Country

TURKEY

Name of the organization

Çanakkale 18 Mart University

Name of the contact

Prof. Dr. Kemal Melih TAŞKIN, Asist. of Prof. Fatih SEZER

Phone

+90 286 2180030 (Ext. 2320)

Email

kmtaskincomu.edu.tr, fatihsezercomu.edu.tr

We are working with natural apomicts plant species Boechera. Apomixis, an asexual mode of reproduction, results in embryo formation without fertilization of the egg. We are investigating the morphogenic potential of various Boechera tissues to establish an efficient regeneration system. Hypocotyls, cotyledons, roots, leaves from 7-days old in vitro growing seedlings, and immature cotyledons from 6 months old plants are tested. The effect of various concentrations of the PGRs on in vitro regeneration of these explants is also investigated and an efficient Agrobacterium-mediated transformation method is developed. We are also investigating the effects of genomic imprinting on the seed development of the Boechera species. The imprinted genes of Boechera species are not reported in the literature. Therefore, we select the Arabidopsis thaliana L. genes known as imprinted as a candidate. Among these genes, the genomic sequences of paternally expressed imprinted genes in FASTA format are obtained from databases, and the existence of these genes in the SRA databases for Boechera species is revealed by using bioinformatic methods. The expression profiles of these candidate genes are also examined with RT-PCR in different development stages of flower and silique tissues in diploid apomict Boechera divaricarpa. We are also determined the structure of DNA methyltransferase (DNMT) genes in apomict and sexual Boechera species and investigated the expression levels during seed development. We determined three DNMT genes; for Boechera spp. METHYLTRANSFERASE1 (MET1), CHROMOMETHYLASE 3 (CMT3), and DOMAINS REARRANGED METHYLTRANSFERASE 1/2 (DRM2) and examined the structure of these genes with bioinformatic tools and compared with other DNMT genes in plants. We also determined the levels of expression in silique tissues after fertilization by semi-quantitative PCR. We isolated and sequenced SWI1 orthologs from Boechera species, including apomictic and sexual species. Boechera species. The SWI1 cDNAs were obtained by RT-PCR from apomictic and sexual Boechera young flower buds and sequenced. We also used available genome data and amplified genomic sequences for SWI1 orthologs in B. holboellii and B. stricta. Recently, we have studied characterized the structure and expression profiles of CENH3 orthologs in diploid Boechera spp...

We are now collaborating with Dr. Vladimir Brukhin (St. Petersburg State University, Russia) to study the genetic and molecular mechanisms that control apomixis by transcriptional and functional analysis methods. We will also study the phylogeny of these genes and the influence of evolutionary selection and expression analysis of candidate genes, cloning, complementation analysis of the mutated genes in a model plant Arabidopsis.

Plant Metabolic Pathways

The molecular mechanisms controlling Plant Metabolic pathways are very diverse and identification of relevant genes is necessary for metabolic engineering. We are recently working with Olive (Olea europaea L.)  which is a widely cultivated economically important Mediterranean plant with high quality of oils and rich compounds. Although genes related to diverse processes were recently discovered via transcriptomic research, genes involved in the biosynthesis of metabolic pathways, have not been characterized in olive. Genomic information is also very limited for this species. Vitamin E constitutes of metabolites with high antioxidant effects, known as tocopherols. Vitamin E is mostly synthesized by oil plants and reported for its beneficial effects on human diseases like coronary heart disease and cancer. A group of methyltransferase and cyclase enzymes has roles in tocopherol biosynthesis. It has been known that these enzymes produce various tocopherols by modifying 2-methyl-6phytyl-1,4-benzoquinol, the precursor of all tocopherols. Among these α tocopherols and γ tocopherol are the most abundant forms found in oil plants. Therefore in our recent, we obtained the full-length transcripts of genes involved in olive tocopherol biosynthesis with RACE (Rapid Amplification of cDNA Ends) method, identified and compared the gene expression levels through fruit development with Real-Time PCR and analyzed tocopherol content with HPLC for the first time in Olive. The project revealed gene/genes involved in tocopherol biosynthesis. These genes will be used to obtain olive genotypes with high vitamin E content and higher productivity/quality by molecular breeding strategies. Strigolactones are plant growth regulators which have been recently identified to control stem and root development. Although SLs were determined in a few agriculturally important and model species, they have not been studied in olive. Olive (Olea europaea L.) is an economically important, widely cultivated Mediterranean plant that is produced for oil and table, is a subject for its beneficial effect on human health. With this project, molecular structures of the genes involved in SLs biosynthesis and signaling are characterized, gene expression profiles are determined. We also investigated the effects of GR24, SLs analog, and TIS108, SLs inhibitor, on parameters such as seed germination, root development, lateral branching, internode length in tissue culture conditions, micropropagation of single node explants and Ayvalık and Domat cutting rooting ability are determined. Transcript sequences of the SLs biosynthesis (MAX1, MAX3, MAX4, D27), perception (D14), and signaling (MAX2) genes were revealed with RACE method for the first time in olive Ayvalık cultivar. Additionally, the effects of GR24 and TIS108 on seed germination, root length, lateral branching, and internode length in Ayvalık and Ak Delice cultivars in vitro are also determined. In tissue culture conditions, GR24 and TIS108 applications did not affect seed germination percentage and root length, however, GR24 inhibited lateral branching when endosperm removed in Ak Delice. Besides, as a result of GR24 and TIS108 applications on single node explants of Ayvalık and Domat cultivars which are used for micropropagation, GR24 inhibited shoot development in vitro conditions. GR24 and TIS108 applications on Ayvalık and Domat cuttings revealed that the TIS108 applications increased the rooting percentage of difficult to root Domat. With this project, we identified and published reference genes (UBC1 and CLATHRIN) that could be used for normalization of gene expression data qPCR studies in olive. SLs gene expression profiles were determined in various tissues in Ayvalık cultivar and these results are in concord with the results from model species.

We are recently working with genes that involve Phytosterol biosynthesis in Olive. With this project, genes controlling olive phytosterol biosynthesis will be identified for the first time and factors controlling this process like fruit maturity, differences between cultivars, gene expression, and single nucleotide polymorphism will be determined. Thus, cultivars, ripening and harvest stages with higher phytosterol content will be identified, sequences of olive phytosterol biosynthesis genes which could be a reference for molecular breeding studies and gene expression changes that are associated with phytosterol content will be determined.

Please list the relevant skills you have in your research area

Plant molecular biology and biotechnology, Gene transfer, Transformation, Plant Tissue culture, Plant development, Seed development, Gene expression, Gene cloning, Apomixis, Plant metabolic pathways, Plant breeding

Project acronym / project no/starting date

Funded by

Main objectives

Main activities

Role in the project

PhyloFunApomixis

119N384

2020

The Scientific and Technological Research Council of Turkey (TÜBİTAK) and

the Russian Foundation of Basic Research (RFBR)

Joint Project

obtain extensive knowledge about apomixis gained with a natural apomict Boechera and to engineer apomixis in sexual crop plants using the model system Arabidopsis thaliana. This project will provide a functional method to analyze apomixis associated genes in natural apomicts for the first time.

Characterize the structure of the apomixis associated genes Boechera spp. using genome data and determine the copy number and polymorphisms

Compare the transcriptome of sexual and apomict accessions to understand which copies are express during gametophyte development.

Check for the tissue-specific expression levels of apomixis associated genes.

Clone best candidates

Perform complementation analysis in Arabidopsis mutants

Project Leader

OLIVER

119Z924

2020

TÜBİTAK

Determine the structure and expression levels of  genes responsible for adventitious root formation in Olive

Characterize the structure of AOX2, AOX1, IBR1, IBR3, IBR10 and PtAIL1 genes using bioinformatic tools

Design primers

Determine the expression levels AOX2, AOX1, IBR1, IBR3, IBR10, and PtAIL1 genes after IBA treatment

Identify germplasm specific SNPs

Project Leader

PhytosterOL

118O405

2018-

TÜBİTAK

With this project, genes controlling olive phytosterol biosynthesis will be identified for the first time and factors controlling this process like fruit maturity, differences between cultivars, gene expression, and single nucleotide polymorphism will be determined.

Identify the genes with key roles in phytosterol biosynthesis using molecular and bioinformatic methods

Analyze the expression of these genes on different olive cultivars and 8 different ripening stages including harvest stages

Analyze the different phytosterol types and total phytosterol content in different olive cultivars and 8 different ripening stages including harvest stages

Project Leader

OeSLs

215O543

2016-2019 (completed)

TÜBİTAK-

COST (European Cooperation in Science and Technology) 

This project aims to investigate the genes responsible for Strigolactones (SLs) biosynthesis and signalling and determine to the effects of SLs as plant growth regulators on in Olive.

Determined the structure and the expression levels of genes involved in SLs biosynthesis and signalling

Revealed the effects of SLs on rooting efficiency

Revealed the effects of SLs on apical dominancy, germination rate and speed

Project Leader

1. Güngör T., Cömert Önder F. , Sezer F., Özbilen A., Taşkin K.M., Ay M., "Synthesis of SMZ Derivatives and Investigation of Effects on Germination, Root and Plant Growth of Arabidopsis thaliana L.", TURKISH JOURNAL OF CHEMISTRY, no.1, pp.1-1, 2019
2. Hürkan K., Sezer F., Özbilen A., Taşkin K.M., "Identification of reference genes for real-time quantitative polymerase chain reaction based gene expression studies on various Olive (Olea europaea L.) tissues", JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY, pp.1-8, 2018
3. Tumer T.B., Yilmaz B., Ozleyen A., Kurt B., Tok T.T., Taşkin K.M., et al., "GR24, a synthetic analog of Strigolactones, alleviates inflammation and promotes Nrf2 cytoprotective response: In vitro and in silico evidences", COMPUTATIONAL BIOLOGY AND CHEMISTRY, vol.76, pp.179-190, 2018
4. Taşkin K.M., Özbilen A., Sezer F., Hürkan K. , Güneş Ş. , "Structure And Expression Of DNA Methyltransferase Genes From Apomictic And Sexual Boechera Species ", Computational Biology And Chemistry, vol.67, pp.15-21, 2017
5. Sezer F., Taşkin K.M., "Molecular characterization of tocopherol biosynthesis genes from Olea europaea (L.) cv. Ayvalık", TURKİSH JOURNAL OF BOTANY, vol.41, pp.559-568, 2017
6. SEZER Fatih,YÜZBASIOGLU Gözde,ÖZBILEN Aslıhan,TASKIN Kemal Melik Genome-wide identification and expression analysis of SWI1 genes in Boechera species. Computational Biology and Chemistry, 62, 75-81., Doi: 10.1016/j.compbiolchem.2016
7. TAŞKİN K.M., ÖZBİLEN A., SEZER F., ÇÖRDÜK N. , ERDEN D., Determination Of The Expression Levels Of DNA Methyltransferase Genes During A Highly Efficient Regeneration System Via Shoot Organogenesis In The Diploid Apomict Boechera divaricarpa, Plant Cell Tissue And Organ Culture, no.121, pp.335-343, 2015
8. Yılmaz Sibel,GÖZÜKIRMIZI NERMIN,Scott Rod,TASKIN KEMAL MELIK. Structure And Expression Analyses of the Fertilization Independent Seed (FIS) Gene Orthologs of the Apomict Boechera species. Plant Cell Biotechnology and Molecular Biology, 16(1-2), 74-83. 2015
9. K.M. TAŞKIN, K. TURGUT, R.J. SCOTT. Apomeiotic pollen mother cell (PMC) development in the apomict Boechera species, Biologia Plantarum, 53 (3), 468-474, 2009.
10. TAŞKIN K.M., TURGUT K., SCOTT R.J. Apomictic development in Arabis gunnisoniana. Israel Journal of Plant Sciences, 52, 2, 155-160, 2004.

Country

TURKEY

Name of the organisation

Name of the contact

Tugba TÜMER

Phone

+90 286 218 0030 (Ext. 1844)

Email

tumertbcomu.edu.tr

Tugba Tümer: tumertbcomu.edu.tr

Tel: 905063017679

 My team focuses on understanding the molecular effects of plant-derived compounds on chronic diseases and developing botanical therapeutics that promote health and wellness.  We are particularly interested in insulin resistance, chronic inflammation, and neuroinflammation as degenerative chronic diseases. Lead compounds from botanicals also inspire us for the design and synthesis of new small molecules.  We use modern research tools such as in silico computation, modelling and ADMET approaches for rational lead discoveries and whole genome transcriptomics for the elucidation of action mechanisms. We have a network of national and international collaborations and major funding from the Scientific and Technological Research Council of Turkey. In our lab, we use in vitro screening and in vivo assays, spectrometry, biochemistry and molecular biology tools to identify bioactive phytochemicals and to study their biological effects and mode of action. We seek for the collaborators who are working on the synthesis of small molecules inspired from the structures found in natural compounds especially lactones and isothiocynates like pharmacophores as well as experts working on molecular simulations in the area of drug discovery.   

Please list the relevant skills you have in your research area

In our lab we routinely use different molecular biology and biochemistry techniques as listed below :

Advanced mammalian cell culture techniques  including cellular apoptosis/cytotoxicity, proliferation assays, Cell-based assays (cell motility, cell migration and cell invasiveness), PCR/Quantitative real time PCR, In vitro plasmid DNA damage and COMET assay, use of siRNA/shRNA constructs for post-transcriptional silencing, electrophoretic techniques: SDS-PAGE, coomassie & silver staining, Immunoprecipitation/Western blot, ELISA, Enzyme characterization and kinetics, Enzyme inhibition kinetics,, UV/Vis Spectroscopy, Enzyme activity measurements (spectrophotometric, spectrofluometric)

Project acronym / starting date

Main objectives

Main activities

Role in the project

March 2018

1. Title of the project: In Silico Design, Synthesis and Screening of New Generation Anti-inflammatory Molecules with Secondary Anticarcinogenic Properties and Elucidation of Mechanisms

Design, synthesis and in vitro evaluations of new generations NSAIDs with secondary anticancer properties

Project Leader

Tugba Tümer

September 2019

2. Title of the project : Elucidation of potential anti-neuroinflammatory effects of novel strigolactone analogs and their mechanism of action in in vitro neuroinflmmation models

the elucidation of potential anti-neuroinflammatory effects and action mechanisms of some

strigolactone analogs on in vitro neuroinflammation models. 

Project Leader

Tuğba Tümer

September 2019

An Optimization of Bioactive Peptides-Enriched Fermented Spirulina Product and Determination of in vitro

Bioaccessibility 

Development of Spiruluna based fermented functional foods and bioactive peptides with anti-inflammatory and anticancer properties

Project Supervisor

Tuğba Tümer Publications:

Kurt B, Ozleyen A, Antika G, Yılmaz YB, Tumer TB. Multitarget Profiling of a Strigolactone Analogue for Early Events of Alzheimer’s Disease: In Vitro Therapeutic Activities against Neuroinflammation. ACS Chemical Neuroscience. 2020 11 (4), 501-507 doi: 10.1021/acschemneuro.9b00694

Sharifi-Rad J, Ozleyen A, Tumer TB, Adetunji CO, El Omari N, Balahbib A, Taheri Y, Bouyahya A, Martorell M, Martins N, C. Cho W. Natural Products and Synthetic Analogs as a Source of Antitumor Drugs. Biomolecules 2019 Nov, 9, 679. doi: 10.3390/biom9110679

Kulabas SS, Onder FC, Yılmaz YB, Ozleyen A, Durdagi S, Sahin K, Ay M, Tumer TB. In vitro and in silico studies of nitrobenzamide derivatives as potential anti-neuroinflammatory agents. J Biomol Struct Dyn. 2019 Oct 23:1-18. doi: 10.1080/07391102.2019.1684368.

Salehi B, Yılmaz YB, Antika G, Tumer TB et al., Insights on the Use ofα-Lipoic Acid for Therapeutic Purposes. Biomolecules2019,9, 356; doi:10.3390/biom9080356.

Salehi, B., Tumer, T. B., Ozleyen, A., Peron, G., Dall’Acqua, S., Rajkovic, J., ... & Milella, L. (2019). Plants of the genus Spinacia: From bioactive molecules to food and phytopharmacological applications. Trends in Food Science & Technology.

Salehi, B., Zakaria, Z. A., Gyawali, R., Ibrahim, S. A., Rajkovic, J., Shinwari, Z. K., Khan T., Sharifi-Rad ., Ozleyen A., Tumer TB…, & Valussi, M. (2019). Piper Species: A Comprehensive Review on Their Phytochemistry, Biological Activities and Applications. Molecules, 24(7), 1364

Tumer TB, Yılmaz YB, Kurt B, Kurt BS, Taskin KM, Kulabas SS. GR24, a synthetic analog of Strigolactones, alleviates inflammation and promotes Nrf2 cytoprotective response: In vitro and in silico evidences. Computational Biology and Chemistry, 2018; 76:179-190. doi: 10.1016/j.

Kulabas SS, Ipek H, Tufekci AR, Arslan S, Demirtas I, Ekren R, Sezerman U, Tumer TB. Ameliorative Potential of Lavandula stoechas in metabolic syndrome via multitarget interactions.  Journal of Ethnopharmacology, 2018, 223:88-98. doi: 10.1016/j.jep.2018.04.043. 

Kapche DWFG, Lekane NM, Kulabas SS, Ipek H, Tok TT, Ngadjui BT, Demirtas I, Tumer TB. Aryl benzofuran derivatives from the stem bark of Calpocalyx dinklagei attenuate inflammation. Phytochemistry, 2017, 141:70-79.

Tumer TB, Onder FC, Ipek H, Gungor T, Savranoglu S, Ay M, Tok TT, Celik A. Biological Evaluation and Molecular Docking Studies of Nitro Benzamide Derivatives with Respect to in vitro Anti-inflamatory Activity. International Journal of Immunopharmacology, 2017, 43:129-139.

Country

TURKEY

Name of the organisation

Name of the contact

Hilal Ozkilinc

Phone

+90 286 218 0030 (Ext. 1838)

Email

hilalozkilinccomu.edu.tr

Dr Ozkilinc has been directing evolutionary biology questions on fungal plant pathogens by using population genetics, phylogenetics and genomics approaches. Collaborate with plant pathologists, evolutionary biologists, bioinformaticians.

Please list the relevant skills you have in your research area

Fungal plant pathogens, genomics, population genetics, evolution, molecular phylogeny, pathogenicity, mitogenomics, bioinformatics, host-pathogen co-evolution, fungicide resistance

Project acronym / starting date

Main objectives

Main activities

Role in the project

TUBITAK/1001

2018- Continuing

Sensitivity of Monilinia Pathogens Causing Brown Rot of Peach Against to Respiration Inhibitor Fungicides Having Specific Mode of Action Mechanisms, Characterization of Mitochondrial Genomes and Investigating Relation Between Fungicide Resistance and Mutations on Mitochondrial Genome

In vitro fungicide tests, mitogenomics, phylogenetics

Principical investigator (PI)

TUBITAK-COST

2015-2018

Idendification of genetic variation by DNA sequence-based comparative genomics of Fusarium oxysporum isolates through Next Generation Sequencing (NGS) method, detemination of phylogenetic relationships and comparison of genes for pathogen effector protein

Genomics, molecular markers, phylogenetics

Researcher

TUBITAK-1010

2013-2016

Molecular and Pathogenic Characterization of Alternaria spp. causing Alternaria Blight of Pistachio (Pistacia vera) and Other Pistacia Species in Turkey and Investigation of Disease Epidemiology

Pathogenicity, phylogenetics, species identification

Principle Investigator

(PI)

TUBITAK-1003

2013-2016

Population Characterization of Chickpea Ascochyta Blight for Developing Chickpea Genotypes Having Resistance/Tolerance through Conventional and Molecular Methods

Population genetics based analyses

Researcher

National Science Foundation of U.S.A

2010-2012

Collaborative Research: Estimating speciation/reticulation boundaries in asexual Alternaria: a genomics approach

Phylogenetics, genomics

Postdoctoral researcher

• Ozkilinc, H., Yildiz, G., Silan, E., Arslan K., Guven, H., Altinok, H. H., Altindag, R., Durak, M. R. (2020). Species Diversity, Mating Type Assays and Aggressiveness Patterns of Monilinia Pathogens Causing Brown Rot of Peach Fruit in Turkey. European Journal of Plant Pathology, DOI: 10.1007/s10658-020-02040-7.
• Ozkilinc H. and Can C. (2019) The most recent status of genetic structure of Didymella rabiei (Ascochyta rabiei) populations in Turkey and the first genotype profile of the pathogen from the wild ancestor, Cicer reticulatum. Phytoparasitica, https://doi.org/10.1007/s12600-019-00721-6.
• Ozkilinc, H. & Sevinc, U. Molecular phylogenetic species in Alternaria pathogens infecting pistachio and wild relatives. (2018) 3 Biotech, 8: 250. https://doi.org/10.1007/s132.
• Ozkilinc H., Sarpkaya K., Kurt S., Can C., Polatbilek H., Yasar A., Sevinc U., Uysal A., Konukoglu F. (2017) Pathogenicity, Morpho-Species and Mating Types of Alternaria spp. causing Alternaria blight in Pistacia spp. in Turkey. Phytoparasitica, 45:719-728 https://doi.org/10.1007/s12600-017-0624-8.
• Ozkilinc, H., Rotondo, F., Pryor, B. M. and Peever, T. L. (2017) Contrasting species boundaries between sections Alternaria and Porri of the genus Alternaria. Plant Pathology, 67:303-314. doi:10.1111/ppa.12749.
• Infantino A, Zaccardelli M., Costa C., Ozkilinc H., Habibi H., Peever T. (2016) A New Disease of grasspea (Lathyrus sativus) caused by Ascochyta lentis var. lathyri. Journal of Plant Pathology, 98 (3): 541-548.
• Ozkilinc, H., Thomas, K., Abang, M. and Peever, T. L. (2015). Population structure and reproductive mode of Didymella fabae in Syria. Plant Pathology. 64:110-1119.
• Ozkilinc H., Akamatsu H., Abang M, Thomas K., Chilvers M. I., Peever T. L. (2011). Development, characterization and linkage analysis of microsatellite loci for the Ascochyta blight pathogen of faba bean, Didymella fabae. Journal of Microbiological Methods, 87: 128-130.
• Ozkilinc H., Frenkel O., Abbo S., Shtienberg D., Sherman A., Kahraman A., Can C. (2011). Aggressiveness of eight Didymella rabiei isolates from domesticated and wild chickpea native to Turkey and Israel, a case study. European Journal of Plant Pathology, 131:529-537.
• Ozkilinc H., Frenkel O., Abbo S., Shtienberg D., Sherman A., Ophir R., Can C (2010). A comparative study of Turkish and Israeli populations of Didymella rabiei, the ascochyta pathogen of chickpea. Plant Pathology, 59:492-503.

Country

TURKEY

Name of the organisation

ÇOMÜ/Department of Molecular Biology and Genetics

Name of the contact

Assoc. Prof. Ozge KARAKAŞ METİN

Phone

+90 286 218 0030 (Ext. 1837)

Email

ozgekarakasmetingmail.com

ozgekarakasmetincomu.edu.tr

• Biotechnological studies for plants
• Plant genetics and genomics studies
• Identification of plant gene sources
• Stress tolerance studies in plants
  •  Application of molecular marker studies for plant breeding
  • Gene transfer and tissue culture systems

Please list the relevant skills you have in your research area

• Biotechnological studies for plants
• Plant genetics and genomics studies
• Identification of plant gene sources
• Stress tolerance studies in plants
  •  Application of molecular marker studies for plant breeding
  • Gene transfer and tissue culture systems

Project acronym / starting date

Main objectives

Main activities

Role in the project

Evaluation of Yellow Rust Disease Resistance in Turkish and Syrian Bread Wheat Germplasm (TUBİTAK Bilateral Project 110O539) 01.07.2011-01.01.2012

The project aimed,

to construct genome-wide association mapping to determine the yellow rust resistance genomic loci in Turkish and Syrian bread wheat germplasm.

to characterize strains of yellow rust that appeared in Syria and Turkey during 2010 season and compare these strains with already known strains, then performing pathogenecity test for Turkish and Syrian bread wheat germplasm, and

to identify genomic loci releated with yellow rust resistance genes (Yr) by using genome wide assosiation mapping in Turkish and Syrian bread wheat germplasm.

*Identification of experimental plant materials.

* Pathology studies for phenotyping and genotyping.

* Molecular marker studies for genotyping of plant material

* Data evaluation- Association mapping studies

Genotyping analysis  performed by using over 400 co-dominant markers including 242 SSR (Simple Sequence Repeats) and 155 EST-SSR (Expressed Sequence Tag-Simple Sequence Repeats) markers and known Yr gene linked SSR/EST-SSR markers.

Director

Determination of cultivation methods for Turkey’s Genotypes and Bringing of new species and cultivars to the related sectors

110G007

(TUBİTAK 1007)

4 years (2010-2014)

Conservation of Turkey’s geophytes, developments of new varieties by using Turkish natural resources, molecular characterization of new varieties and determination of  their biological activities for pharmacetical purposes

By this project,

At least one population of very important 850 geophyte taxons of Turkish flora identified and 10 plants for each taxons conserved ex-situ in the ‘Gardens of the Turkish Geophytes’.

New variety candidate developed,

Phytochemical proporties of bulbous plant species examined.

DNA fingerprinting data determined.

AFLP, species spesific SSR, ISSR and EST-SSR were used as a molecular markers.  Also three noncoding region of chloroplast were used.

Researcher

•T. Taşçıoğlu, Y. Aydin, K. Akan, S. Kumar Verma, Ö. Karakaş Metin, A. Altinkut Uncuoğlu. Wheat stripe rust disease: Quantitative profiling of Yr10 gene. FRESENIUS ENVIRONMENTAL BULLETIN, 2017, 26(7)-4859-4866.

 •T. Talaş Oğraş, E. Koban Baştanlar, Ö. Karakaş Metin, İ. Kandemir, H. Özçelik. Assessment of genetic diversity of rose genotypes using ISSR markers. TURKISH JOURNAL OF BOTANY, 2017, 41: 347-355 DOI: 10.3906/bot-1608-32.

• T. Taşçıoğlu, Ö. Karakaş Metin, Y. Aydin, M. Şakiroğlu, K. Akan, A. Altinkut Uncuoğlu. Genetic Diversity, Population Structure, and Linkage Disequilibrium in Bread Wheat (Triticum aestivum L.). BIOCHEMICAL GENETICS, 2016, 54:421–437 DOI: 10.1007/s10528-0169729-x.

• A. Onay, E. Tilkat, V. Süzerer, Ö. Karakaş Metin, Y. Özden Çiftçi, F. M. Kılınç, İ. Koç, M. Şakiroğlu, H. Yıldırım, A. Altınkut Uncuoğlu, N. Çalar, Ö. F. Akdemir. Rejuvenation of Mature Lentisk by Micrografting and Evaluation of Genetic Stability. TURKISH JOURNAL OF BIOLOGY, 2016, 40: 781-796, DOI: 10.3906/biy-1510-25.

• E. Filiz, A. Distelfeld, T. Fahima, Ö. Karakaş Metin, E. Nevo, S. Weining, A. Altinkut Uncuoğlu. Barley Molybdenum Cofactor Sulfurase (MCSU):sequencing, modeling and its comparison to other higher plants. TURKISH JOURNAL OF AGRICULTURE AND FORESTRY, 2015, 39: 786-796 DOI:10.3906/tar-1411-68.

• F.M Kılınc, V. Süzerer, Y. Özden Çiftçi, A. Onay, H. Yıldırım, A. Altınkut Uncuoğlu, E. Tilkat, İ. Koç, Ö.F. Akdemir, Ö. Karakaş Metin. Clonal micropropagation of Pistacia lentiscus L. and assessment of genetic stability using IRAP markers. PLANT GROWTH REGULATION, 2014, 75:75–88, DOI: 10.1007/s10725-014-9933-9.

• A H. Balta, Ö. Karakaş Metin, F. Şentürk Akfırat, F. Ertuğrul, S. Hasançebi, Y. Aydın, K. Akan, Z. Mert, M. Türet and A. Altınkut Uncuoğlu. Identification of an AFLP marker linked with yellow rust resistance in wheat (Triticum aestivum L.). TURKISH JOURNAL OF BIOLOGY, 2014, 38: 371-379, DOI: 10.3906/biy-1311-8.

• Ö. Karakaş Metin, M. Türktaş, F. Ertuğrul, E. Kaya. Use of fluorescent-based amplified  fragment length polymorphism to resolve phylogenetic relationships of Colchicum species from Turkey. GENETICS AND MOLECULAR RESEARCH, 2014, 13 (1):1480-1490, DOI: 10.4238/2014.March.6.6.

• Ö. Karakaş Metin, M. Türktaş,  M. Aslay, E. Kaya. Evaluation of genetic relationship between Fritillaria species from Turkey’s flora using fluorescent-based AFLP. TURKISH JOURNAL OF BIOLOGY, 2013, 37:273-279, DOI: 10.3906/biy-1207-62.

• M. Türktaş, Ö. Karakaş Metin, B. Baştuğ, F. Ertuğrul, Y. İzgi Saraç, E. Kaya. Molecular phylogenetic analysis of Tulipa (Liliaceae) based on non-coding plastid and nuclear DNA sequences with an emphasis on Turkey. BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, 2013, 172:270–279, DOI: 10.1111/boj.12040.

Country

TURKEY

Name of the organisation

Canakkale Onsekiz Mart University

Name of the contact

Assoc. Prof Sercan Karav

Phone

+90 286 218 0030 (Ext. 2317)

Email

sercankaravcomu.edu.tr

Host-Microbiome Interactions, Metagenomics, Probiotics&Prebiotics, Glycobiology, Enzymology, Microbial Biotechnology

Please list the relevant skills you have in your research area

- Shotgun metagenomics analysis

- Recombinant production and characterization gut microbiome associated novel enzymes

- Advanced mass spectrometry analysis for milk glycans and metabolites

- Prebiotic activity characterization of unknown compounds

Project acronym / starting date

Main objectives

Main activities

Role in the project

Selective Prebiotics

October 2018

Production of selective prebiotics

- Recombinant production of microbiome associated enzymes

- Isolation of novel compound from milk

PI

NanoPreGlycan

October 2020

France Centre National de la Recherche Scientifique (CNRS)

Delivery of glycans by nanoparticles

-Isolation of glycans from different milk sources

- Preparation of EndoBI-1/inorganic nanoflowers

-  Test prebiotic activity of immobilized N-glycans

PI

GlycoMicrobiome

October 2020

King’s College London

Understanding How Glycans Shape Gut Microbiome with Machine Learning

-Evaluate the N-glycome of bovine colostrum and compare the effects of bovine colostrum on the calf gut microbiome

- Determine the relative importance of conjugation to N-glycan and gut microbiome interactions.

PI

1. Karav S, Casaburi G, Arslan A, Kaplan M, Sucu B, Frese S. N-glycans from human milk glycoproteins are selectively released by an infant gut symbiont in vivo. J Funct Foods. 2019; 61: 103485. doi: 10.1016/j.jff.2019.103485

2. Karav S, Casaburi G, Frese SA. Reduced colonic mucin degradation in breastfed infants colonized by Bifidobacterium longum subsp. infantis EVC001. FEBS Open Bio. 2018; 8(10): 1649-57. doi: 10.1002/2211-5463.12516

3. Karav S, Salcedo J, Frese SA, Barile D. Thoroughbred mare’s milk exhibits a unique and diverse free oligosaccharide profile. FEBS Open Bio. 2018; 8(8): 1219-29. doi: 10.1002/2211-5463.12460

4. Karav S, Le Parc A, de Moura JMLN, Frese SA, Kirmiz N, Block DE, et al. Oligosaccharides released from milk glycoproteins are selective growth substrates for infant-associated bifidobacteria. Appl Environ Microbiol. 2016; 82(12): 3622-30. doi: 10.1128/AEM.00547-16

5. Karav S, Bell JM, Parc AL, Liu Y, Mills DA, Block DE, et al. Characterizing the release of bioactive N-glycans from dairy products by a novel endo-beta-N-acetylglucosaminidase. Biotechnol Prog. 2015; 31(5): 1331-39. doi: 10.1002/btpr.2135

6. Karav S, Parc AL, Moura Bell JM, Rouquie C, Mills DA, Barile D, et al. Kinetic characterization of a novel endo-beta-N-acetylglucosaminidase on concentrated bovine colostrum whey to release bioactive glycans. Enzyme Microb Technol. 2015; 77: 46–53. doi: 10.1016/j.enzmictec.2015.05.007

7.Parc AL, Karav S, Rouquié C, Maga EA, Bunyatratchata A, Barile D. Characterization of recombinant human lactoferrin N-glycans expressed in the milk of transgenic cows. PLoS One Press. 2017; 12(2): e0171477. doi: 10.1371/journal.pone.0171477

8. Cohen JL, Karav S, Barile D, de Moura Bell JMLN. Immobilization of an endo-β-N-acetylglucosaminidase for the release of bioactive N-glycans. Catalysts. 2018; 8(7): 278. doi: 10.3390/catal8070278

9.        Karav S, German JB, Rouquié C, Le Parc A, Barile D. Studying lactoferrin N-glycosylation. Int J Mol Sci. 2017; 18(4): 870. doi: 10.3390/ijms18040870

10.      Karav S, Cohen JL, Barile D, de Moura Bell JMLN. Recent advances in immobilization strategies for glycosidases. Biotechnology Progress. 2017; 33(1): 104-12. doi: 10.1002/btpr.2385