathogenic Vibrio cholerae (V. cholerae) bacteria in environmental waters, including drinking water, which may pose a potential health risk to humans, an ultrasensitive electrochemical DNA biosensor for rapid detection of V. cholerae DNA in the environmental sample was developed. Silica nanospheres were functionalized with 3-aminopropyltriethoxysilane (APTS) for effective immobilization of the capture probe, and gold nanoparticles were used for acceleration of electron transfer to the electrode surface. The aminated capture probe was immobilized onto the Si-Au nanocomposite-modified carbon screen printed electrode (Si-Au-SPE) via an imine covalent bond with glutaraldehyde (GA), which served as the bifunctional cross-linking agent. The targeted DNA sequence of V. cholerae was monitored via a sandwich DNA hybridization strategy with a pair of DNA probes, which included the capture probe and reporter probe that flanked the complementary DNA (cDNA), and evaluated by differential pulse voltammetry (DPV) in the presence of an anthraquninone redox label. Under optimum sandwich hybridization conditions, the voltammetric genosensor could detect the targeted V. cholerae gene from 1.0 × 10-17-1.0 × 10-7 M cDNA with a limit of detection (LOD) of 1.25 × 10-18 M (i.e., 1.1513 × 10-13 µg/µL) and long-term stability of the DNA biosensor up to 55 days. The electrochemical DNA biosensor was capable of giving a reproducible DPV signal with a relative standard deviation (RSD) of <5.0% (n = 5). Satisfactory recoveries of V. cholerae cDNA concentration from different bacterial strains, river water, and cabbage samples were obtained between 96.5% and 101.6% with the proposed DNA sandwich biosensing procedure. The V. cholerae DNA concentrations determined by the sandwich-type electrochemical genosensor in the environmental samples were correlated to the number of bacterial colonies obtained from standard microbiological procedures (bacterial colony count reference method).
  17. Detection of high-risk HPV 16 genotypes in cervical cancers using isothermal DNA amplification with electrochemical genosensor
    Nakowong P, Chatchawal P, Chaibun T, Boonapatcharoen N, Promptmas C, Buajeeb W, et al.
    Talanta, 2024 Mar 01;269:125495.
    PMID: 38043336 DOI: 10.1016/j.talanta.2023.125495
    Cervical cancer emerges as the third most prevalent types of malignancy among women on a global scale. Cervical cancer is significantly associated with the persistent infection of human papillomavirus (HPV) type 16. The process of diagnosing is crucial in order to prevent the progression of a condition into a malignant state. The early detection of cervical cancer through initial stage screening is of the utmost significance in both the prevention and effective management of this disease. The present detection methodology is dependent on quantitative polymerase chain reaction (qPCR), which necessitates the use of a costly heat cycler instrument. In this study, we report the development of an electrochemical DNA biosensor integrated with an isothermal recombinase polymerase amplification (RPA) reaction for the detection and identification of the high-risk HPV-16 genotype. The electrochemical biosensor exhibited a high degree of specificity and sensitivity, as evidenced by its limit of detection (LOD) of 0.23 copies/μL of HPV-16 DNA. The validity of this electrochemical platform was confirmed through the analysis of 40 cervical tissues samples, and the findings were consistent with those obtained through polymerase chain reaction (PCR) testing. Our straightforward electrochemical detection technology and quick turnaround time at 75 min make the assay suitable for point-of-care testing in low-resource settings.
  18. Fulltext Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the Hedgehog Mushrooms (Hydnum L.)
    Feng B, Wang XH, Ratkowsky D, Gates G, Lee SS, Grebenc T, et al.
    Sci Rep, 2016 May 06;6:25586.
    PMID: 27151256 DOI: 10.1038/srep25586
    Hydnum is a fungal genus proposed by Linnaeus in the early time of modern taxonomy. It contains several ectomycorrhizal species which are commonly consumed worldwide. However, Hydnum is one of the most understudied fungal genera, especially from a molecular phylogenetic view. In this study, we extensively gathered specimens of Hydnum from Asia, Europe, America and Australasia, and analyzed them by using sequences of four gene fragments (ITS, nrLSU, tef1α and rpb1). Our phylogenetic analyses recognized at least 31 phylogenetic species within Hydnum, 15 of which were reported for the first time. Most Australasian species were recognized as strongly divergent old relics, but recent migration between Australasia and the Northern Hemisphere was also detected. Within the Northern Hemisphere, frequent historical biota exchanges between the Old World and the New World via both the North Atlantic Land Bridge and the Bering Land Bridge could be elucidated. Our study also revealed that most Hydnum species found in subalpine areas of the Hengduan Mountains in southwestern China occur in northeastern/northern China and Europe, indicating that the composition of the mycobiota in the Hengduan Mountains reigion is more complicated than what we have known before.
  19. Machine Learning-Assisted Real-Time Polymerase Chain Reaction and High-Resolution Melt Analysis for SARS-CoV-2 Variant Identification
    Promja S, Puenpa J, Achakulvisut T, Poovorawan Y, Lee SY, Athamanolap P, et al.
    Anal Chem, 2023 Jan 12.
    PMID: 36633573 DOI: 10.1021/acs.analchem.2c05112
    Since the declaration of COVID-19 as a pandemic in early 2020, multiple variants of the severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) have been detected. The emergence of multiple variants has raised concerns due to their impact on public health. Therefore, it is crucial to distinguish between different viral variants. Here, we developed a machine learning web-based application for SARS-CoV-2 variant identification via duplex real-time polymerase chain reaction (PCR) coupled with high-resolution melt (qPCR-HRM) analysis. As a proof-of-concept, we investigated the platform's ability to identify the Alpha, Delta, and wild-type strains using two sets of primers. The duplex qPCR-HRM could identify the two variants reliably in as low as 100 copies/μL. Finally, the platform was validated with 167 nasopharyngeal swab samples, which gave a sensitivity of 95.2%. This work demonstrates the potential for use as automated, cost-effective, and large-scale viral variant surveillance.
  20. Fulltext Using VigiBase to Identify Substandard Medicines: Detection Capacity and Key Prerequisites
    Juhlin K, Karimi G, Andér M, Camilli S, Dheda M, Har TS, et al.
    Drug Saf, 2015 Apr;38(4):373-82.
    PMID: 25687792 DOI: 10.1007/s40264-015-0271-2
    Substandard medicines, whether the result of intentional manipulation or lack of compliance with good manufacturing practice (GMP) or good distribution practice (GDP), pose a significant potential threat to patient safety. Spontaneous adverse drug reaction reporting systems can contribute to identification of quality problems that cause unwanted and/or harmful effects, and to identification of clusters of lack of efficacy. In 2011, the Uppsala Monitoring Centre (UMC) constructed a novel algorithm to identify reporting patterns suggestive of substandard medicines in spontaneous reporting, and applied it to VigiBase(®), the World Health Organization's global individual case safety report database. The algorithm identified some historical clusters related to substandard products, which were later able to be confirmed in the literature or by contact with national centres (NCs). As relevant and detailed information is often lacking in the VigiBase reports but might be available at the reporting NC, further evaluation of the algorithm was undertaken with involvement from NCs.
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