The main purpose of TUBITAK UME Bioanalysis Laboratory is to provide SI traceability in the field of biometrology, in other words, in the measurements of large biological molecules (DNA, RNA, peptide and protein) and cells, thus increasing the quality of the measurements in this field.
For this purpose, new methods are developed as required by newly developed technology and required standards, the developed methods are validated, and the necessary reference materials, needed in our country, are prepared and presented to the use of the stakeholders.
Other purposes of the laboratory are to organize various activities and studies in order to raise awareness of metrology in our country and to increase awareness in the field of biometology, to support the production of primary level reference materials at national and international level and to establish the SI traceability chain of the produced materials.
TUBITAK UME Bioanalysis Laboratory cooperates and provides support with relevant institutions and organizations for the accurate and reliable conduct of industrial, legal and scientific activities at national and international level. At the international level, in the field of biometrology, the laboratory represents Turkey at EURAMET TC-MC, JCTLM, CIPM CCQM Nucleic Acid Analysis Working Group (NAWG), Protein Analysis Working Group (PAWG) and Cell Analysis Working Group (CAWG) activities and participates to annual meetings.
Additionally, the laboratory collaborates in international projects such as EMPIR and participates in international measurement comparisons since 2010. In order to ensure SI traceability of the produced certified reference materials, after participation in international comparisons, the measurement capability (CMC), is approved and recognized at the international level.
The Bioanalysis Laboratory continues its activities in the field of biometrology in 3 different sub-disciplines:
- Nucleic acid based research: Research and development studies are carried out in this field in order to perform DNA and RNA measurements in biological structures with high accuracy and low uncertainty. The main research areas are listed below, and the primary level measurement services provided can be found on the "Services" page:
- Determination of genetically modified organisms (GMO) in agricultural products by digital PCR (dPCR), which is accepted as the reference DNA measurement method,
- Production of reference materials and organizing proficiency tests within the scope of halal food analysis (meat authentication and gelatin authentication),
- Development of primary methods with dPCR for detecting DNA mutations in cancer tissues and liquid biopsy samples,
- Development of new measurement methods for methylated DNA used in the early diagnosis of cancer,
- Development of methods to measure variable mRNA levels with high accuracy used in the early diagnosis of diseases.
New measurement methods have been developed and several measurement capability have been approved by participating in the measurement comparisons organized between metrology institutes under CCQM NAWG and given in the list below:
- CCQM-P199.b: SARS-CoV-2 RNA copy number quantification, 2020
- CCQM-P199: HIV-1, Copy number concentration of HIV-1 RNA genomic sequences, 2019
- CCQM-K86.c: Relative quantification of genomic DNA fragments extracted from high oil matrix , 2018
(Mester, Z., Corbisier, P., Ellison, S., Gao, Y., Niu, C., Lee, F., Pérez-Urquiza, M., Suárez, A., Burns, M., Milavec, M., Wiangnoon, K., Grififths, K., Mclaughlin, J., Shibayama, S., Takatsu, A., Akgoz, M., Vonsky, M., Runov, A., Guerrero, J. Final Report of CCQM-K86.c. Relative Quantification of Genomic DNA Fragments Extracted from a Biological Tissue, Metrologia, 57:Technical Supplement 1A (2020) : Article number 08004. https://doi.org/10.1088/0026-1394/57/1A/08004)
- CCQM-P184: Copy number concentration and fractional abundance of a mutation (SNV: EGFR or INDEL: BRAF) mixed with wt DNA, 2018
- CCQM-K86.b: Relative quantification of Bt63 in GM rice matrix sample, 2016
(Dong, L., Sui, Z., Wang, J., Tang, V., Chum, W., Lee, F., Sim, D., Perez-Urquiza, M., Burns, M., Milavic, M., Prawettongsopon, C., Grififths, K.R., Mclaughlin, J.L., Shibayama, S., Akyurek, S., Akgoz, M. Final Report for CCQM-K86.b Relative Quantification of Bt63 in GM Rice Matrix Sample, Metrologia, 55:Technical Supplement (2018) : 08017. https://doi.org/10.1088/0026-1394/55/1A/08017)
- CCQM-P155: Multiple cancer cell biomarker measurement , 2016
- CCQM-P154: Absolute Quantification of DNA, 2015
(Yoo, H., Park, S., Dong, L., Sui, Z., Pavsic, J., Milavec, M., Akgoz, M., Mozioglu, E., Corbisier, P., Janka, M., Cosme, B., De V. Cavalcante, J.J., Flatshart, R.B., Burke, D., Smith, M., Mclaughlin, J., Emslie, K., Whale, A., Huggett, J.F., Parkes, H., Kline, M.C., Harenza, J.L., Vallone, P.M. International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction, Analytical Chemistry, 88:24 (2016): 12169-12176. https://doi.org/10.1021/acs.analchem.6b03076)
- CCQM-P94.2: Quantification of DNA methylation II, 2014
- CCQM-P103.1: Measurement of multiplexed biomarker panel of RNA transcripts, 2013
(Devonshire, A.S., Sanders, R., Whale, A.S., Nixon, G.J., Cowen, S., Ellison, S., Parkers, H., Pine, P.S., Salit, M., Mcdaniel, J., Munro, S., Lund, S., Matsukura, S., Sekiguchi, Y., Kawaharasaki, M., Granjeiro, J.M., Lotsch, P.F., Saraiva, A.M., Couto, P., Yang, I., Kwon, H., Park, S., Demsar, T., Akyurek, S., Akgoz, M. An International Comparability Study on Quantification of mRNA Gene Expression Ratios: CCQM-P103.1, Biomolecular Detection and Quantification, 8:- (2016) : 15-28. https://doi.org/10.1016/j.bdq.2016.05.003)
- CCQM-K86: Relative Quantification of Genomic DNA Fragments Extracted from a Biological Tissue, 2013
(Corbisier, P, Vincent, S., Schimmel, H., Kortekaas, A.M, Trapmann, S., Burns, M., Bushell, C., Akgoz, M., Akyurek, S., Dong, L., Fu, B., Zhang, L., Wang, J., Perez Urquiza, M., Bautista, J. L., Garibay, A., Fuller, B., Baoutina, A., Partis, L., Emslie, K., Holden, M., Chum, W. Y., Kim, H. -H., Phunbua, N., Milavec, M., Zel, J., Vonsky, M., Konopelko, L. A., Lau, T.L.T., Yang, B., Hui, M.H.K., Yu, A.C.H., Viroonudomphol, D., Prawettongsopon, C., Wiangnon, K., Takabatake, R., Kitta, K., Kawaharasaki, M., Parkes, H., CCQM-K86/P113.1: Relative quantification of genomic DNA fragments extracted from a biological tissue, Metrologia, 2012. https://doi.org/10.1088/0026-1394/49/1A/08002 )
Bioanalysis Laboratory conducts measurement comparison studies with its international partners at CCQM NAWG.
- CCQM-NAWG “Quantification (and fractional abundance) of genomic DNA extracted from a protein matrix” International Measurement Comparison Study is prepared jointly with Thailand Metrology Institute (NIMT). The samples were prepared within the scope of halal food by mixing beef and pork matrix and DNA ratios will be mesured. The samples have been prepared and will be sent to participating laboratories in 2021.
- The CCQM-NAWG DNA Methylation Measurement Comparison Study is being prepared jointly with the South Korean Metrology Institute (KRISS).
Additionally, the articles about new developed measurement methods are given below:
- Yalcinkaya, B., Coşkun, K., Akgoz, M., Pence, S. (2020). A simple silica based DNA isolation method for cell-free DNA analysis from liquid biopsy, Turkish Journal of Biochemistry (published online ahead of print 2020), 000010151520200253. https://doi.org/10.1515/tjb-2020-0253
- Yalcinkaya, B., Yumbul, E., Mozioglu, E. Comparison of DNA Extraction Methods for Meat Analysis, Food Chemistry, 221: (2017): 1253-1257. https://doi.org/10.1016/j.foodchem.2016.11.032
- Mozioglu, E., Akgoz, M., Tamerler, C., Kocagoz, Z.T. A Simple Guanidinium Isothiocyanate Method for Bacterial Genomic DNA Isolation, Turkish Journal of Biology, :38 (2014) : 125-129. https://doi.org/10.3906/biy-1308-7
- Kocagoz, T., Altin, S., Turkyilmaz, O., Tas, I., Karaduman, P., Bolaban, D., Yesilyurt, E., Oktem, S., Aytekin, N., Sinik, G., Mozioglu, E., Silier, T. Efficiency of the TK Culture System in the Diagnosis of Tuberculosis", Diagnostic Microbiology and Infectious Disease, 72:4 (2012) : 350-357. https://doi.org/10.1016/j.diagmicrobio.2011.12.004
Scientific publications, national and international patent applications on biosensors developed for rapid diagnosis of biological molecules are given below:
- Mozioglu, E., Akyurek, S., Gunduz, S., Akgoz, M., Goren, A.C., Kocagoz, T. Oligomer Based Real-Time Detection of Microorganisms Producing Nuclease Enzymes, The Analyst, 144:4 (2019) : 1379-1385. https://doi.org/10.1039/C8AN02129E
- International patent: Erkan Mozi̇oğlu, Sema Akyürek, Simay Gündüz, Müslüm Akgöz, Ahmet Ceyhan GÖREN, Zühtü Tanıl KOCAGÖZ. Method for rapid identification of microorganisms producing nuclease enzymes (PCT/IB2018/051664)
- National patent: Erkan Mozioğlu, Sema Akyürek, Simay Gündüz, Müslüm Akgöz, Ahmet Ceyhan Gören, Zühüt Tanıl Kocagöz. Nükleaz Enzimlerini Üreten Mikroorganizmaların Hızlı Tanısı için Yöntem (2017/03901)
- Mozioglu, E., Akgoz, M., Kocagoz, T., Tamerler, C. Detection of Nuclease Activity Using a Simple Fluorescence Based Biosensor, Analytical Methods, 8: (2016): 4017-4021. doi.org/10.1039/C5AY02310F. https://doi.org/10.1039/C5AY02310F
- International patent: Erkan Mozioğlu, Muslum Akgoz, Candan Tamerler, Tanıl Kocagöz. Fluorescence method for detecting nuclease activity (PCT/IB2013/ 059297)
National Patent: Erkan Mozioğlu, Özgür Gökmen, Muslum Akgoz, Candan Tamerler, Tanıl Kocagöz. Nükleaz Enzim Etkinliğinin Belirlenmesinde Işımalı Yöntem (2013/07628)
- Mozioglu, E., Gokmen, O., Tamerler, C., Kocagoz, T., Akgoz, M. Selection of Nucleic Acid Aptamers Specific for Mycobacterium Tuberculosis, Applied Biochemistry and Biotechnology, 178:4 (2016) : 849-864.
- International patent: Erkan Mozioğlu, Özgür Gökmen, Müslüm Akgöz, Tanıl Kocagöz, Candan Tamerler. DNA aptamers to diagnose Mycobacterium tuberculosis bacteria and treat tuberculosis disease, specific for M. tuberculosis bacteria (PCT/EP2013/ 071003)
- National patent: Erkan Mozioğlu, Muslum Akgoz, Candan Tamerler, Tanıl Kocagöz. M. tuberculosis Bakterisinin Tanısında ve Yol Açtığı Verem (Tüberküloz) Hastalığının Tedavisinde Kullanılacak M. tuberculosis Bakterisine Özgü DNA Aptamerleri (2013/04224)
- National patent: Özgür Gökmen, Müslüm Akgöz. S. pneumoniae Bakterisinin Tanısında ve Yol Açtığı Zatürre Hastalığının Tedavisinde Kullanılacak S. pneumoniae Bakterisine Özgü DNA Aptamerleri (2013/06123)
- Protein and peptide-based research: Research and development studies are carried out in order to quantify the polymeric biomolecules such as proteins and peptides and the activities of enzymes, with high accuracy and low uncertainty. The main research areas are given below, and the primary level measurement services provided by the laboratory can be accessed on the "Services" page:
- Providing Industrial Service in the Field of Proteomics
- LC-MS / MS Method Based protein identification
- Complex Proteome Analysis - Relative quantification (LFQ-TMT),
- Identification of common protein modifications (methylation, acetylation, phosphorylation etc.)
- Peptide fragmentation (HCD)
- Measurement of peptide / protein amounts based on immunological and mass spectrometry
- Development of new methods for protein activity measurements
- Production of certified reference materials needed by clinical laboratories and organization of proficiency tests.
New measurement methods have been developed and measurement capability have been gained approved by participating in the measurement comparisons organized between metrology institutes under CCQM PAWG and given in the list below:
- CCQM-115c: HbA1c Absolute Quantification, 2020
- CCQM-P201: Total Hemoglobin in Serum, 2020
- CCQM-K115.2018: Peptide purity - synthetic hexapeptide of HbA0 (VE), 2019
- CCQM-K115c: Peptide purity - synthetic glycated hexapeptide of HbA1c (GE), 2019
- CCQM-K115b: Peptide purity - synthetic oxytocin, (OXT)), 2018
(Josephs RD, Li M, Daireaux A, Choteau T, Martos G, Westwood S, Wielgosz RI, Li H, Wang S, Li X, Shi N, Wu P, Feng L, Huang T, Zhang T, Li S, Beltrão, PJ, Saraiva AM, Garrido BC, Scapin SMN, Wollinger W, Sade YB, Thibeault M-P, Stocks BB, Melanson JE, Kinumi T, Rezali MF Bin, Öztug M, Akgöz M, Quaglia M. Key comparison study on peptide purity - synthetic oxytocin. Metrologia 57:08014–08014. (2020). https://doi.org/10.1088/0026-1394/57/1A/08014)
- CCQM-K151: Determination of the amount content of a purity-assessed recombinant protein in an aqueous calibration solution - Insulin, 2018
- CCQM-P164: Mass fraction of human growth hormone in serum, 2018
- CCQM-K 115/P55.2: Peptide Purity Determination - Synthetic Human C Peptide, 2017
(Josephs, R.D., Li, M., Song, D., Westwood, S., Stoppacher, N., Flatschart, R., Oliveira, R., Melanson, J.E., Ohlendorg, R., Henrion, A., Kinumi, T., Wong, L., Liu, Q., Oztug Senal, M., Vatansever, B., Un, I., Goren, A.C., Akgoz, M., Quaglia, M., Warren, J. Key Comparison Study on Peptide Purity Synthetic Human C-Peptide, Metrologia, 54:Technical Supplement (2017) : 08007, 2017, Volume 54, https://doi.org/10.1088/0026-1394/54/1A/08007)
- CCQM-P137: Activity of alpha amylase in human serum, 2016
- CCQM-P58.1: Immunoassay Quantification of Human Cardiac Troponin I, 2012
Additionally, the scientific articles about newly developed measurement methods are given below:
- Oztug M, Kilinc E, Akgoz M, Karaguler NG. Thermal Proteome Profiling and Meltome Analysis of a Thermophilic Bacterial Strain, Geobacillus thermoleovorans ARTRW1: Toward Industrial Applications. Omi A J Integr Biol 24:omi.2020.0115 (2020). https://doi.org/10.1089/omi.2020.0115
- Oztug, M., Cebeci, A., Mumcu, H., Akgoz, M., Karaguler, N.G. Whole-Genome Sequence of Geobacillus Thermoleovorans ARTRW1, Isolated from Armutlu Geothermal Spring, Turkey, Mıcrobıology Resource Announcements, 9:24 (2020): Article Number: e00269-20 https://doi.org/10.1128/MRA.00269-20
- Josephs, R.D., Martos, G., Li, M., Liqing, W., Melanson, J.E., Quaglia, M., Beltrao, P.J., Prevoo-Franzsen, D., Boeuf, A., Delatour, V., Oztug Kilinc, M., Henrion, A., Jeong, J., Park, S. Establishment of Measurement Traceability for Peptide and Protein Quantification Through Rigorous Purity Assessment-a Review, Metrologia, 56:4 (2019) : Article Number: 044006. https://doi.org/10.1088/1681-7575/ab27e5
- Ralf D. Josephs, Norbert Stoppacher, Steven Westwood, Robert I. Wielgosz, Ming Li, Milena Quaglia, Jeremy Melanson, Gustavo Martos, Desiree Prevoo, Liqing Wu, Sandra Scapin, Merve Öztug Sena, Lingkai Wong, Ji-Seon Jeong, Kelly Wai Yi Chan, Cristian G. Arsene and Sang-Ryoul Park Concept paper on SI value assignment of purity model for the classification of peptide/protein purity determinations J. Chem. Metrol. 11:1 (2017) 1-8. http://doi.org/10.25135/jcm.1.17.02.030
- Vatansever, B., Muñoz, A., Klein, C.L., Reinert, K. Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis. Journal of Analytical and Bioanalytical Chemistry, 409:4 (2017) : 989-997. https://doi.org/10.1007/s00216-016-0013-z
- Tutuncu HE, Oztug M, Balci NC, Tuter M, Gul N. Function Based Metagenomics Approach for Obtaining Lipase from Acid Mine Drainage Site. Int J Ser Eng Sci Arch Biotechnol Bioeng 3:1–20 (2017). http://old.ijseries.com/index.php/IJSES/article/view/129/100
- Vatansever, B., Senal, M.O., Akgoz, M. et al. Development and validation of a generic method for quantification of collagen in food supplement tablets using liquid chromatography coupled with time-of-flight mass spectrometry. Anal Bioanal Chem 407, 1981–1987 (2015). https://doi.org/10.1007/s00216-014-8443-y
- Cell-based research: In this field, it is aimed to develop new measurement methods based on microscope and flow cytometry instruments for the characterization and counting of different cells such as stem cells, blood cells, cancer cells.
The laboratory has attended to a comparison study under CCQM CAWG and new measurement methods are being developed:
- CCQM-P165:(Quantification of CD34+ cell counts), 2016
- Saraiva, L., Wang, L., Kammel, M., Kummrow, A., Atkinson, E., Lee, J.Y., Yalcinkaya, B., Akgoz, M., Hockner, J., Ruf, A., Engel, A., Zhang, Y., OShea, O., Paola Sassi, M., Divieto, C., Lekishvili, T., Campbell, J., Liu, Y., Wang, J., Stebbings, R., Gaigalas, A.K., Rigsby, P., Neukammer, J., Vessillier, S. Comparison of Volumetric and Bead Based Counting of CD34 Cells by Single Platform Flow Cytometry, Cytometry Part B: Clinical Cytometry, 96:6 (2019):508-513. https://doi.org/10.1002/cyto.b.21773