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Fulltext An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies

Axtner J, Crampton-Platt A, Hörig LA, Mohamed A, Xu CCY, Yu DW, et al.

Gigascience, 2019 Apr 01;8(4).
PMID: 30997489 DOI: 10.1093/gigascience/giz029

BACKGROUND: The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation.
FINDINGS: Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples.
CONCLUSIONS: Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.

Matched MeSH terms: Laboratories
Fulltext Clinical and Laboratory Features of JAK2 V617F, CALR, and MPL Mutations in Malaysian Patients with Classical Myeloproliferative Neoplasm (MPN)

Zulkeflee RH, Zulkafli Z, Johan MF, Husin A, Islam MA, Hassan R

Int J Environ Res Public Health, 2021 Jul 16;18(14).
PMID: 34300032 DOI: 10.3390/ijerph18147582

Mutations of JAK2V617F, CALR, and MPL genes confirm the diagnosis of myeloproliferative neoplasm (MPN). This study aims to determine the genetic profile of JAK2V617F, CALR exon 9 Type 1 (52 bp deletion) and Type 2 (5 bp insertion), and MPL W515 L/K genes among Malaysian patients and correlate these mutations with clinical and hematologic parameters in MPN. Mutations of JAK2V617F, CALR, and MPL were analyzed in 159 Malaysian patients using allele-specific polymerase chain reaction, including 76 polycythemia vera (PV), 41 essential thrombocythemia (ET), and 42 primary myelofibrosis (PMF) mutations, and the demographics of the patients were retrieved. The result showed that 73.6% JAK2V617F, 5.66% CALR, and 27.7% were triple-negative mutations. No MPL W515L/K mutation was detected. In ET and PMF, the predominance type was the CALR Type 1 mutation. In JAK2V617F mutant patients, serum LDH was significantly higher in PMF compared to PV and ET. PV has a higher risk of evolving to post PV myelofibrosis compared to ET. A thrombotic event at initial diagnosis of 40.9% was high compared to global incidence. Only one PMF patient had a CALR mutation that transformed to acute myeloid leukemia. JAK2V617F and CALR mutations play an important role in diagnostics. Hence, every patient suspected of having a myeloproliferative neoplasm should be screened for these mutations.

Matched MeSH terms: Laboratories
Fulltext Debilitating Pain and Fractures: a Rare Case of Hypophosphatemic Osteomalacia with Concomitant Vitamin D Deficiency in Neurofibromatosis Type 1

Nagaratnam S, Karupiah M, Mustafa N

J ASEAN Fed Endocr Soc, 2020;35(1):105-108.
PMID: 33442176 DOI: 10.15605/jafes.035.01.17

Hypophosphatemic osteomalacia is a rare form of metabolic bone disorder in neurofibromatosis type 1 (NF1). The exact disease mechanism of this disorder in NF1 is yet to be established. We present a 44-year-old female known to have NF1, who presents with debilitating bone pain, weakness and multiple fractures. Laboratory investigations showed persistent hypophosphatemia with renal phosphate wasting suggestive of hypophosphatemic osteomalacia. She also had concomitant vitamin D deficiency which contributed to the disease severity. Medical therapy with oral phosphate and vitamin D improved her symptoms without significant changes in fracture healing or phosphate levels.

Matched MeSH terms: Laboratories
Fulltext Historical development of the renal histopathology services in Malaysia

Looi LM, Cheah PL

Malays J Pathol, 2009 Jun;31(1):11-6.
PMID: 19694308 MyJurnal

Western-style medicine was introduced to Malaya by the Portuguese, Dutch and British between the 1500s and 1800s. Although the earliest pathology laboratories were developed within hospitals towards the end of the 19th Century, histopathology emerged much later than the biochemistry and bacteriology services. The University Departments of Pathology were the pioneers of the renal histopathology diagnostic services. The Department of Pathology, University of Malaya (UM) received its first renal biopsy on 19 May 1968. Hospital Universiti Kebangsaan Malaysia (HUKM) and Hospital Universiti Sains Malaysia (HUSM) started their services in 1979 and 1987 respectively. It is notable that the early services in these University centres caterred for both the university hospitals and the Ministry of Health (MOH) until the mid-1990s when MOH began to develop its own services, pivoted on renal pathologists trained through Fellowship programmes. Currently, key centres in the MOH are Kuala Lumpur Hospital, Sultanah Aminah Hospital Johor Bahru and Malacca Hospital. With the inclusion of renal biopsy interpretation in the Master of Pathology programmes, basic renal histopathology services became widely available throughout the country from 2000. This subsequently filtered out to the private sector as more histopathologists embraced private practice. There is now active continuing professional development in renal histopathology through clinicopathological dicussions, seminars and workshops. Renal research on amyloid nephropathy, minimal change disease, IgA nephropathy, fibrillary glomerulonephritis, lupus nephritis and microwave technology have provided an insight into the patterns of renal pathology and changing criteria for biopsy. More recently, there has been increasing involvement of renal teams in clinical trials, particularly for lupus nephritis and renal transplant modulation.

Matched MeSH terms: Laboratories/history*; Laboratories/organization & administration
Guidelines on safe laboratory practice (version 1/2004)

College of Pathologists, Academy of Medicine of, Malaysia

Malays J Pathol, 2005 Jun;27(1):71-2.
PMID: 16676698
Matched MeSH terms: Laboratories/standards*
Laboratory accidents--a matter of attitude

Karim N, Choe CK

Malays J Pathol, 2000 Dec;22(2):85-9.
PMID: 16329540

This is a prospective study on accidents occurring in the Pathology laboratories of Hospital Ipoh over the 3-year period from January 1996 to October 1999. 15 mishaps were recorded. The location of the accidents were the histology (40%), microbiology (33%), haematology (20%) and cytology (7%) laboratories. No mishaps were reported from the clinical chemistry, blood bank and outpatient laboratories. Cuts by sharp objects were the most common injuries sustained (47%) followed by splashes and squirts by fluid such as blood or chemicals (27%). There was 1 case each of contact with biohazardous fluid, burn, allergy and accidental drinking of disinfectant. 67% of the accidents involved medical laboratory technicians, 20% involved attendants and the rest were medical officers and the junior laboratory technicians. Although the accidents reported appeared trivial, it is vital to document them and bring them to the attention of all concerned in the laboratory, in order to prevent major accidents and also because of medico-legal implications. The role of the Laboratory Safety Committee cannot be overemphasised. Modification of staff attitude is considered an important remedial goal.

Matched MeSH terms: Laboratories, Hospital*
External quality assurance in Malaysia

Nawawi H, Lim HH, Zakiah I

Southeast Asian J. Trop. Med. Public Health, 1999;30 Suppl 3:39-45.
PMID: 10926257

An activity supportive of the MOH QA Programme, the National EQAS for clinical chemistry monitors for analytical performance in core routine biochemical testing by the pathology laboratories, with unsatisfactory performance scores serving to alert against deficiencies or problems and the scores in subsequent challenges providing the feedback of effectiveness of remedial actions taken. While unacceptable individual analyte performance score (variance index score, VIS) indicated problems in instruments, reagent and calibrators, or the use of inherently poorer methods, repeated occurrence of unsatisfactory OMRVIS was traceable to generally poor laboratory management of usually inadequately-equipment small laboratories. The outcome has been one of slow but gradual improvement in the overall performance of participating laboratories, with a move towards methods upgrading and standardization to achieve greater concordance of results. Presently, the programme is limited to 61 government and 4 private hospital laboratories in the country for 12 commonly assayed clinical biochemistry analytes. It is hoped that the NEQAS could be extended to the other private laboratories and that of academic institutions. However, this is dependent to a large extent on the manpower and financial support obtainable by the organizing body of the programme in the future. Belk and Sunderman, 1947 demonstrated that laboratories participating in an quality assessment scheme could rapidly and dramatically improve their analytical performance. In some countries, participation has become mandatory, and acceptable performance is a requirement in laboratory accreditation. The need and value of the NEQAP is, therefore, evident. While there may be limitations in the national programme. efforts are being made at improving the programme within the means and resources of the organising body. The goals of the NEQAP are not just to monitor performance but also to educate. On this, matters related to and supportive of these goals have also been pursued. The annual workshop/forum on quality controls had allowed exchange of information between representatives of participating laboratories and the organising body. Recently in the 1997 MOH Quality Improvement evaluation, Quality Control has been evaluated together with the other 17 such activities. The study on knowledge, attitude and practice has provided the necessary feedback and will be used for future planning in making efforts at increasing the effectiveness and benefits of the all QC activities including this NEQAP for clinical chemistry. In addition, there is a need to look into areas such as selection of methods and test systems, and improvement of continuing education, training as well as research in quality improvement as suggested by the Quality Improvement evaluation.

Matched MeSH terms: Laboratories, Hospital/standards*
The pattern of bacteriological cultures in a state laboratory

Lim Swee Eng, Bin Mohamed Hussain AH

Med J Malaysia, 1973 Dec;28(2):103-8.
PMID: 4276266
Matched MeSH terms: Laboratories*
Exploring ligand-protein interaction: A laboratory exercise on herbicide binding to plasma transport protein

Roslan AA, Tayyab S

Biochem Mol Biol Educ, 2019 03;47(2):156-160.
PMID: 30629781 DOI: 10.1002/bmb.21207

A laboratory exercise on the interaction between the herbicide pendimethalin (PM) and goat serum albumin (GSA), a carrier protein present in mammalian blood circulation, is described. Fluorescence spectroscopy was used to study the binding reaction between PM and GSA. Titration of a constant amount of the protein (GSA) with increasing ligand (PM) concentrations produced a consecutive decrease in the protein's fluorescence. Treatment of the fluorescence quenching data according to the Stern-Volmer equation yielded the values of the Stern-Volmer constant (Ksv ) and bimolecular quenching rate constant (kq ), whereas values of the binding constant (Ka ) and number of binding sites (n) were obtained from the double logarithmic plot. This experiment provides an exciting opportunity for undergraduate students to independently perform ligand binding studies with a protein, in addition to providing the means for the determination of their binding parameters. © 2019 International Union of Biochemistry and Molecular Biology, 47(2): 156-160, 2019.

Matched MeSH terms: Laboratories*
Sunway Medical Laboratory Quality Control Plans Based on Six Sigma, Risk Management and Uncertainty

Jairaman J, Sakiman Z, Li LS

Clin. Lab. Med., 2017 Mar;37(1):163-176.
PMID: 28153364 DOI: 10.1016/j.cll.2016.09.013

Sunway Medical Centre (SunMed) implemented Six Sigma, measurement uncertainty, and risk management after the CLSI EP23 Individualized Quality Control Plan approach. Despite the differences in all three approaches, each implementation was beneficial to the laboratory, and none was in conflict with another approach. A synthesis of these approaches, built on a solid foundation of quality control planning, can help build a strong quality management system for the entire laboratory.

Matched MeSH terms: Laboratories/standards*
Fulltext Reliability and validity of job content questionnaire for university research laboratory staff in Malaysia

Nehzat F, Huda BZ, Tajuddin SH

Southeast Asian J. Trop. Med. Public Health, 2014 Mar;45(2):481-9.
PMID: 24968690

Job Content Questionnaire (JCQ) has been proven a reliable and valid instrument to assess job stress in many countries and among various occupations. In Malaysia, both English and Malay versions of the JCQ have been administered to automotive workers, schoolteachers, and office workers. This study assessed the reliability and validity of the instrument with research laboratory staff in a university. A cross sectional study was conducted among 258 research laboratory staff in Universiti Putra Malaysia (UPM). Malaysian laboratory staff who have worked for at least one year were randomly selected from nine faculties and institutes in the university that have research laboratory. A self-administered English and Malay version of Job Content Questionnaire (JCQ) was used. Three major scales of JCQ: decision latitude, psychological job demands, and social support were assessed. Cronbach's alpha coefficients of two scales were acceptable, decision latitude and psychological job demands (0.70 and 0.72, respectively), while Cronbach's alpha coefficient for social support (0.86) was good. Exploratory factor analysis showed five factors that correspond closely to the theoretical construct of the questionnaire. The results of this research suggest that the JCQ is reliable and valid for examining psychosocial work situations and job strain among research laboratory staff. Further studies should be done for confirmative results, and further evaluation is needed on the decision authority subscale for this occupation.

Matched MeSH terms: Laboratories/manpower*
A large exposure to Brucella melitensis in a diagnostic laboratory

Sam IC, Karunakaran R, Kamarulzaman A, Ponnampalavanar S, Syed Omar SF, Ng KP, et al.

J Hosp Infect, 2012 Apr;80(4):321-5.
PMID: 22237130 DOI: 10.1016/j.jhin.2011.12.004

Brucella species are easily transmitted by aerosols and can be acquired in the laboratory.

Matched MeSH terms: Laboratories, Hospital*
Fulltext Simultaneous optimization of nanocrystalline SnO2 thin film deposition using multiple linear regressions

Ebrahimiasl S, Zakaria A

Sensors (Basel), 2014;14(2):2549-60.
PMID: 24509767 DOI: 10.3390/s140202549

A nanocrystalline SnO2 thin film was synthesized by a chemical bath method. The parameters affecting the energy band gap and surface morphology of the deposited SnO2 thin film were optimized using a semi-empirical method. Four parameters, including deposition time, pH, bath temperature and tin chloride (SnCl2·2H2O) concentration were optimized by a factorial method. The factorial used a Taguchi OA (TOA) design method to estimate certain interactions and obtain the actual responses. Statistical evidences in analysis of variance including high F-value (4,112.2 and 20.27), very low P-value (<0.012 and 0.0478), non-significant lack of fit, the determination coefficient (R2 equal to 0.978 and 0.977) and the adequate precision (170.96 and 12.57) validated the suggested model. The optima of the suggested model were verified in the laboratory and results were quite close to the predicted values, indicating that the model successfully simulated the optimum conditions of SnO2 thin film synthesis.

Matched MeSH terms: Laboratories
Fulltext A survey of therapeutic drug monitoring services in Malaysia

Ab Rahman AF, Ahmed Abdelrahim HE, Mohamed Ibrahim MI

Saudi Pharm J, 2013 Jan;21(1):19-24.
PMID: 23960816 DOI: 10.1016/j.jsps.2012.01.002

In Malaysia, therapeutic drug monitoring (TDM) service was started in the 1980s. Since then, the number of hospitals that offer the service has increased. In this paper, we report the findings of a nationwide survey describing the practice of TDM in these hospitals. Questionnaires were mailed to 128 government hospitals. Data were collected for general characteristics of the hospitals, administrative, and laboratory activities related to TDM service. One hundred and twenty-one hospitals responded to the survey. Thirty-four hospitals (28.1%) provided the service with their own TDM laboratories, 44 hospitals (36.4%) provided the service using other hospitals' laboratories and 43 hospitals (35.5%) did not provide the service at all. TDM services were more likely to be offered in larger hospitals with various medical specialties. Since it is managed entirely by hospital pharmacists, these pharmacists assume an important role in ensuring optimum use of the TDM service.

Matched MeSH terms: Laboratories, Hospital
Fulltext Clinically lesser known entity in India: A Report of two cases of Melioidosis

Barman P, Kaur R, Kumar K

Indian J Crit Care Med, 2013 Jan;17(1):46-8.
PMID: 23833477 DOI: 10.4103/0972-5229.112146

Melioidosis is endemic in the South Asian regions, like Thailand, Singapore Malaysia and Australia. The disease is more pronounced in the southern part of the country. It is caused by Burkholderia pseudomallei which causes systemic involvement, morbidity and mortality associated with the disease is high. Due to highly varied clinical presentation, and low general awareness this infection is largely underdiagnosed and under reported in our country. Most laboratories in the country still rely on conventional culturing methods with their low sensitivity, adding to the under reporting. To enhance physician awareness we describe here two cases who presented to our institute after months of misdiagnosis.

Matched MeSH terms: Laboratories
A shelf-stable fluorogenic isothermal amplification assay for the detection of Burkholderia pseudomallei

Michelle Wong Tzeling J, Yean Yean C

Analyst, 2016 Feb 21;141(4):1246-9.
PMID: 26783560 DOI: 10.1039/c5an01741f

A shelf-stable loop-mediated isothermal amplification (LAMP) reagent for Burkholderia pseudomallei detection is described. The coupling of LAMP reagents with the indirect colorimetric indicator and consequently its lyophilization enable the simple evaluation of results without the need for any advance laboratory instruments. The reagents were found to have a stable shelf life of at least 30 days with well-maintained sensitivity and specificity.

Matched MeSH terms: Laboratories
Fulltext Chest Radiograph Findings In Novel Swine-Origin Influenza A (H1N1) Virus (S-OIV) Infection: A UKMMC Experience

Norzailin AB, Norhafizah E

Med J Malaysia, 2015 Apr;70(2):93-7.
PMID: 26162384 MyJurnal

OBJECTIVE: 1.To evaluates and recognizes findings in chest radiograph in patients with laboratory-confirmed S-OIV (H1N1) infection treated at UKMMC. 2. To evaluate whether the findings on initial chest radiographs of influenza A (H1N1) patients can help to predict the prognosis.

MATERIAL AND METHODS: Total of 109 adult patients presenting to the Universiti Kebangsaan Malaysia Medical Centre (UKMMC) with flu-like symptoms who were positive for influenza A and these patients had underwent chest radiographs (CXR). The initial CXRs were evaluated for the pattern (consolidation, ground-glass, and reticulation), distribution, and extend of abnormality. The disease is classifies by the clinical severity (mild, moderate or severe illness) and adverse outcome (ventilated, death or recovered well).

RESULTS: The initial CXRs were normal in 56% of cases. The predominant radiographic finding was consolidation, most commonly involving the middle and lower zones (35% of cases). There is no significant association between initial CXR findings with the patient clinical outcome either fully recovered or death/ ventilated.

CONCLUSION: Normal chest radiographs is the most common radiographic finding in S-OIV (H1N1) infection and the most common abnormal lung finding is consolidation. Initial chest radiographs did not determine the patient clinical outcome and a normal initial radiograph could not exclude adverse outcome.

Matched MeSH terms: Laboratories
Fulltext Fine Particle Emissions From Tropical Peat Fires Decrease Rapidly With Time Since Ignition

Roulston C, Paton-Walsh C, Smith TEL, Guérette ÉA, Evers S, Yule CM, et al.

J Geophys Res Atmos, 2018 May 27;123(10):5607-5617.
PMID: 30167349 DOI: 10.1029/2017JD027827

Southeast Asia experiences frequent fires in fuel-rich tropical peatlands, leading to extreme episodes of regional haze with high concentrations of fine particulate matter (PM2.5) impacting human health. In a study published recently, the first field measurements of PM2.5 emission factors for tropical peat fires showed larger emissions than from other fuel types. Here we report even higher PM2.5 emission factors, measured at newly ignited peat fires in Malaysia, suggesting that current estimates of fine particulate emissions from peat fires may be underestimated by a factor of 3 or more. In addition, we use both field and laboratory measurements of burning peat to provide the first mechanistic explanation for the high variability in PM2.5 emission factors, demonstrating that buildup of a surface ash layer causes the emissions of PM2.5 to decrease as the peat fire progresses. This finding implies that peat fires are more hazardous (in terms of aerosol emissions) when first ignited than when still burning many days later. Varying emission factors for PM2.5 also have implications for our ability to correctly model the climate and air quality impacts downwind of the peat fires. For modelers able to implement a time-varying emission factor, we recommend an emission factor for PM2.5 from newly ignited tropical peat fires of 58 g of PM2.5 per kilogram of dry fuel consumed (g/kg), reducing exponentially at a rate of 9%/day. If the age of the fire is unknown or only a single value may be used, we recommend an average value of 24 g/kg.

Matched MeSH terms: Laboratories
Impact of the COVID-19 pandemic on cytology practice: An international survey in the Asia-Pacific region

Wang YH, Bychkov A, Chakrabarti I, Jain D, Liu Z, He S, et al.

Cancer Cytopathol, 2020 Dec;128(12):895-904.
PMID: 32931161 DOI: 10.1002/cncy.22354

BACKGROUND: The purpose of the current study was to examine the impact of coronavirus disease 2019 (COVID-19) on various aspects of cytology practice in the Asia-Pacific region.
METHODS: An online questionnaire was distributed to cytopathology laboratories in 24 Asia-Pacific countries to explore the impact of restrictive measures on access to health care, use of general and personal protective equipment (PPE), and changes in cytology workflow and workload from February to April 2020.
RESULTS: A total of 167 cytopathology laboratories from 24 countries responded to the survey; the majority reported that restrictive measures that limited the accessibility of health care services had been implemented in their cities and/or countries (80.8%) and their hospitals (83.8%). The respondents noted that COVID-19 had an impact on the cytologic workflow as well as the workload. Approximately one-half of the participants reported the implementation of new biosafety protocols (54.5%) as well as improvements in laboratory facilities (47.3%). Rearrangement or redeployment of the workforce was reported in 53.3% and 34.1% of laboratories, respectively. The majority of the respondents reported a significant reduction (>10%) in caseload associated with both gynecological (82.0%) and nongynecological specimens (78.4%). Most laboratories reported no significant change in the malignancy rates of both gynecological (67.7%) and nongynecological specimens (58.7%) compared with the same period in 2019.
CONCLUSIONS: The results of the survey demonstrated that the COVID-19 pandemic resulted in a significant reduction in the number of cytology specimens examined along with the need to implement new biosafety protocols. These findings underscore the need for the worldwide standardization of biosafety protocols and cytology practice.

Matched MeSH terms: Laboratories, Hospital/organization & administration*; Laboratories, Hospital/standards; Laboratories, Hospital/statistics & numerical data
Fulltext Evaluation of the Effects of Cement and Lime with Rice Husk Ash as an Additive on Strength Behavior of Coastal Soil

Eliaslankaran Z, Daud NNN, Yusoff ZM, Rostami V

Materials (Basel), 2021 Feb 28;14(5).
PMID: 33670914 DOI: 10.3390/ma14051140

Coastal accretion and erosion are unavoidable processes as some coastal sediments undergo modification and stabilization. This study was conducted to investigate the geotechnical behavior of soil collected from Bagan Lalang coast and treated with lime, cement, and rice husk ash (RHA) to design a low-cost alternative mixture with environmentally friendly characteristics. Laboratory tests were carried out to analyze the physical properties of the soil (Atterberg limits and compaction properties), together with mechanical characteristics (direct shear and unconfined compressive strength (UCS) tests) to determine the effect of different ratios of stabilizer/pozzolan on the coastal soil and the optimum conditions for each mixture. Part of the purpose of this study was also to analyze the shear behavior of the coastal soil and monitor the maximum axial compressive stress that the treated specimens can bear under zero confining pressure. Compared to the natural soil, the soil treated with lime and rice husk ash (LRHA) in the ratio of 1:2 (8% lime content) showed a tremendous increase in shear stress under the normal stress of 200 kPa. The strength parameters such as the cohesion (c) and internal friction angle (ϕ) values showed a significant increase. Cohesion values increased considerably in samples cured for 90 days compared to specimens cured for 7 days with additional LRHA in the ratio of 1:2 (28%).

Matched MeSH terms: Laboratories

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