Research

Research Fields

DNA obtained from biological materials found in archaeological excavations and forensic events sheds light on the past. Ancient DNA (aDNA) studies conducted in this context have an interdisciplinary character. DNA isolations are carried out from fossils (human, animal, plant, etc.) excavated from archaeological excavations, gender determination and bioinformatics-based polymorphism studies are carried out. In addition, an archaeological excavation, and the soil samples from the other samples (streams, Hot Springs, soil, human samples, etc.) in the samples metagenomics analysis, bacteria, and eukaryotic organisms at the molecular level of archeae identification, disease diagnosis and treatment phase in order to create a token, at dating in archaeological studies are carried out.


Laboratory Equipment

– Gradient PCR – PCR
- Real-time PCR

- Laminar flow cabinet


Research Group

Prof. Dr. Ercan ARICAN 
Umut BÜYÜK (PhD.Student) 
Neşe AKÇAY (PhD.Student) 
Sultan Fidan PEDÜK (PhD Student)

Fahri PAT (PhD Student)
Sevgi BİNAY (PhD.Student) 
Zehra ÖZDEMİR (Ph.D.Student) 
Gülnur ÇIRAK (PhD Student)


Services:

- Identification of organism microbiota by metagenomic techniques (16s rRNA) - Species designation of organisms by DNA sequencing and analysis (NGS)
- Sex Determination (human, animals)

- Haplogroup Determination from skeletons
- Determination of species from seeds or other part of plants

Contact:

Prof. Dr. Ercan ARICAN : 0212 455 57 00 / 15113; earican@istanbul.edu.tr





The Animal Cell Culture Laboratory, which was founded by Prof. Dr. Avni Kuru for the first time in 1992 within the Faculty of Science, was completely renovated in 2007 with a research project supported by the Scientific Research Projects Unit of Istanbul University and started its activities in the Department of Molecular Biology and Genetics.The Animal Cell Culture Laboratory, reorganized according to international rules, continues to serve as a modern laboratory where many dissertations and research projects are conducted. The Animal Cell Culture Laboratory has supported and mentored many units with its wide cell collection, advanced equipment and trained researchers.

Research Fields

Its main research interests include testing the cytotoxic effects of various plant extracts and pure substances, evaluating their antioxidant and antiviral activities and apoptotic effects. Damages in intracellular oxidative stress and cellular molecules (DNA, protein and lipid) as a result of oxidative stress are detected. Researches are carried out to elucidate the mechanisms of antioxidation and detoxification in biological systems.

The laboratory's cell collection includes HeLa, Vero, C6 glioma, NRK 52E, MDCK, and VHF93 cells. In addition to the cell collection, there is also a virus collection (Influenza and Parainfluenza type 2 viruses) in our laboratory.

Laboratory Equipment

– pH meter (Jenco)
– Benchtop Centrifuge (Nüve, NF-400)
– Vortex Shaker (Fisons)
– Benchtop Mini Autoclave (Nüve, OT-012)
– Refrigerator
– Carbon dioxide incubator (HeraCell 240 ve HeraCell 150i, Thermo Scientific)
– Incubator (Nüve, FN-055)
– Laminar Flow Cabinet (Class II, Bilser)
– Vacuum System (Integra Vacusafe)
– Microscope (Prior)
– Inverted Microscope (CK ve CK-31, Olympus)

Research Group


Prof.Dr. Nazlı ARDA Prof. Dr. Ali KARAGÖZ Prof.Dr. EVREN ÖNAY UÇAR Asst. Prof. Dr. MURAT PEKMEZ
Res. Asst. Dr. ELİF MERTOĞLU KAMALI

Contact


Prof.Dr. Nazlı ARDA 0212 455 57 00/15212, 15113; narda@istanbul.edu.tr
Prof. Dr. Ali KARAGÖZ 0212 455 57 00/15116; sanicula@istanbul.edu.tr
Prof. Dr. EVREN ÖNAY UÇAR 0212 455 57 00/15117, 15107; evrenonay@istanbul.edu.tr
Asst. Prof. Dr. MURAT PEKMEZ 0121 455 57 00/15468, 15107; muratpekmez@hotmail.com

Projects


BAP Projects

“Evaluation of Antiviral and Antitumoral Activities of Various Medicinal Plants Used Among the Population” (Project No: 1603/30042001, Completed, Prof. Dr. Ali KARAGÖZ)  

      *    "Fluorometric and Electrophoretic Analysis of Protein Carbonyls Formed as a Result of Oxidative Stress in Cell Cultures” (Project No: 268/23082004, Completed, Prof.Dr. Nazlı ARDA )

           
      *    The Effects of Viscum album Extract on DNA Damage/Repair Caused by Oxidative Stress in Cell Culture” (Project No: 1462, Completed, Project Manager: Prof. Dr. Ali KARAGÖZ)


      *    “Proteomic Approach in Determination of Oxidative Protein Damages and Antioxidant Activity” (Project No: 4120, Continues, Project Manager: Prof. Dr. Nazlı ARDA)


      *    “Effects of Sanicula europaea Extract on the Repair of Damages Caused by Oxidative Stress in Cell Culture“ (Project No: 22649, Continues, Project Manager: Prof. Dr.Evren ÖNAY UÇAR) 


      *    “Investigation of Differentiation Mechanisms of Pancreatic Stem Cells, Acinar Cells and Pancreatic Duct Cells into Beta Cells in Conditions of Glucotoxicity, Lipotoxicity and Glucolipotoxicity“ (Project No: 25275, Continues, Project Manager: Prof.Dr.Şehnaz BOLKENT)

      *    “Cytotoxic effects of Viscum album extracts on cell cultures” (Project No: 27484, Continues, Project Manager: Prof. Dr. Evren ÖNAY UÇAR)


TÜBİTAK Projects


“Determination of Antioxidant, Antiviral and Antimicrobial Activities of Milk Serum Proteins and Hydrolysates and Clarification of Their Structural Properties” (Project no: 104S507 (SBAG-2972), Completed, Project Manager: Prof.Dr.Süha YALÇIN) 

       *    “Determination of the Chemical Content of Some Endemic Cephalaria Species Grown in Turkey, Investigation of Antioxidant and Antimicrobial Activities of Extracts and Compounds to be Identified” (Project no: 107T028, 2006-2010, Project Manager: Prof.Dr.Süheyla Kırmızıgül)
     
       *    “Investigation of the Effects of CoenzymeQ10 and Beta-Carotene Applications on HSP27 Expression in Rat C6 Glioma Cells” (TÜBİTAK Student Project, completed)  “Proteomic Analysis of HSP70 Heat Shock Protein in C6 Rat Glioma Cell Line Treated with CoenzymeQ10 and Beta-Carotene” (TÜBİTAK Student Project, completed)

Ph.D. Thesis Projects


“The Effect of Viscum album Extract on Expression of Stress Proteins in C6 Rat Glioma Cells” (completed) (Evren ÖNAY UÇAR) 

     *    “DNA Damages Caused by Oxidative Stress in Cell Culture and Protective Effect of Olive Oil” (completed) (Özlem EROL) 

     *    “Effects of Vitamin E on Molecular Damage Caused by Indomethacin in Glioma Cells” (completed) (Murat PEKMEZ) 

     *    “The Apoptosis-Inducing Effect of Vitamin E on Rat C6 Glioma Cells” (completed) (Zeynep OKTAY) 

     *    “Evaluation of Cytotoxic Activities of Some Papaver Alkaloids” (completed) (Recep DEMİRGAN)
 
     *    “Evaluation of microRNAs as Markers in Patients Diagnosed with Hepatitis B Virus- Infected Hepatocellular Carcinoma” (continued) (Recep DEMİRGAN)
   
     *    “Evaluation of In Vitro Antiviral Activities of Some Plant Extracts” (continued) (Furkan BÖLÜKBAŞI)





Molecular Biology and Genetics Department-Plant Biotechnology Laboratory was founded by Prof. Dr. Emine Bilge, Prof. Dr. Güler Temizkan and Prof. Dr. Nermin Gözükırmızı.The scientific background of our laboratory is based on genetic studies initiated in plants from the 1950's. Our laboratory has been continuing its scientific activities with national, international and industrial projects supported by using today's technologies such as tissue culture, molecular biology, gene and -omics technologies. Within the scope of these activities, 25 national and international PhD, over 35 MSc thesis and many graduation projects have been completed so far, contributing to the production and applications of knowledge in molecular biology, genetics and biotechnology.

Studies are carried out with institutions such as the Ministry of Agriculture and Forestry, TUBITAK Marmara Research Center Genetic Engineering and Biotechnology Institute, IU Rectorate of Biotechnology and Genetic Engineering Application Research Center. These studies are performed for such as comprehensive education and training, and the transfer of methods, technology and current practices in the field of plant biotechnology to researchers and participants from public and private institutions. Our working group, which carries out pioneering studies and practices in its field, has more than 500 national and international books, chapters, research articles etc.

Laboratory Equipment

– pH Meter
– Refrigerated Centrifuge
– Magnetic Stirrer with Heating
– Desktop Mini Autoclave
– Refrigerator, Freezer
– Shaking Incubator
– Laminar Flow
– Microscope
– Gradient PCR
– Real Time PCR
– Nanodrop Spectrophotometer
– Gel Imaging System
– Plant Growth Chamber
– Ultrapure Water System


Research Group

Faculty Members Internal                                         Internal

 
Prof. Dr. Şule Arı                                                           20309
Prof. Dr. Neslihan Turgut Kara                                   20307
Assoc. Prof. Dr. Özgür Çakır
Assoc. Prof. Dr. Aslıhan Temel
Asst. Prof. Dr. Fatma Elif Çepni Yüzbaşıoğlu
Res. Asst. Dr. Cüneyt Uçarlı
Res. Asst. Burcu Arıkan

* Istanbul University Contact Number: 0212 455 57 00
**Address: IU Bioengineering Building, Molecular Biology and Genetics Department, MB-Z02
Examples of Multicenter Projects of the Plant Biotechnology Laboratory


 * Bazı pestisidlerin farklı organizmalardaki mutagenik etkileri (TÜBİTAK, Grant No: TBAG 515)
 * Mutation experiments on barley tissue culture (The Research Foundation of İstanbul University, Science 181-212/030186) 
   * Trakya bölgesine uygun yüksek verimli arpa hatlarının ıslahı (TÜBİTAK; Grant No: TBAG 623)
 * A comparative study on callus induction, plant regeneration and chromosomal variations from different explant of barley (Hordeum vulgare L.) (NATO-TU Biotechnology, Subproject 1.2.2. Grant No: 842)  

   * Kağıtlık hammadde nitelikleri biyogenetik olarak geliştirilmiş olarak kavak klonlarının üretimi (SEKA, 2001) 
   * Sorgum bitkisinin biyoteknolojik yöntemlerle ıslahı (MSG, 1998) 
   * EUREKA, Cerealstresstol -1322 (1999) 
   * Bitki Biyoteknolojisi (62-1 001, TÜBİTAK, Gen Mühendisliği ve Biyoteknoloji Araştırma Enstitüsü) 
   * Paulownia elongata’ nın doku kültürü sistemlerinin optimizasyonu, mikroüretimi (62- 2-002, TÜBİTAK, GMBAE-Teknogen) 
   * Pamuğun biyoteknolojik yöntemlerle ıslahı (TÜBİTAK, GMBAE-Türk Tekstil Vakfı) 
   * Biyodizel endüstrisi atıksularının fiziksel, kimyasal ve biyolojik yöntemlerle arıtılabilirliğinin incelenmesi (TÜBİTAK- ÇAYDAG Proje No: 108Y039) 
   * Endophytes in Biotechnology and Agriculture, FA COST Action FA1103 [(European Cooperation in Science and Technology) Tübitak Proje No. 111O835]    
   * Monokotil Bitkilerde Transformasyon Çalışmaları (TÜBİTAK, TBAG-1404)


For Current Projects and Publications


Faculty Members                                                                     WEB Adress

Prof. Dr. Şule Arı                                                                      https://avesis.istanbul.edu.tr/sari
Prof. Dr. Neslihan Turgut Kara                                              https://avesis.istanbul.edu.tr/neslihantk
Assoc. Prof. Dr. Özgür Çakır                                                   https://avesis.istanbul.edu.tr/ozgurckr
Assoc. Prof. Dr. Aslıhan Temel                                               https://profil.istanbul.edu.tr/tr/p/atemel
Asst. Prof. Dr. Fatma Elif Çepni Yüzbaşıoğlu                        https://avesis.istanbul.edu.tr/ecepniyuzbasioglu









As studies on the exploration of the atmosphere of planets other than Earth increase, the responses of biological systems to these environmental conditions are better understood. In the light of this information, different atmospheric pressure systems have been developed that are known to be effective on plant physiology and development. With the idea of establishing greenhouses on Mars and the moon, the difficulty of low atmospheric pressure engineering and system installation emerged. Low pressure systems were first tested within the framework of the United States Human Space Programs and special tools were developed to reduce the structural and physiological effects of low pressure. For example, the Mercury, Gemini, and Apollo vehicles were built to create a pressure of 34 kilopascals (kPa) with pure oxygen for astronauts in space. However, the shuttle and space station Alpha are generally designed to operate at near normal pressure (101 kPa), while EVA is designed to operate at 70 kPa. Skylab is manufactured to create a pressure of 34 kPa (70% O2 /30% N2 Gas mixture). It has been determined that humans cannot live at pressures less than 30-40 kPa, whereas plants have the ability to live at pressures as low as 5-10 kPa. It has been found that plants are able to adapt to changes in O2, CO2 and total gas pressure. In addition, the effect of plants on the ability to tolerate low pressure, as well as increase growth, productivity and storage of fruits in such conditions, is also known.

In the Low Pressure Unit, the responses of different organisms (bacteria, yeast, plants, animals, humans) under different pressure and atmospheric conditions are examined at the molecular level.

Laboratory Equipment
* Computer Controlled Low Pressure Cabinet
* Equipment in Department of Molecular Biology and Genetics
Responsible Researcher
Prof. Dr. Ercan ARICAN

Contact: 0212 455 57 00 / 15119, earican@istanbul.edu.tr





Proteomics laboratory was established in 2010 in the Department of Molecular Biology and Genetics within the scope of project no. 4120 supported by Istanbul University Scientific Research Projects Unit and supported by TUBITAK projects, It is an analysis laboratory used in many scientific research, graduate education and thesis studies with its sophisticated equipment and infrastructure investments.

The purpose of the establishment of the proteomics laboratory is to carry out qualified and comprehensive scientific research and to have a say in this field by using sophisticated devices and new methods at international standards in protein studies, which constitute an important part of molecular biology. In addition, by educating a large number of postgraduate students, it is to bring competent researchers who can work in this field both to our university and our country.


Research Topics

In this laboratory, proteome analysis is performed on materials obtained from various biological sources (human, animal, plant and microorganism). Stress proteins and oxidative protein damages are determined by proteomic techniques. The activities of various enzymes are measured, electrophoretic and chromatographic separation of polypeptides is performed.


Laboratory Equipment

*   pH meter (Inolab)

*   Magnetic Stirrer with Heating (Heidolph)

*   Scale (Precisa)

*   Precision Scale (Man)

*   Isoelectric Focusing Device (Protean IEF Cell, Bio-Rad)

*   Refrigerated Centrifuge (Sigma 3-30K)

*   Western Blot System (Semi-Dry Blotter, Bio-RAD)

*   Tube mixer (Velp Scientifica)

*   Vertical Electrophoresis Systems (Bio-Rad, ATTO)

*   Ultrasonic Water Bath (Wise Clean)

*   Tube Roller (Vural Medical)

*   Plate Shaker (Heidolph Unimax 1010)

*   Molecular Imager ChemiDoc XRS System (Bio-Rad)

*   Spectrofluorometer (Biotek FLX-800)

*   Gel Imaging System (GS-800 Calibrated Densitometry, Bio-Rad)

*   Protein Purification Device (Profinia, Bio-Rad)

*   Gel Drying System (Clever Scientific)

*   Automatic Electrophoresis System (Experion, Bio-Rad) o Deep freeze o Fridge

*   HPLC (Schimadzu)  Qubit Spectrofluorometer (Invitrogen)


Research Group

*   Prof. Dr. Nazlı ARDA
*   Prof. Dr. Ali KARAGÖZ
*   Prof. Dr. Evren ÖNAY UÇAR
*   Asst. Prof. Murat PEKMEZ
*   Res. Asst. Dr. Elif MERTOĞLU

Contacts

Prof. Dr. Nazlı ARDA : 0212 455 57 00/15212, 15113; narda@istanbul.edu.tr
Prof. Dr. Evren ÖNAY UÇAR : 0212 455 57 00 / 15117; evrenonay@istanbul.edu.tr

Projects

BAP Projects

*   “Fluorometric and Electrophoretic Analysis of Protein Carbonyls Formed as a Result of Oxidative Stress in Cell Cultures” (Project No: 268/23082004, completed, Director: Prof.Dr. Nazlı ARDA)
*   “Effects of Viscum album Extract on DNA Damage/Repair Caused by Oxidative Stress in Cell Culture” (Project No: 1462, completed, Director: Assistant Prof. Dr. Ali KARAGÖZ)
*   “Investigation of Allergenicity and Immunohistochemical Properties of Some Tree Pollens in Istanbul Parks, Gardens and Groves” (Project No: 3063, Ongoing, Director: Prof.Dr.Suna Büyüköztürk)
*   “Proteomic Approach in the Determination of Oxidative Protein Damages and Determination of Antioxidant Activity” (Project No: 4120, completed, Director: Prof. Dr.
Nazlı ARDA)
*   “Effects of Sanicula europaea Extract on the Repair of Damages Caused by Oxidative Stress in Cell Culture” (Project No: 22649, ongoing, Director: Dr. Evren ÖNAY UÇAR) *   “Investigation of Differentiation Mechanisms of Pancreatic Stem Cells, Acinar Cells and Pancreatic Duct Cells into Beta Cells in Conditions of Glucotoxicity, Lipotoxicity and Glucolipotoxicity“(Project No: 25275, ongoing, Director: Prof.Dr.Şehnaz BOLKENT)
*   “Demonstration of intracellular phosphorylation in Schizosaccharomyces pombe” (Project No: 20423, ongoing, Director: Assist.Prof. Bedia Palabıyık)

TÜBİTAK Projects

*   “Determination of Antioxidant, Antiviral and Antimicrobial Activities of Milk Serum Proteins and Hydrolysates and Clarifying Their Structural Properties” (Project no: 104S507 (SBAG-2972), completed, Director: Prof. Dr. Süha YALÇIN)
*   “Investigation of Aerobic Granular Sludge Structure and Stability” (Project No:107Y137, completed, Director: Asst. Prof. Gülsüm YILMAZ)
*   "Determination of Chemical Contents of Some Endemic Cephalaria Species Growing in Turkey, Investigation of Antioxidant and Antimicrobial Activities of Extracts and Compounds to be Identified" (Project no: 107T028, 2006-2010, Executive: Prof. Dr. Süheyla KIRMIZIGÜL)
*   “Investigation of the Effects of CoenzymeQ10 and Beta-Carotene Applications on HSP27 Expression in Rat C6 Glioma Cells” (TÜBİTAK Student Project, completed) 
*   “Proteomic Analysis of HSP70 Heat Shock Protein in C6 Rat Glioma Cell Line Treated with CoenzymeQ10 and Beta-Carotene” (TÜBİTAK Student Project, completed)

PhD Thesis Projects

*   “Protective Effect of Antioxidants Against Protein Oxidation in Schizosaccharomyces pombe Under Oxidative Stress”, İsmail HAMAD (completed).
*   “Effect of Viscum album Extract on Expression of Stress Proteins in C6 Rat Glioma Cells”, Evren ÖNAY UÇAR (completed).
*   “DNA Damages Caused by Oxidative Stress in Cell Culture and Protective Effect of Olive Oil”, Özlem EROL (completed).
*   “Effects of Vitamin E on Molecular Damages Caused by Indomethacin in Glioma Cells”, Murat PEKMEZ (completed).
*   “Examination of Oxidative Stress-Associated Gene Expressions in Human Thoracic Aortic Aneurysms”, Zelal ADIGÜZEL (completed).

Master Thesis Projects

*   “Apoptosis Inducing Effect of Vitamin E on Rat C6 Glioma Cells”, Zeynep OKTAY (completed).
*   “Proteomic Analysis of Yellow Rust Resistant Wheat (Triticum aestivum L.)”, Cihan İNAN (completed).
*   “White Mulberry (Morus alba L.) and Blue Atlas Cedar in Istanbul [Cedrus atlantica (Endl.) Carr. cv. Glauca] Pollens Allergenic Proteins”, Demirhan ÇETEREİSİ, (completed).

“Allergenic Proteins of Pollens of Mediterranean Sycamore (Cupressus sempervirens L.) and Sabin Juniper (Juniperus sabina L.) in Istanbul”, Şahin Taş (completed).







Genetic Diseases and Molecular Analysis Research Laboratory conducts genomic and transcriptomic studies on human diseases. It is focused on finding biomarkers in order to elucidate the pathophysiology of diseases and to make an early diagnosis.

Researches are conducted on prenatal diagnosis, in vitro fertilization (IVF), recurrent miscarriages, ovarian cancer and sports genetics. In our researches, DNA, RNA and small RNA (miRNA, piRNA) expressions from blood, tissue, amniotic fluid, peritoneal fluid and other body samples are analyzed using advanced technological methods such as microarray, PCR, digital PCR and sequencing. In the field of prenatal diagnosis, 4 important miRNA patents were obtained, which can be used as a marker for early diagnosis of diseases such as preeclampsia, which affects both the baby and the mother. In order to investigate the molecular causes of recurrent miscarriages and IVF failures, tissue and blood samples were taken from these patients and different miRNA, mRNA and gene profiles were obtained.

In our laboratory, we are trying to detect genes, mRNAs and miRNAs, which are effective in the formation and progression of ovarian cancer, by non-invasive methods (liquid biopsy) in the early stages. In addition, we continue to work on the effect and analysis of cancer stem cells, which cause cancer recurrence, in ovarian cancer.

Genetic Diseases and Molecular Analysis Research Laboratory also works on sports and exercise science with the study of polymorphisms in the genome. In order to discover molecular markers for the diagnosis and treatment of these diseases of genetic origin, we conduct academic studies by training students at the master's and doctoral levels with researchers who have received bachelor's degrees from different disciplines. The results of our researches carried out in all these areas have been published in international journals with high scientific impact factor. Our team, which produces at least 4 articles every year, continues its studies intensively and contributes to the scientific world for the molecular analysis of human diseases.

Contacts


Prof. Dr. Tuba GÜNEL 0212 455 57 00 / 20305, gunel@istanbul.edu.tr
Res. Asst. Ece GÜMÜŞOĞLU 0212 455 57 00 / 20305, ece.gumusoglu@istanbul.edu.tr





Research Topics

In this laboratory, Schizosaccharomyces pombe strain, which is used as a model organism in researches on diseases related to heavy metal metabolism, aging and cancer, is used to determine the targets and activities of active pharmaceutical ingredients.

In addition, glucose suppression and oxidative stress response metabolisms in this organism are tried to be clarified. Investigation of glucose sensing, intracellular transport, signal transduction and stress response pathways in Schizosaccharomyces pombe yeast, which is a eukaryotic model organism, are carried out both by transcriptome analysis and expression analysis of target genes using qPCR technique, as well as using biochemical techniques. In addition to these studies, synthesis and destruction rates of storage carbohydrates against oxidative stress and heat shock researhes are carried out in our laboratory. In the same conditions, transcription analysis of genes related to thiamine metabolism is also performed. to these studies, investigating the synthesis and destruction rates of storage carbohydrates against oxidative stress and heat shock, transcription analysis of genes related to thiamine metabolism is also carried out under the same conditions. Besides, structural and transcriptional analyzes of the genes that play role in glucose sensing and glucose uptake into the cell are performed.

Laboratory Equipment


*   Eukaryotic cell counter
*   Cell lysis tools
*   Gel imaging systems
*   Shaking incubator
*   Biosafety cabinet


Research Group

*   Prof. Dr. Bedia Gemici PALABIYIK
*   Asst. Prof. Dr. Semian KARAER UZUNER
*   Asst. Prof. Dr. Çağatay TARHAN
*   Res. Asst. Dr. Merve YILMAZER


Contacts

Asst. Prof. Semian KARAER UZUNER: 0212 455 57 00/15108; semka@istanbul.edu.tr
Prof. Dr. Bedia Gemici PALABIYIK: 0212 455 57 00/15467; bediag@istanbul.edu.tr

Projects


*   Investigation of zinc carrier proteins specific to superoxide dismutase enzyme in yeast
*   Studies on cellular senescence in Schizosaccharomyces pombe
*   Investigation of the Relationship between Glucose Metabolism and Oxidative Stress Response in Glucose Suppression-Resistant Invertase Mutants of Schizosaccharomyces pombe, İ.Ü. Scientific Research Projects Executive Secretariat.
*   enome-Dimensional Investigation of the Relationship Between Glucose Signaling and Oxidative Stress in Schizosaccharomyces pombe Invertase Mutants, İ.Ü. Scientific Research Projects Executive Secretariat.
*   Investigation of Glucose Suppression and Stress Response Pathways in Schizosaccharomyces pombe, TÜBİTAK-TBAG, Project No: 211T178.






Bioinformatics can be defined as the use of information technologies in the solution of biological problems. In its narrowest definition, it is the creation and operation of biological databases that support genomic sequences. In its broadest definition, it is understood as the use of all existing computer applications in solving biological problems.

Bioinformatics encompasses two main streams of knowledge in modern biology:

1. Genetic information flow: The information flow from determining the characteristics of an organism by examining its DNA, to the characteristic features of the communities formed by this organism species. The obtained DNA information is used again to define the genetic pool.

2. Experimental information flow: The information obtained by observing biological events is described with explanatory models, then the accuracy of these models is tested with new experiments.

In the last two decades, the impact of basic biological research on clinical medicine applications and clinical medicine information systems has been more decisive and has led to the emergence of a new generation of epidemiological, diagnostic, diagnostic and therapeutic modules. Although bioinformatics studies seem to be aimed at basic scientific research, they will be indispensable for clinical informatics in the next ten years. For example, DNA sequence information will be included in the medical forms of patients with increasing frequency. Today, some insurance companies in the USA can request current genetic screening test results when determining risk premiums.

The bioinformatics working group carries out studies to investigate different DNA structures (Z-DNA, G-Quadruplex, etc.) in the genome of yeast (S. cerevisiae and S. pombe) and to determine the interactions between related structures and gene functions. Since it is a model organism, this information to be obtained especially from the S. pombe genome; will present new approaches for animal and human molecular studies (cancer, apoptosis, systems biology, etc.). The working group also works on bioinformatics-supported molecular marker determination in plants.

Project:

Detection of Z-DNA occurrences in S. pombe genome by web-based programs.


Members of Bioinformatics Working Group

*   Prof. Dr. Ercan ARICAN

*   Asst. Prof. Dr. Andres ARAVENA

Research and Development (R&D) Units 

Faculty Members


*   Prof. Dr. Gülruh Albayrak 
*   Asst. Prof. Terje Marken Steinum

R&D Personnel

*   Asst. Prof. Elif Çepni Yüzbaşıoğlu
*   Res. Asst. Gülin İnci Varol

Department/Faculty/University Collaborations

*  Faculty of Aquatic Sciences, Department of Aquaculture and Diseases, Department of Fisheries Diseases

National Collaborations

*   Istanbul Yeni Yüzyıl University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics
*   Istanbul Yeni Yüzyıl University, Faculty of Medicine, Department of Medical Biology and Genetics
*   On Dokuz Mayıs University, Faculty of Agriculture, Department of Plant Protection

International Collaborations

*   University of Turku, Department of Biochemistry and Food Chemistry (Finland)
*   Isfahan University of Technology, Faculty of Agriculture (Iran)
*   University of Punjab (Pakistan)

Study Team

*   Specialist Aylin Gazdağlı (PhD Student)
*   Specialist Tuğba Teker (PhD Student)
*   Specialist Mebruke Saba Akpir Ulusoy (PhD Student)
*   Specialist Inji Shikhaliyeva (PhD Student)
*   Büşra Nur Çetin (Master Student)
*   Mehmet Arslan (Master Student)
*   Çağatay Yetim (Master Student)
*   Özlem Sefer (Master Student)
*   Serhat Yağmur Ofluoğlu (Master Student)
*   Syeda Anum Khalid (Exchange Student)


Research Areas



Research area 1 (Molecular Mycology)
*   Genotyping, chemotyping, secondary metabolite production, investigation of antifungal effects of natural vegetable oils, microbial transformation and gene silencing studies in plant pathogenic fungi

Research area 2 (Molecular Bacteriology)

*   Studies on the characterization of virulence mechanisms of bacteria causing disease in fish  Studies on inhibition of virulence of bacteria responsible for disease in humans

Research area 3 (Molecular Biology)

*   Investigation of the effects of mycotoxins on stem cells

Techniques
 Basic molecular biology and basic microbiology techniques; recombinant DNA technology, amplification by polymerase chain reaction (PCR) and real-time PCR, cationic polymer-mediated and vector-mediated quelling, gel electrophoresis, MIC and MBK determination, antibiogram (disk diffusion-mediated), API-mediated biochemical diagnosis, viability tests, etc.
Laboratory Equipment
 Class II biosafety cabinet
 Temperature and light controlled growth chamber  PCR Thermal Cycler  Shaker incubator  Desktop centrifuge  Gel electrophoresis systems  Water bath  Light microscope  Fluorescent microscope (Common use)  Real-time PCR device (Common use)  Electroporation device (Common use)  Gel imaging system (Common use)  Incubator (Common use)  Refrigerated centrifuge (Common use)  Fume hood (Common use)  Spectrophotometer (Common use)  Ultrasonicator (Common use)
Examples from Research Projects
 Studies on Development of New Generic Microsatellite Markers that Can Be Used in Genotyping of Fusarium Species (IU BAP- 2014 completed)  Genotyping of Fusarium graminearum Isolates with CAPS Markers (IU BAP- 2014)  Cessation of Trichothecene Production in Fusarium Species (İ.Ü. BAP- 2014)  Mitochondrial DNA variation analysis of Fusarium graminearum isolates (İ.Ü. BAP- 2015)
 Genotyping of Fusarium culmorum Isolates with CAPS Markers (IU BAP- 2016)  Retrotransposon-based molecular marker screening in Fusarium graminearum (IU BAP- 2016)
 Determination of Mycotoxin Production Potential in Fusarium Species by PCR Analysis (IU BAP- 2017)  ISSR marker-based genetic typing of Fusarium graminearum and Fusarium culmorum isolates (İ.Ü. BAP- 2017)  Molecular Analysis of Mycelium Coloration in Fusarium Species (TÜBİTAK 3001- 2018)
 Investigation of Nikita and Succula Retrotransposons in Fusarium Species (IU BAP- 2017 continues)  Molecular characterization of virulence genes in Lactococcus garvieae” (IU BAP- 2017)
 Investigation of Phylogenetic and Enzymatic Characteristics of T. maritimum isolates (IU BAP- 2016 continues)  Determination of Bacterial Microbiota of Some Octacoral Species Living in the Sea of Marmara (TÜBİTAK-2017 continues).
Examples from Current Master's and Doctoral Thesis Titles
Master Thesis Titles
 • Molecular Characterization of Virulence Genes in Lactococcus garvieae  • Targeted Genotype Analysis of Fusarium Isolates in 3ADON Chemotype
PhD Thesis Title
 • Molecular Analysis of Mycelium Coloration in Fusarium Species  Transcriptomic Screening of the Effects of Mycotoxins on Survival and Division of Mesenchymal Stem Cells
Examples from Publications
 Yörük E., Albayrak G., “siRNA quelling of tri4 and tri5 genes related to deoxynivalenol  synthesis in Fusarium graminearum and F. culmorum”, Journal of Environmental
 Biology, https://doi.org/10.22438/jeb/, basımda, 2019
 Teker T., Albayrak G., Akayli T., Urku C., “Detection of Haemolysin Genes as Genetic Determinants of Virulence in Lactococcus garvieae”, Turk. J. Fish.& Aquat.
Sci. https://doi.org/10.4194/1303-2712-v19_7_09, 19(7), basımda, 2019
 Gazdağlı A., Sefer Ö., Yörük E., Varol G.İ., Teker T., Albayrak G., “Investigation of Camphor Effects on Fusarium graminearum and F. culmorum at Different Molecular Levels”, Pathogens, 7, 90: 1-11, 2018  Yörük E.,Gazdağlı A., ALBAYRAK G., “Effects of Growth Conditions on tri4 Gene Expression in Fusarium culmorum”, Journal of Agricultural Faculty of Gaziosmanpasa University, 34 (2): 91-97, 2017  Albayrak G., Yörük E., Gazdağlı A., Sharifnabi B., "Genetic Diversity Among Fusarium graminearum And F. culmorum Isolates Based on ISSR Markers", Archives of Biological Sciences, vol.68, pp.333-343, 2016  Yörük E., Albayrak G., "Geneticin (G418) resistance and electroporation-mediated transformation of Fusarium graminearum and F. culmorum", BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT, vol.29, pp.268-273, 2015  Yörük, E., Karlik, E., Gazdagli, A., Kayis, M., Kaya, F., & Albayrak, G. “PKS13, FG08079. 1 and PKS10 gene expression analysis in Fusarium graminearum and Fusarium culmorum by real time PCR.”, Iranian Journal of Biotechnology, 13(2), 53- 57, 2015
 Yörük E., Gazdağlı A., Albayrak G., "Class B Trichothecene Chemotyping In Fusarium Species By PCR Assay", GENETIKA-BELGRADE, vol.46, pp.661-669, 2014
 Albayrak G., Yörük E., "Genetic Characterization of Fusarium graminearum and F. culmorum Isolates From Turkey By Using Random-Amplified Polymorphic DNA", Genetıcs And Molecular Research, no.2, pp.1360-1372, 2013  Yörük, E., and Albayrak, G., Chemotyping of Fusarium graminearum and F. culmorum isolates from Turkey by PCR assay. Mycopathologia, 173(1), 53-61, 2012  Olsen AB, Gulla S., Steinum TM, Colquhoun DJ, Nilsen HK and Duchaud E. (2017) Multilocus sequence analysis reveals extensive genetic variety within Tenacibaculum spp. associated with ulcers in sea-farmed fish in Norway. Veterinary Microbiology; Volume 205, pp. 39-45.  Steinum TM, Karataş S, Tandstad Martinussen N, Meirelles PM, Thompson FL and Colquhoun DJ (2016) Multi-Locus Sequence Analysis of the close relatives Vibrio anguillarum and Vibrio ordalii Appl. Environ. Microbiol. 82(18) pp. 5496-5504.  Turgay E, Steinum TM, Gul AG and Karatas S (2015) An outbreak of scuticociliatosis in cultured common dentex (Dentex dentex) in Turkey. Bull. Eur. Ass. Fish Pathol., 35(3) pp. 104-109.
 Mitchell SO, Steinum TM, Toenshoff ER, Kvellestad A, Falk K, Horn M and Colquhoun DJ (2013) ‘Candidatus Branchiomonas cysticola’ is a common agent of epitheliocysts in seawater farmed Atlantic salmon (Salmo salar) in Norway and Ireland. Dis Aquat Organ. 103(1): pp. 35-43.
Services
 Pathogenic bacteria species diagnosis, 2018