Automated nucleic acid extractors machines which prepare samples efficiently from a variety of materials using purification System, which offers highly versatile, automated magnetic-particle processing for DNA/RNA, protein or cell purification from virtually any source. Using revolutionary magnetic particle separation technology, this system provides excellent reproduciblity and quality.
Real-time PCR, also known as quantitative PCR (qPCR), is the gold-standard for sensitive, specific detection and quantification of nucleic acid (DNA/RNA) targets. Real-time PCR/qPCR assays have become the tool of choice for the rapid and sensitive determination and quantitation of nucleic acid in various biological samples, with diverse applications such as, molecular diagnostics, gene expression analysis and cancer phenotyping. AICBU have powerful, precise, and flexible real-time PCR detection systems with advanced optical technology to deliver sensitive, reliable detection for singlexplex or multiplex reactions.
Droplet PCR is a second-generation digital PCR system provides absolute quantification of target DNA or RNA molecules using EvaGreen or TaqMan Hydrolysis Probes. Unmatched sensitivity and precision for various applications such as Cancer biomarker studies and copy number variation, Pathogen detection, Gene expression analysis etc
Ariyaratne, D., Gomes, L., Jayadas, T.T.P., Kuruppu, H., Kodituwakku, L., Jeewandara, C., Pannila Hetti, N., Dheerasinghe, A., Samaraweera, S., Ogg, G. and Malavige, G., 2022. Epidemiological and virological factors determining dengue transmission in Sri Lanka during the COVID-19 pandemic. PLOS Global Public Health, 2(8), p.e0000399.
Jeewandara, C., Guruge, D., Pushpakumara, P., Madhusanka, D., Jayadas, T.T.P., Chaturanga, I., Aberathna, I., Danasekara, S., Pathmanathan, T., Jayathilaka, D., Somathilaka, G., Kuruppu, H., Gomes, L., Gunasekara, V., Wijayamuni, R., Ogg, G. and Malavige, G., 2022. Sensitivity and specificity of two WHO approved SARS-CoV2 antigen assays in detecting patients with SARS-CoV2 infection. BMC Infectious Diseases, 22(1).
Gomes, L., Jeewandara, C., Jayadas, T.T.P., Dissanayake, O., Harvie, M., Guruge, D., Withanage, V., Mahesh, P., Rajapakse, W., Ramachandran, R., Dharmarajan, V., Pathiraja, I., Sanjeewani, A., Bandara, P., Nanayakkara, G., Francis, V., Kithsiri, A., Edirisinghe, D., De Silva, K., Wijayamuni, R., Ogg, G., Waggoner, J. and Malavige, G. ( 2021). Surveillance of SARS-CoV2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. Journal of Virological Methods, 300, p.114374.
The instrument
Illumina’s “sequencing by synthesis” (SBS) chemistry is a widely adopted sequencing technique in the modern scientific world which has generated ~90% of the publicly available genome sequencing data. SBS chemistry uses fluorescently labeled nucleic acid bases that bind to the complementary bases of the original DNA strand from the sample at each sequencing cycle generating a sequence with an accuracy of 99.9% (Q30). NextSeq550 is one of the mid-high range benchtop sequencers of Illumina that supports massively parallel (120 Gigabase output) sequencing and DNA microarray experiments.
External uses
NextSeq550 platform can be used to perform targeted sequencing, metagenomics, whole genome sequencing of viruses and bacteria, and even human transcriptome and exome sequencing for research purposes.
The instrument
The iSeq100 is a small benchtop sequencer that uses semiconductor chip sequencing technology combined with a single channel of Illumina’s proprietary sequencing by synthesis (SBS) chemistry. Even though the iSeq100 cannot generate a high throughput like other Illumina sequencers, its output of 1.2 Gigabases is sufficient for small-scale sequencing experiments without the loss of accuracy.
External uses
The iSeq 100 System is capable of handling small whole-genome experiments such as bacteria, viruses, and plasmid sequencing as well as targeted sequencing of a set of genes or gene regions, gene expression analysis, or 16S metagenomics.
Ranasinghe, D, Jayathilaka, D., Jeewandara, C, Gunasinghe, D, Ariyaratne, D, Pramanayagam Jayadas, T, Kuruppu, H, Wijesinghe, A, Bary, F, Madusanka, D, Darshana, P, Guruge, D, Wijayamuni, R, Ogg, G. and Malavige, G. Molecular epidemiology of AY.28 and AY.104 delta sub-lineages in Sri Lanka (2022). 10.3389/fpubh.2022.873633
Ranasinghe D, Jayadas TTP, Jayathilaka D, Jeewandara C, Dissanayake O, Guruge D, Ariyarathne D, Gunasinghe D, Gomes L, Wijesinghe A, Wijayamuni R, De Silva T, Ogg GS, Malavige GN. Comparison of different sequencing techniques with multiplex real-time PCR for detection of SARS-CoV-2 variants of concern (2021). 10.1371/journal.pone.0265220
Jeewandara C, Jayathilaka D, Ranasinghe D, Hsu NS, Ariyaratne D, Jayadas TT, Panambara Arachchige DM, Lindsey BB, Gomes L, Parker MD, Wijewickrama A, Karunaratne M, Ogg GS, de Silva TI and Malavige GN (2021) Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka. Microbiol. 12:722838. doi: 10.3389/fmicb.2021.722838
Deshni Jayathilaka, Chandima Jeewandara, Diyanath Ranasinghe, Dinuka Ariyaratna, Laksiri Gomes, AnandaWijewickrama, Graham S. Ogg, Gathsaurie Neelika Malavige; Comparison of Respiratory Microbiome in patients who cleared virus early vs prolong shedders in COVID 19 disease; British Society of Immunology virtual conference, December 2020
Jeewandra C, Jayathilaka DC, Ranasinghe D, Ariyaratne MHJD, Gomes L, Wijewickrama A, Karunaratne M, Malavige GN; WGS Metagenomics Vs Targeted sequencing: which is better for pathogen identification and characterization; COVIDCON, February 2021
Jeewandara C, Jayathilaka DC, Ariyaratne MHJD, Ranasinghe D, Gomes L, Wijewickrama A, Karunaratne M, Ogg GS, Malavige GN; D614g mutation associated with higher transmission in Sri Lankan SARS-COV2 virus strains; The Asia-Pacific Academic Consortium for Public Health (APACPH) virtual conference, December 2020
Jeewandara C, Jayathilaka DC, Ariyaratna MHJD, Gomes L, Ranasinghe D, Wijewickrama A, Karunaratne M, Ogg G.S, Silva T, Malavige GN; Characterization of SARS-CoV2 strains in Sri Lanka by whole genome sequencing; Ceylon College of Physicians Annual Conference November 2020.
Jeewandara, D. Jayathilaka, D. Ranasinghe, D. Ariyaratne, T.T.P. Jayadas, Madhusanka D, L. Gomes, B. Lindsey, M. Parker, A. Wijewickrama, M. Karunaratne, G. Ogg, T. de Silva, G.N. Malavige; A new SARS-CoV-2 lineage (B.1.411) is driving the recent large pandemic; European Congress of Clinical Microbiology & Infectious Diseases (ECCMID), July 2021
The instrument
MinION is a powerful portable sequencing device that delivers immediate access to gigabases of long-read data. The pocket-sized, USB-powered MinION allows us to sequence anything, anywhere-from the bench to the field, with real time analysis providing immediate access to actionable results.
External uses
The MinION is capable of sequencing whole genomes/exomes, whole transcriptome(cDNA), smaller transcriptomes (direct RNA) and can be used in targeted sequencing, metagenomics and multiplexing for smaller samples.
Ranasinghe, D, Jayathilaka, D., Jeewandara, C, Gunasinghe, D, Ariyaratne, D, Pramanayagam Jayadas, T, Kuruppu, H, Wijesinghe, A, Bary, F, Madusanka, D, Darshana, P, Guruge, D, Wijayamuni, R, Ogg, G. and Malavige, G. Molecular epidemiology of AY.28 and AY.104 delta sub-lineages in Sri Lanka (2022). 10.3389/fpubh.2022.873633
Ranasinghe D, Jayadas TTP, Jayathilaka D, Jeewandara C, Dissanayake O, Guruge D, Ariyarathne D, Gunasinghe D, Gomes L, Wijesinghe A, Wijayamuni R, De Silva T, Ogg GS, Malavige GN. Comparison of different sequencing techniques with multiplex real-time PCR for detection of SARS-CoV-2 variants of concern (2021). 10.1371/journal.pone.0265220
Diyanath Ranasinghe, Chandima Jeewandara, Deshni Jayathilaka, Dinuka Ariyaratne, Tibutius Thanesh Jayadas, Deshan Madushanka, Laksiri Gomes, Matthew D. Parker, Ananda Wijewickrama , Malika Karunaratne , Graham S. Ogg , Gathsaurie Neelika Malavige; Sub-genomic RNA Expression in SARS-CoV-2 B.1.411 and B.1.1.7 Infections in Sri Lanka; International Society for Infectious Diseases (IMED), November, 2021.
The instrument
The cobas e 411 analyzer is a fully automated analyzer which uses Electrochemiluminescence (ECL) technology for immune assays. Our analyzer has a disk sample handling system. oth quantitative and qualitative in vitro assay determinations for a broad range of applications
External uses
ECL technology has a wide range of applications in quantitative and qualitative in vitro assay determinations including anemia; bone, cardiac and tumor markers; critical care; fertility/hormones; maternal care; and infectious diseases
Jeewandara C, Aberathna IS, Gomes L, Pushpakumara PD, Danasekara S, Guruge D, Ranasinghe T, Gunasekera B, Kamaladasa A, Kuruppu H, Somathilake G, Dissanayake O, Gamalath N, Ekanayake D, Jayamali J, Jayathilaka D, Mudunkotuwa A, Harvie M, Nimasha T, Wijayamuni R, Schimanski L, Rijal P, Tan TK, Dong T, Townsend A, Ogg GS, Malavige GN. Jeewandara C, et al. Immun Inflamm Dis. 2022 Apr;10(4):e592. doi: 10.1002/iid3.592. Immun Inflamm Dis. 2022. PMID: 35349749 Free PMC article.
Instrument
ELLA (version 3.4.0.52, Protein Simple, USA) is a fully automated immunoassay instrument that allows fast performance of ELISA assays without any manual steps. This system uses cartridges that allow the measurements of biomarkers in different types of samples. The cartridges use microfluidics based technology that enables the measurements of single analytes, multiple analytes and also multiplexed analytes. The results obtained using the ELLA is highly sensitive and reproducible. This system allows the researcher to perform an automated immunoassay and automatically process the data acquired. It also allows the researcher to view, analyse, and extract and save fluorescence and concentration data to be used for further analysis.
Dayarathna, S., Jeewandara, C., Gomes, L. et al. Similarities and differences between the ‘cytokine storms’ in acute dengue and COVID-19. Sci Rep 10, 19839 (2020). https://doi.org/10.1038/s41598-020-76836-2
The basic 96- and 384-well plate EliSpot & FluoroSpot Reader
The AID iSpot is one of the most successful EliSpot/FluoroSpot Reader developments in recent years. The AID iSpot for the first time allows analyzing both: Enzymatic and fluorescent (FluoroSpot) based EliSpot assays. The AID iSpot comprises the same outstanding functionality, such as layout-generator, rule-compiler, various export possibilities etc., as the AID Classic. Beside all of the popular functions of the AID Classic, the AID iSpot simultaneously allows for 1-, 2- or even 3-color FluoroSpot analysis. A simple “one-click switch” between enzymatic and fluorescent mode, without the need of hardware changes, is enough to switch from one mode to the other.
ELISA is an abbreviation for “Enzyme Linked Immunosorbent Assay” and is a common laboratory technique. We use this technique to measure the analyte’s (antibodies or antigens most likely) concentration in solutions. The wavelength of the coloured end product is the indicator of the amount of analytes in the original sample which is then measure via the ELISA plate reader.
Jeewandara et al., “Immune responses following the first dose of the Sputnik V (Gam-COVID-Vac),” Sci. Reports 2022 121, vol. 12, no. 1, pp. 1–10, Feb. 2022, doi: 10.1038/s41598-022-05788-6.
P. D. Pushpakumara et al., “Identification of Immune Responses to Japanese Encephalitis Virus Specific T Cell Epitopes,” Front. Public Heal., vol. 8, Feb. 2020, doi: 10.3389/fpubh.2020.00019.
C. Jeewandara et al., “Persistence of immune responses to the Sinopharm/BBIBP-CorV vaccine,” Immunity, Inflamm. Dis., vol. 10, no. 6, p. e621, Jun. 2022, doi: 10.1002/IID3.621.
C. Jeewandara et al., “Immune responses to a single dose of the AZD1222/Covishield vaccine in health care workers,” Nat. Commun., vol. 12, no. 1, Dec. 2021, doi: 10.1038/s41467-021-24579-7.
C. Jeewandara et al., “Immune responses to Sinopharm/BBIBP-CorV in individuals in Sri Lanka,” Immunology, vol. 167, no. 2, pp. 275–285, Oct. 2022, doi: 10.1111/IMM.13536.
P. D. Pushpakumara et al., “Development and validation of an assay for detection of Japanese encephalitis virus specific antibody responses,” PLoS One, vol. 15, no. 10, p. e0238609, Oct. 2020, doi: 10.1371/journal.pone.0238609.
C. Jeewandara et al., “Seroprevalence of SARS-CoV-2 Infection in the Colombo Municipality Region, Sri Lanka,” Front. public Heal., vol. 9, Nov. 2021, doi: 10.3389/FPUBH.2021.724398.
The instrument
Luminex is a multiplex bead-based immunoassay technology based on internally dyed microspheres. Unlike ELISA, the immune complexes are developed on unique fluorescent magnetic microspheres enabling the simultaneous detection of multiple analytes in a single reaction mixture.
External uses
Luminex MAGPIX ® System is ideal when it’s required to detect multiple analytes such as cytokines and antibodies in samples with limited volume.
Deshni Jayathilaka, Chandima Jeewandara, Laksiri Gomes, Tibutius Thanesh Pramanayagam Jayadas, Achala Kamaladasa, Gayasha Somathilake, Dinuka Guruge, Pradeep Darshana Pushpakumara, Thushali Ranasinghe, Inoka Sepali Aberathna, Saubhagya Danasekara, Buddini Gunathilaka, Heshan Kuruppu, Ananda Wijewickrama, Ruwan Wijayamuni, Lisa Schimanski, T K Tan, Graham S Ogg, Alain Townsend, Gathsaurie Neelika Malavige, Kinetics of immune responses to SARS-CoV-2 proteins in individuals with varying severity of infection and following a single dose of the AZD1222, Clinical and Experimental Immunology, Volume 208, Issue 3, June 2022, Pages 323–331
Peggy Sue (bio-techne, Proteinsimple, USA) is a fully automated system performing simple Western assays i.e., automated Western without gels, transfer devices, blots and films. It is capable of performing both size-based and charge-based assays. Upon completion of the run, complete run report with an automated analysis can be obtained which can be further analysed using Compass SW software. 384 well plate in which protein samples are loaded with primary and secondary antibodies, luminol peroxide, antibody diluents, sample buffers along with stacking and separation matrices in separate wells is kept in the sample tray. Running and washing buffers are loaded into the resource tray along with capillary boxes. Peggy Sue automates all the steps of the traditional SDS-PAGE and Western blot, from loading the samples into capillaries, protein separation, immunoprobing/labelling, washing, detection and data analysis. Up to 96 samples can be processed in a single run of 8 cycles (12×8).
Jeewandara, C., Aberathna, I. S., Dayarathna, S., Nimasha, T., Ranasinghe, T., Jayamali, J., … & Malavige, G. N. (2022). Comparison of the kinetics and magnitude of antibody responses to different SARS-CoV-2 proteins in Sinopharm/BBIBP-CorV vaccinees following the BNT162b2 booster or natural infection. Plos one, 17(10), e0274845.
The AICBU flow cytometry lab is equipped with state-of-the-art technology. Flow cytometry is frequently used in research projects involving infections (Dengue, SARS-CoV2), immunodeficiency and vaccine studies.
The guava EasyCyte is fitted with 3 lasers (405, 488, 642) and can analyze up to 10 colours. This is an easy-to-use flow cytometer which is better suited for smaller sample numbers.
The FACSARIA III is a high-speed fixed-alignment benchtop cell sorter which is highly sensitive and can handle high-throughput. This is equipped with 3 lasers (488, 561, 633) and can assay up to 13 colours. Cell sorting can be done to tubes or 96-well plates.
Jeewandara C, Guruge D, Pushpakumara PD, Kamaladasa A, Aberathna IS, Ramu ST, Gunasekera B, Wijesinghe A, Dissanayake O, Kuruppu H, Ranasinghe T, Jayathilaka D, Dayarathna S, Ekanayake D, Jayamali J, Gamalath N, Mudunkotiwa A, Somathilake G, Dissanayake M, Harvie M, Nimasha T, Madusanka D, Jayadas T, Wijayamuni R, Schimanski L, Rijal P, Tan TK, Townsend A, Ogg GS, Malavige GN. Immune Responses to a Single Dose of the AZD1222/Covishield Vaccine at 16 Weeks in Individuals in Sri Lanka. J Immunol 2021 Dec 1;207(11):2681-2687. doi: 10.4049/jimmunol.2100762. Epub 2021 Nov 8. PMID: 34750205.
Jayaratne, H.E., Wijeratne, D., Fernando, S., Kamaladasa, A., Gomes, L., Wijewickrama, A., Ogg, G.S. and Malavige, G.N. (2018), Regulatory T-cells in acute dengue viral infection. Immunology, 154: 89-97. https://doi.org/10.1111/imm.12863
This is used as the gold standard for allergy diagnosis. The Phadia 250 instrument provides the kind of flexibility that enables medium-sized labs to run ImmunoCAP™ tests in a variety of workflow settings. A Large allergen test menu covering more than 500 whole allergens and mixes and 100 allergen components is available. Throughput up to 60 results/hour.
LuxScan 10K Microarray Scanner is a compact high performance system for microarray imaging and data analysis of DNA, protein and cell arrays. Its advanced systems for optics, signal processing and motion control provide superior scan accuracy, and high detection sensitivity over a wide linear dynamic range. With optimized signal acquisition and processing elements, it is an ideal tool for profiling fluorescent-labelled microarrays.
In this laboratory it is used to tread the ISAC ImmunoCAP test chip which can read 112 allergens with one serum sample.
The EUROBlotOne is a compact tabletop device for complete processing of immunoblots. Following the fast and convenient software-guided loading, the system performs the identification and dilution of samples as well as all incubation and wash steps. Eight reagent channels allow the combination of tests from the areas of autoimmune and infection diagnostics in one run. The incubated strips are then automatically dried and the results are generated through the software programs.
The EUROIMMUN Analyzer I-2P is an open system for fully automated ELISA processing of up to 3 microplates and 144 patient samples in one run. The combination of EUROIMMUN ELISAs and EUROIMMUN Analyzer I-2P enables a quick and simple, but also a secure routine operation, owing to the automatic recognition and allocation of reagents and the import of QC data via Data Matrix codes. The results are automatically generated through the inbuilt software.
The EUROIMMUN Sprinter XL offers a flexible solution for fully automated processing of immunofluorescence tests for medium and high sample volumes. The device performs identification, dilution and transfer of samples, as well as all washing and incubation steps. The Sprinter XL can also be used as combination devices for additional processing of ELISAs.
The LED fluorescence microscope EUROStar III Plus has been precisely tailored to the requirements of indirect immunofluorescence. A camera is attached directly to the integrated photo tube for capturing digital images. The EUROStar III Plus includes a halogen lamp as standard equipment for normal transmitted light microscopy in bright and dark field and can be upgraded for phase contrast work.
The cell culture facilities provided in our lab enable researchers to carry out cell work by providing them with the necessary space, equipment and the necessary reagents and consumables.
The cell culture lab is equipped with the following equipment:
Wijesinghe, A., Gamage, J., Goonewardena, H. et al. Phenotype and functionality of follicular helper T cells in patients with acute dengue infection. J Biomed Sci 27, 50 (2020). https://doi.org/10.1186/s12929-020-00641-2
Olympus FV3000RS (Evident, Olympus life science) utilizes two high sensitivity spectral detectors and one spectral detector and is capable of multichannel Truspectral imaging, enabling simultaneous imaging with flexibility and high sensitivity. Four lasers (405nm, 488nm, 561nm, 640nm) have offered the opportunity to select a vast variety of dyes and detectors. The microscope is equipped with hybrid scanner system, employing a resonant scanner and a galvanometer scanner, for capturing live phenomena with high speed and for recording complex structures with high resolution respectively. Zero drift compensator (ZDC-2) facilitates long term imaging. 2D, 3D and MATL images are acquired via XY, XYZ or XYT and can be mapped or stitched. Tilt adjustment in Z direction has made easier with the FV3000RS. Lambda series can be acquired by a single channel or multiple channels. The system is ideal in performing colocalization, 2D deconvolution, FRAP and FRET analysis.
Dayarathna, S., Jeewandara, C., & Malavige, G. N. (2020, December). Use of Confocal Microscopy to Characterise DENV Infection and NS1 Expression in C6/36 and HepG2 Cells in Utilising Them as Models to Screen for the Efficacy of Antiviral Drugs. In 2020 From Innovation to Impact (FITI) (Vol. 1, pp. 1-5). IEEE.
