ISTANBUL UNIVERSITY · İstanbul University is the first university in Turkey and among the first ten universities founded in Europe, directing the society in areas of health, social

İstanbul University Central Campus34452 Beyazıt / Fatih-İstanbul+90 (212) 440 00 00 [email protected]

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ISTANBUL UNIVERSITY RESEARCH LABORATORIES2014

ContentsLABORATORY OF INTERACTIONS BETWEEN SUBSTANCE AND MIND 10NEUROIMMUNOLOGY and IMMUNOGENETICS LABORATORY 11LABORATORY of COGNITIVE NEUROSCIENCE 12BIOPHYSICS LABORATORY 13LABORATORY of ELECTROENCEPHALOGRAPHY 14GENETIC RESEARCH LABORATORY 15HISTOLOGY and EMBRYOLOGY RESEARCH LABORATORIES 16LABORATORY of CHILD HEALTH and DISEASES, and NUTRITION METABOLISM 17LABORATORY of NEUROPSCHOLOGY 18MICROBIOLOGY RESEARCH LABORATORIES 19PEDIATRIC ENDOCRINOLOGY RESEARCH LABORATORY 20LABORATORY of MEDICAL BIOLOGY 21LABORATORY of BRAIN and NEURODEGENERATIVE/NEUROGENETIC DISEASES 22CENTER for HEARING and SPEECH DISORDERS / LABORATORY of AUDIOLOGY 23SLEEP and WAKE DISORDERS UNIT 24LABORATORY of PEDIATRIC GENETICS 25LABORATORY of MOLECULAR GENETICS 26ANALYTICAL CHEMISTRY RESEARCH LABORATORY 27PHARMACOGNOSY RESEARCH LABORATORY 28PHARMACOLOGY RESEARCH LABORATORY 29PHARMACEUTICAL TECHNOLOGY RESEARCH LABORATORY 30PHARMACEUTICAL TOXICOLOGY RESEARCH LABORATORY 31ISTE (HERBARIUM) 32LABORATORY of ANDROLOGY 33LABORATORY of DNA ANALYSIS 34FOSSIL DNA LABORATORY 35FOOD SCIENCE LABORATORIES 36CELL CULTURE LABORATORY 37IN VITRO FERTILIZATION and EMBRYO TRANSFER LABORATORY 38CARCASS and MEAT QUALITY LABORATORY 39OSTEOARCHAEOLOGY LABORATORY 40VIROLOGY RESEARCH LABORATORY 41 FLOW CYTOMETRY LABORATORY 42

RARE DISEASES RESEARCH LABORATORY 43MOLECULAR HEMATOLOGY RESEARCH LABORATORY 44TUBERCULOSIS MOLECULAR EPIDEMIOLOGY LABORATORY 45LABORATORY of TISSUE CULTURE and PROTEOMICS 46LABORATORY of NEUROIMMUNOLOGY 47LABORATORY for PRODUCTION, PURIFICATION and INVESTIGATION of EXPERIMENTAL ANI-MALS 48MOLECULAR METABOLIC RESEARCH LABORATORY 49ISOLATION and TRANSPLANTATION of ISLETS of LANGERHANS RESEARCH LABORATORY 50HEMATOPOIETIC and STEM CELL LABORATORY 51HULUSİ BEHÇET LIFE SCIENCES RESEARCH LABORATORY 52OBSERVATORY IST60 TELESCOPE 56SOLAR OBSERVATORY 57CELL and TISSUE CULTURE LABORATORY 58MOLECULAR CELL BIOLOGY RESEARCH LABORATORY 59BIOCHEMISTRY RESEARCH LABORATORY 60PRIMARY-STEM CELL and CANCER RESEARCH LABORATORY 61RADIOECOLOGY LABORATORY 62MOLECULAR CANCER BIOLOGY LABORATORY 63IMMUNOHISTOCHEMISTRY RESEARCH LABORATORY 64PHYSIOLOGY RESEARCH LABORATORY 65MOLECULAR RADIOBIOLOGY and BIOMOLECULAR TECHNOLOGY RESEARCH LABORATORY 66PLANT BIOTECHNOLOGY and GENETICALLY MODIFIED ORGANISMS LABORATORY 67ENVIRONMENTAL and INSTRUMENTAL ANALYSIS LABORATORY 68FUNDAMENTAL and INDUSTRIAL MICROBIOLOGY RESEARCH LABORATORY 69MOLECULAR RADIOBIOLOGY and PLANT BIOTECHNOLOGY RESEARCH LABORATORY 70PLANKTON CULTURE LABORATORY 71ISTF (HERBARIUM) 72NANO and OPTOELECTRONIC RESEARCH LABORATORY 73ADVANCED LITHOGRAPHIC METHODS LABORATORY 74HIGH MAGNETIC FIELD and LOW TEMPERATURE LABORATORY 75MOLECULAR SPECTROSCOPY LABORATORY 76LASER SPECTROSCOPY LABORATORY 77DIELECTRIC SPECTROSCOPY LABORATORY 78

NUCLEAR PHYSICS RESEARCH LABORATORY 79ANCIENT DNA RESEARCH LABORATORY 80PLANT BIOTECHNOLOGY LABORATORY 81PROTEOMICS LABORATORY 82MOLECULAR DIAGNOSIS in HUMAN DISEASES LABORATORY 83PLANT GENOMIC RESEARCH LABORATORY 84BIOINFORMATICS LABORATORY 85GENETICALLY MODIFIED ORGANISMS LABORATORY 86PLANT PATHOLOGY LABORATORY 87PLANT SECONDARY METABOLISM ENGINEERING LABORATORY 88YEAST GENETICS,TECHNOLOGY and GENOMIC RESEARCH LABORATORY 89WASTE TECHNOLOGY RESEARCH LABORATORY 90ORGANIC CHEMISTRY RESEARCH LABORATORY 91FOOD ANTIOXIDANTS MEASUREMENT APPLICATION and RESEARCH CENTER 92BIOCHEMISTRY RESEARCH LABORATORY 93PROCESS and REACTOR DESIGN RESEARCH LABORATORY 94GEOCHRONOLOGICAL SAMPLE PREPARATION and MINERAL SEPARATION LABORATORY 95SOIL SCIENCE (AGROLOGY) and ECOLOGY LABORATORY 96LABORATORY and THERMAL ANALYSIS LABORATORY 97PROF. DR. A. YILMAZ BOZKURT WOODEN MATERIALS COMBUSTION TEST and ANALYSIS LAB-ORATORY 98ANNUAL RING RESEARCHES and WOOD ANATOMY LABORATORY 99PROF. DR. A. YILMAZ BOZKURT WOOD ANATOMY LABORATORY 100FORESTRY PRODUCTS CHEMISTRY and TECHNOLOGY RESEARCH LABORATORY and CELLU-LOSE, PAPER and CARDBOARD ANALYSIS LABORATORY 101BASIN MANAGEMENT LABORATORY 102INSTRUMENTAL ANALYSIS LABORATORY 103ECOTOXICOLOGY and CYANOTOXIN LABORATORY 104TECHNOLOGY TRANSFER APPLICATION AND RESEARCH CENTER CENTRAL RESEARCH LABORATORY (MERLAB) 105PRODUCTION and POST-PRODUCTION LABORATORY 108PREHISTORY LABORATORY 109SHIP CONSERVATION and RECONSTRUCTION LABORATORY 110

PREFACE

İstanbul University is the first university in Turkey and among the first ten universities founded in Europe, directing the society in areas of health, social sciences, natural science and engineering as well as culture and art throughout its 561-year history. It is the biggest and the most established university in Turkey, running 767 diploma programs, with its 20 Faculties, 17 Institutes, 3 Colleges, 1 Conservatoire, 7 Vocational Schools, 41 Application and Research Centers, and 3 Departments. It has a unique training and education potential with its approximately 18,000 graduates.

The objectives of İstanbul University, among world’s top 500 universities (ARWU ranking) for the past eight years, for the near future are to be among the world’s top 100 universities and maintain its greatest role in shaping our past/history since 1453 as a “Bridge of Science from the Past into the Future”.

Istanbul University has the highest number of publications in Turkey, the number of publications per faculty member increases approximately by 5% each year. It was the serious support attempts for improving the research facilities of scientists at the international level and for strengthening their motivation that led to the attainment of this success. What plays a key role in the progress of nations in the scientific arena is the support given to fundamental scientific research. However, in a globalized world, research that benefits the society is the only way to achieve sustainable development, welfare the whole society enjoys, and a future for a world where we can live. The achievement of this objective is through collaboration of all relevant institute and institutions in areas of research on applied sciences, without neglecting fundamental scientific research.

In the last five years, İstanbul University has recognized it as its primary objective to carry its research capacity beyond scientific publications and transform it into new technology and products offering solutions to the problems of our country, region and world society. Our mission is to produce sustainable solutions to the problems in the fields of environment, energy sources, social area, health and culture by research relevant for the society, on the other hand, our vision is to achieve this objective through regional and academic cooperation and in ten years to carry this process to a level that will draw attention of the international academic community.

The aim, in preparing the Catalogue of Research Laboratories at İstanbul University, is to enhance our collaboration with our national and international partners in the fields of health, science, engineering, and social sciences by presenting our university’s research inventory and facilities for research to universities, state institutions, private sector establishments, and the public.

We present our research inventory as well as vast opportunities of our laboratories to the attention of universities, state institutions, private sector entities and society through our catalogue, The Catalogue of Research Laboratories of İstanbul University, in order to increase our cooperation with our stakeholders in the fields of health, science, engineering and social sciences.

Prof. Dr. Yunus SÖYLET RECTOR

HEALTH SCIENCES RESEARCH LABORATORIES

Laboratory Supervisor and Contact Information

Prof. Dr. Sacit Karamürsel+90 212 4142000 - [email protected]

Research Infrastructure of the Laboratory

Modulated transcranial electrical stimulation system,

EEG-Neurofeedback system, Visual stimulation Po-

tential/Electroretinography System (8-channel pol-

ygraph, Analog/digital converters, Visual stimulus

presentation systems).

Collaborations and Projects

The laboratory took part in the project titled “Elec-

trical Neuronal Oscillations and Cognition” within

the scope of the COST program by European Union.

A joint project has been conducted with Macedonian

Academy of Sciences on EEG-Neurofeedback within

the scope of TÜBİTAK’s (Scientific and Technolog-

ical Research Council of Turkey) Macedonia-Turkey

bilateral research support.

Research on impact of modulat-ed transcranial electrical stimula-tion on assertiveness, studies on

measurement of thresholds of sensa-tion and pain by electrical stimulation, investigation of impact of transcranial electrical stimulation on sensation-pain threshold and sympathetic system, fol-low-up using neuromonitarization dur-ing brain and nervous system surger-ies and comparative electrophysiology studies in invertebrates are conducted, and design and construction of devices as well as development of measuring techniques for these experimental stud-ies continue.

ISTANBUL FACULTY of MEDICINE LABORATORY OF INTERACTIONS BETWEEN SUBSTANCE AND MIND

10



Laminar flow cabinet, CO2 incubator, Inverted mi-

croscope, Fluorescent microscope, ELISA reading

device, Centrifuge, Thermal cycler, Real time ther-

mal cycler (Light thermal cycler), Nanodrop, Hori-

zontal electrophoresis equipment, Gel imaging and

documentation device.


We run collaborative studies with Heidelberg Uni-

versity (Germany), Mannheim University (Germa-

ny) and Petras University (Greece).

Among autoimmune diseases, im-munologic mechanisms of nerv-ous system diseases are predom-

inantly investigated. Firstly, biological materials of multiple sclerosis, myas-thenia gravis and other related disease groups are stored as in a data bank, evaluated and developed as a multidis-ciplinary cooperation environment. Re-search is conducted by evaluation of cellular immune response and genetic examinations.

Prof. Dr. Güher Saruhan Direskeneli +90 212 4142000 - [email protected]

ISTANBUL FACULTY of MEDICINE NEUROIMMUNOLOGY and IMMUNOGENETICS LABORATORY

11


Prof. Dr. Tamer Demiralp+90 212 4142000 - [email protected]

Brain structures and mechanisms activated during such cognitive processes as perception, atten-

tion, memory and language in human beings by methods of Electroencepha-logram (EEG), Event Related Brain Po-tentials (ERPs) and Navigated Transcra-nial Magnetic Stimulation (TMS) are investigated. Laboratory’s main field of research is integration of functional MRI (fMRI) or TMS methods with EEG and ERP measurements by using TMS and Magnetic Resonance Imaging (MRI) compatible EEG/ERP systems. Beside basic brain research, neurobiological mechanisms of various dementias and psychiatric diseases, including primari-ly Alzheimer’s disease and Parkinson’s disease, as well as effects of cardiovas-cular factors posing a risk for cognition are investigated


EEG/ERPs Laboratory (electromagnetic and sound

isolation room, 32 and 64-channel digital EEG am-

plifier, visual/auditory stimulus presentation systems

and software, EEG/ERPs analysis software), MR and

TMS compatible 32-channel EEG/ERPs System,

Navigated Transcranial Magnetic Stimulation (TMS)

System.


We have collaborations and joint projects with Bre-

men University (Germany), Munich Ludwig-Maxi-

milian University (Germany), Max Planck Institute

for Human Cognitive And Brain Sciences (Leipzig,

Germany), Berlin School of Mind and Brain (Ger-

many) and Cuban Neuroscience Institute. We also

conduct joint TÜBİTAK (Scientific and Technologi-

cal Research Council of Turkey) project with Ankara

University and joint İSTKA (İstanbul Development

Agency) project with İstanbul Şehir University (Tur-

key) and joint research with Boğaziçi University

(Turkey).

ISTANBUL FACULTY of MEDICINE LABORATORY of COGNITIVE NEUROSCIENCE

12


Important studies on cell and tissue cultures, and stem cells have been performed for many years. It has

played a pioneering role in production of Hybridoma and monoclonal anti-body in our country. Important studies are performed on purification of pro-teins, nucleic acids (DNA-RNA (mRNA, tRNA)) and any organelles from cells and tissues, cell and tissue-level imag-ing by molecular methods (immunoflu-orescence), recombinant protein pro-duction by biotechnological methods, development and purification of poly-clonal antibodies, protein-protein/ pro-tein-ligand interactions, intracellular pro-tein trafficking, in vitro protein synthesis, description of post-translational modifi-cations (ADP-ribosylation, phosphoryl-ation) and eukaryotic and prokaryotic protein synthesis mechanisms. There are studies on apoptosis, oxidative stress, effects of antioxidants on oxida-tive stress, mitochondrial damage, C++ metabolisms and ion channels, mesen-

chymal stem cell isolation, culture from tissue and organs, hematopoietic stem cells and cancer stem cell isolation and tissue engineering.

Prof.Dr. Muhammet Bektaş

+90 212 4142000 - [email protected]

Prof. Dr. Işıl Albeniz+90 212 4142000 - [email protected]


Cold room, Hot room, Dark room, Laminar flow

cabinet, CO2 incubator, Inverted microscope, Flu-

orescence microscope, Thermal cycler, Semi-dry

“Western Blot”, Vertical and horizontal electrophore-

sis equipment, Lyophilizer, Viscometer, Mixer (vor-

tex), Liquid chromatography purification system,

Fluorescence spectrophotometer, UV-Vis spectro-

photometer, Transilluminator, Electrophoresis tank.


We conduct collaborative studies with MD Ander-

son Cancer Research Center (USA) and Semmelweis

University (Hungary).

ISTANBUL FACULTY of MEDICINE BIOPHYSICS LABORATORY

13


Prof. Dr. Betül Baykal+90 212 41420000 - [email protected]

Routine and urgent EEG recording for diagnosis and differential diag-nosis of neurological diseases are

performed. Hyperventilation and photic stimulation are performed for each pa-tient. Polysomnography and other re-flex triggers are used when required. Both short-term and long-term Vid-eo-EEG stimulant recordings are used for diagnosis of pseudoseizures and sei-zure types. Moreover, 24-hour and con-tinuous preoperative monitorization for epilepsy surgery is performed. It is used as a supportive method for such devel-oping and internal diseases as psychiat-ric disorders and encephalography. Oth-er than diagnostic recordings, we also conduct scientific projects for research purposes.


EEG, Video-EEG device and short-term and long-

term continuous Video-EEG.


Projects and studies are conducted with 31 centers

primarily including Germany, Italy and France with-

in the frame of Epicure 6th Framework European Un-

ion Integrated Project as well as with Munich Ludwig

Maximilian University (Germany), Genoa Universi-

ty (Italy) on genetic epilepsies with the project titled

Reflex seizures in different epilepsies, and lastly with It-

aly and the Netherlands on photosensitive epilepsies

within the frame of Marie-Curie Programme.

ISTANBUL FACULTY of MEDICINE LABORATORY of ELECTROENCEPHALOGRAPHY

14


For postnatal and prenatal diagno-sis, chromosome obtainment with short-term and long-term cell cul-

tures, chromosome analysis in different tissues, FISH and a-CGH analyses, DNA isolation, Sanger Sequencing, MLPA real time PCR, enzyme cutting, target muta-tion in genes, and STR and bioinformat-ic analyses are performed.

Prof. Dr. Seher Başaran+90 212 4142000 - [email protected]


Sterile cabinet, Inverted microscope, Hybridization

device (Hybridizer), Microcentrifuge, Automatic

metaphase finder, FISH microscope with fluores-

cence attachment, PCR device, Hybridization oven,

magnetic mixer, Microarray scanner, Microarray dry-

er, Genetic Analyzer (Sequencer), Microcentrifuge,

Vortex, Plate centrifuge, Nanodrop, Digital dry bath,

DNA isolation device.


There are collaborations with Cologne University

(Germany), University of Paris (France), University

of Duisburg Essen (Germany) and Hacettepe Uni-

versity (Turkey) as part of international projects,

CRANIRARE and SBAG-ERA-NET. Joint studies

are carried out with San Diego University on central

nervous system abnormalities and exon sequencing.

ISTANBUL FACULTY of MEDICINE GENETIC RESEARCH LABORATORY

15


Prof. Dr. Seyhun Solakoğlu+90 212 4142000 - [email protected]

Supplementary analyses for differ-ential diagnosis of nephropatho-logic diseases and dermatolog-

ical bullous diseases, primary ciliary dyskinesia and some metabolic neuro-degenerative diseases as well as etio-pathogenesis of spermatozoa-induced infertility cases and malabsorption syn-dromes are performed. Preliminary tests for materials used in practices of fields such as dentistry and orthope-dics, and primary fibroblast culture pro-cedures are performed.

Prof. Dr. Leyla Tapul+90 212 4142000 - [email protected]

Prof. Dr. Bülent Ahıshalı+90 212 4142000 - 32360

[email protected]


Electron microscope (Jeol 1011), ultramicrotome

(Leica EM-UC7), tissue processor (Leica EM-TP),

Knifemaker (Leica EM-KMR3), EM-Trim 2, lam-

inar flow cabinet, CO2 incubator, inverted phase

contrast microscope, fluorescence microscope and

cyto-counter.


There are research projects conducted with Leibniz

Molecular Pharmacology Institute (Germany), Open

University (UK) and Karolinska Institute (Sweden).

ISTANBUL FACULTY of MEDICINE HISTOLOGY and EMBRYOLOGY RESEARCH LABORATORIES

16


Screening, determination of phe-nylalanine-tyrosine by HPLC and BH4 challenge tests are per-

formed in Phenylketonuria analysis unit; screening of biotinidase in serum and biotinidase activity, Beutler test, re-ducing substances in the urine, mono-saccharide chromatography, oligosac-charide chromatography, metilmalonic acid determination, nitroprusside test, dinitrophenylhydrazine test, orotic acid determination, sodium hydroxide test, FeCl3 test, ketone determination, and examinations of amino acids and acyl carnitine by tandem mass spectrome-try, HPLC analysis of quantitative amino acids and carbohydrate-deficient glyco-proteins (CDG), organic acid analyses by gas chromatography-mass spectrome-try and enzyme analyses are performed in advanced metabolic tests unit.

Prof. Dr. Gülden Gökçay+90 212 4142000 - [email protected]

Prof. Dr. Ümit D. Türkoğlu+90 212 4142000 - [email protected]


HPLC systems, amino acid analyzer, tandem mass

spectrometry, gas chromatography-mass spectrome-

try and fume hood systems.


We conduct collaborative studies with European

Research Network (Switzerland), Center for Disease

Prevention and Control (USA), Screening-Labor

Hannover (Germany), Heidelberg University (Ger-

many), University of Zurich (Switzerland), Univer-

sity of Nijmegen (Amsterdam), University of Man-

chester (UK) and University of Newcastle (UK).

ISTANBUL FACULTY of MEDICINE LABORATORY of CHILD HEALTH and DISEASES, and NUTRITION METABOLISM

17


Prof. Dr. Hakan Gürvit+90 212 4142000 - [email protected]

It is the first neuropsychology labora-tory of Turkey, where neuropsycholog-ical evaluation and aphasia evaluation

as well as cognitive rehabilitation are conducted. Evaluations are conducted by both traditional neuropsychological batteries and computerized tests.


CANTAB and computerized Stroop WCST tests.


We have collaborations with Northwestern Universi-

ty (USA) and Rutgers University (USA).

ISTANBUL FACULTY of MEDICINE LABORATORY of NEUROPSCHOLOGY

18


It comprises laboratory of bacteriolo-gy, laboratory of mycology/mycobac-teriology, laboratory of parasitology

and laboratories of virology-immunol-ogy. Blood culture, sterile body fluids, cystic fibrosis patient samples and in-terferon-gamma release test in blood samples as well as PCR procedures are performed and Echinococcus granulo-sus IgG, Entemoeba histolytica IgG are studied. Autoantibodies are examined using ELISA, indirect immune fluores-cence and immunoblot method, and immunophenotyping tests and immu-nodeficiency panel are performed.

Prof. Dr. Nezahat Gürler+90 212 4142000 - [email protected]


Ovens operating at various temperatures (incuba-

tors), CO2 oven, Normal and refrigerated centrifug-

es, Normal water bath and water bath with shaker,

Elisa devices, Fully automated blood culture device,

Fluorescence microscope, Dark field microscope, Au-

tomated bacterial identification system, Light cycler

(for molecular tests), Thermal cycler to be used in

PCR tests, Pulsed Field device (for molecular tests),

lyophilizer in culture collection center, Electropho-

resis device, Gel imaging system (transilluminator),

Biosafety cabinets and flow cytometry.


We conduct joint projects with Public Health Agency

of Turkey and World Health Organization on infec-

tious diseases and anti-tuberculosis drug resistance.

We submit data about activity of flu to National Ref-

erence Laboratory for Influenza, Ministry of Health

and World Health Organization. We collaborate

with University of Cologne (Germany) on diagnosis

of HIV drug resistance.

ISTANBUL FACULTY of MEDICINE MICROBIOLOGY RESEARCH LABORATORIES

19


Blood samples and data from pa-tients diagnosed with congenital hyperinsulinism, neonatal diabe-

tes, obesity, congenital adrenal hyper-plasia, thyroid diseases, type 1 diabetes, MODY, multiple pituitary hormone defi-ciencies, idiopathic shortness of stat-ure, excess aromatase and early puber-ty are collected. DNA, RNA, leukocyte and serum are extracted and studied.

Prof. Dr. Firdevs Baş+90 212 4142000 - [email protected]


DNA and RNA extraction robot, PCR, Real time

PCR.


We have collaborations with Exeter University (UK)

about congenital hyperinsulinism and neonatal di-

abetes cases, with Schneider Children’s Medical

Center (Israel) about a genetic analysis in early pu-

berty, with University of Prague (Czech Republic) on

a genetic study of multiple hormone deficiency and

joint studies with TÜBİTAK (Scientific and Techno-

logical Research Council of Turkey).

ISTANBUL FACULTY of MEDICINE PEDIATRIC ENDOCRINOLOGY RESEARCH LABORATORY

20


It consists of Laboratory of Tissue Typ-ing and Immunogenetics and Labora-tories of Serology, Cell Culture, Flow

Cytometry, Molecular Genetics, DNA Sequence Analysis and Immunogenet-ics. Low/high-resolution analyses of HLA tissue groups in patients/donors preparing for transplantation of solid organs and bone marrow/stem cells along with tissue groups considered to be related with autoimmune diseas-es are studied. Cross-match tests and anti-HLA antibody screening and identi-fication tests which can estimate suc-cess of transplantation from living/cadaveric donors to patients are con-ducted. Pre-transplantation HLA tissue typing tests and chimerism assay used in post-transplantation engraftment fol-low-up are conducted on patients/do-nors planned to have stem cell trans-plantation.

Prof. Dr. Fatma Savran Oğuz



CO2 incubator, Inverted microscope, Fluorescence

microscope, Thermal cyclers, Horizontal electropho-

resis equipment, DNA sequencer, Flow cytometry

device and luminex device.


It has been recognized as an accredited laboratory

by European Federation for Immunogenetics (EFI).

It has been appointed by both EFI Quality Control

Committee and Scientific Council for Immunology

of Ministry of Health to organize HLA control tests

among HLA laboratories. International projects are

conducted in the field of Transplantation Immunol-

ogy/Immunogenetics and Ageing.

ISTANBUL FACULTY of MEDICINE LABORATORY of MEDICAL BIOLOGY

21


Primary neuron culture, gene ex-pression analyses, siRNA gene si-lencing, qrtPCR methods, poly-

morphism analyses, Protein analyses with Western Blot, analysis of cytokines, chemokines and hormones from body fluids by ELISA method are performed. Roles of different genes in diseases can be determined by neurodegenerative disease models generated using pri-mary neuron culture, and gene silenc-ing methods. The main fields of study are molecular mechanisms involved in neurodegeneration and genetic basis of Alzheimer’s disease and Parkinson’s disease.

Assoc. Prof. Dr. Erdinç Dursun

+90 212 414 2000 - [email protected]

Assoc. Prof. Dr. Duygu Gezen-Ak

+90 212 414 2000 - [email protected]

Prof. Dr. Selma Yılmazer



Laminar flow cabinet in Class 100 Room, CO2 in-

cubator, Inverted microscope, Fluorescence micro-

scope, Thermal cycler, Real time thermal cyclers

(Light Cycler 480, Light Cycler Nano), Picodrop,

iBlot for Western Blot, Horizontal and vertical elec-

trophoresis equipment, Gel imaging and documen-

tation device.


We conduct collaborative studies with Rutgers Uni-

versity (USA), University of Angers (France), Univer-

sity of Exeter (UK) and Thessaloniki School of Med-

icine of Aristotle University (Greece). Currently a

project on discovery of new biomarkers for Alzheim-

er’s and Parkinson’s diseases, funded by European

Union, is conducted.

CERRAHPAŞA FACULTY of MEDICINE LABORATORY of BRAIN and NEURODEGENERATIVE/NEUROGENETIC DISEASES

22


Such studies as hearing tests for neonates, children and adults, di-agnosis and therapy programs for

speech-voice and language disorders, scholastic follow-up of and support for individuals with hearing loss, prognosis and rehabilitation of balance disorders, noise and hearing conservation pro-grams, hearing screening programs for neonates, preschool and school-aged children, hearing aid, and implants of middle ear, inner ear and brain stem are conducted.

Prof. Dr. Ahmet Ataş+90 212 4143000 - [email protected]


Computerized dynamic posturography, Head im-

pulse, Measurement equipment for cortical audito-

ry evoked potential responses, Multi-frequency im-

mitancemetry, Voice analysis system.


We participate in supporting individuals with hear-

ing loss by the joint project with İstanbul Develop-

ment Agency. We have projects on development of

an analysis algorithm for dynamic vestibular sys-

tem, and medical equipment development within

the scope of TÜBİTAK (Scientific and Technologi-

cal Research Council of Turkey) project conducted

in collaboration with İstanbul Technical University

(Turkey).

CERRAHPAŞA FACULTY of MEDICINE CENTER for HEARING and SPEECH DISORDERS / LABORATORY of AUDIOLOGY

23


Prof. Dr. Derya Karadeniz+90 212 4143000 - [email protected]

Diagnosis and treatment of sleep disorders and polysomnograph-ic examinations for preliminary

diagnosis of epilepsy are performed. It is the only unit in Europe accredited accordind to criteria set by European Sleep Research Society and authorized to deliver training and certification pro-grams for specialists from Europe.


3-channel EEG [F4-M1, C4-M1, O4-M1] for full-

night polysomnography, Two-channel EOG, Super-

ficial EMG of chin, Right/left tibialis anterior, and

body position sensor, Oro-nasal sensor, Nasal pres-

sure sensor, Thoracic and respiratory movements,

ECG, Recording of respiratory sounds, O2 saturation

and synchronous video recording.


We conduct a randomized, double-blind study in

which a comparison of BF2.649 (Pitolisant) and

plasebo in two parallel groups in daytime hypersom-

nia and frequency of weekly cataplexy attacks in nar-

coleptic patients with cataplexy is made, along with

a device development project for detection of car-

dio-respiratory events during sleep by a device other

than polysomnography, that is a multi-center study

as part of a European Union project.

CERRAHPAŞA FACULTY of MEDICINE SLEEP and WAKE DISORDERS UNIT

24


Chromosome analysis from blood, skin, bone marrow and prenatal samples (fetal blood, amnion flu-

id and corion villus biopsy) and diagno-sis of micro-deletions by fluorescence in situ hybridization are performed.

Prof. Dr. Beyhan Tüysüz+90 212 414 3000 - [email protected]


Karyotech PSI Karyotype+FISH analysis system, In-

cubator, Microscope, Thermo-Highmeter, Refriger-

ated centrifuge, CO2 incubator, pH meter, Laminar

flow cabinet, Hybridization unit, Spectrophotome-

ter, Deep freezer.


We conduct the following projects with following

partners: Identification of new genes in different

genetic diseases conducted jointly with Yale Uni-

versity (England), Department of Neurosurgery,

Neurogenetics Program; genetic studies of skeletal

diseases conducted jointly with Université Paris Des-

cartes-Sorbonne Paris Cité, Institut Imagine, Hos-

pital Necker Enfants Malades, France; Department

of Genetics; Research on “cilia” disorders conducted

jointly with Department of Molecular Medicine and

Birth Defects Research Center of University College

London (UCL), England; a study on genetic sub-

structure of Cutis laxa group of disorders jointly con-

ducted with Institut für Medizinische Genetik und

Humangenetik, Charité-Universitätsmedizin Berlin,

Augustenburger Platz 1, Berlin, Germany; Research

on Noonan group (RASopathies) of disorders joint-

ly conducted with Dr. Martin Zenker Institute of

Human Genetics, University Hospital Magdeburg

Leipziger, Germany; Research on diseases accompa-

nied by osteoporosis conducted jointly with Pediatric

Endocrinology and Metabolic Bone Diseases De-

partment of Pediatrics, Helsinki University Hospital,

Finland; arthrogryposis and Cornelia de Lange group

of diseases conducted jointly with Department of

Molecular and Human Genetics, Baylor College of

Medicine, Houston, USA.

CERRAHPAŞA FACULTY of MEDICINE LABORATORY of PEDIATRIC GENETICS

25


Prof. Dr. Mustafa Özen+90 212 4143000 - [email protected]

Beside studies and analyses regard-ing diagnosis and treatment plan-ning of many diseases, including

routine studies on genetics of single gene disorders, infertility tests and ge-netics of cancer and leukemia, projects pertaining to research-development studies are conducted in laboratory of molecular genetics and cell culture.


37°C incubator, Light cycler 480 real time PCR

device, Thermal cycler, Electrophoresis units, Gel

imaging device, Centrifuges (refrigerated, vacuum),

DNA isolation device, -20°C and -80°C cooling

chambers, Microwave, Oven, ABI 3500 sequence

analysis device, Light cycler 2.0 Real Time device,

Pyro sequence (for specific sequencing), Rotor Gene

(real time device) and Laminar Flow cabinet.


Ongoing research & development projects supported

by TÜBİTAK (Scientific and Technological Research

Council of Turkey) are investigation of MiRNAs in

human laryngeal cancer, determination of tongue

cancer-specific miRNAs and investigation of MiR-

NAs in patients with delirium.

CERRAHPAŞA FACULTY of MEDICINE LABORATORY of MOLECULAR GENETICS

26


Development and validation of spectrometric, high performance liquid chromatographic and gas

chromatographic methods for drug analyses constituting the basis of re-search and development, quality con-trol studies, qualitative and quantitative analyses of drug substances and im-purities in pharmaceutical preparations and biological materials are conducted and method validation as well as phar-macopoeia analyses are performed in conformity with international guidelines.

Prof. Dr. Serap Sağlık Aslan+90 212 4400000 - [email protected]


Spectrophotometer, Spectrofluorimetry, Flow injec-

tion system, High performance liquid chromatogra-

phy (UV, diode-array, fluorescence and electrometric

detection, online SPE-LC, UPLC), Gas chromatog-

raphy (with flame ionization and mass spectrometric

detection).


Studies are conducted with Istanbul Technical Uni-

versity (Turkey), Yildiz Technical University (Tur-

key), Bezmialem Foundation University (Turkey),

Yeditepe University (Turkey), Anadolu University

(Turkey), Pamukkale University (Turkey), Namik

Kemal University (Turkey), Dicle University (Tur-

key), Batman University (Turkey), Munich Univer-

sity (Germany), Barcelona University (Spain), Cairo

University (Egypt) and Free University of Brussels

(Belgium). These studies are based on development

and validation of new analytical techniques and

methods.

FACULTY of PHARMACY ANALYTICAL CHEMISTRY RESEARCH LABORATORY

27


Isolation and structural determina-tion of compounds isolated from me-dicinal plants are performed by using

chromatographic methods and con-ducting spectral analyses. Moreover, various biological activities of plant ex-tracts and isolated compounds are in-vestigated.

Prof. Dr. Afife Mat +90 212 4400000 - [email protected]


High performance liquid chromatography (with di-

ode-array and fluorescence detection), Medium pres-

sure liquid chromatography, Flash chromatography,

chromatotron, Vacuum liquid chromatography, Vac-

uum speed concentrator, Lyophilizer, Vacuum oven.


Collaborative studies are done with Anadolu Uni-

versity (Turkey), Marmara University (Turkey), Uni-

versity of Saarland (Germany), University of Paris

(France), University of Mostaganem (Algeria), Free

University of Berlin (Germany) and Institute of Lei-

bniz (Germany). Studies have been conducted on

isolation of active compounds from plant resources

and demonstration of activity.

FACULTY of PHARMACY PHARMACOGNOSY RESEARCH LABORATORY

28


Pharmacology of gastrointesti-nal (i.e. experimental ulcer model) and central nervous systems (ex-

perimental and genetic epileptic mod-els), pharmacological studies [exami-nation of impacts of P-glycoprotein and transporter proteins of ABC gene fam-ily on pharmacokinetics of medicines and determination of levels of medi-cines in plasma and other body fluids by high pressure liquid chromatography (HPLC)] are performed in addition to ex-amination of activities of medicines and active substances of plant/synthetic origin in such areas as pharmacology of cardiovascular system (experimen-tal hypertension, diabetic and glauco-ma models as well as isolated vascular and cardiac preparations obtained from test animals and humans such as aor-ta, mesenteric artery, renal artery, retinal artery, basilar artery, human intra-mam-mary artery, human saphenous vein, human radial artery and heart etc.),.

Prof. Dr. Sönmez Uydeş Doğan



Organ bath system, Myograph system, High per-

formance liquid chromatography, Solid and liquid

phase extraction systems (with UV and fluorescence

detection), Angendorff system, ELISA device and

telemetry system.


Studies conducted with Ege University (Turkey), In-

stitute for Biological Rhythms and Cancer of Uni-

versity of Paris XI (France), and University of Paris

Nord, Inserm UMR-S698 (France). Studies are in

the fields of pharmacology of cardiovascular system

and pharmacokinetics.

FACULTY of PHARMACY PHARMACOLOGY RESEARCH LABORATORY

29


Drug formulation studies (solid dosage forms, disperse systems, topical and transdermal drug de-

livery systems, new drug delivery sys-tems (microspheres, vesicular delivery systems, solid lipid nanoparticles, and polymeric micelles), bio-adhesive sys-tems, ocular, pulmonary, nasal and buc-cal drug delivery systems and radiop-harmaceuticals), drug stability studies and targeted (brain, liver, lungs, bone and colon) drug delivery system studies are carried out.

Prof. Dr. Yıldız Özsoy Erginer



Texture analyzer, Dissolution system, Nano-zetasizer,

Lyophilizer, High performance liquid chromatogra-

phy (with diode-array and fluorescence detection),

Franz diffusion cell system, ATR-FTIR spectrome-

ter, Cell culture laboratory equipment, Tewameter,

Corneometer, Skin pH-meter, Sebumeter and mex-

ameter.


Collaborative studies are conducted with Marmara

University (Turkey), London School of Pharmacy

(England), University of Bath (England), Cardiff

University (England), Trinity College (Universi-

ty of Dublin) (Ireland), University of Pittsburgh

(USA) and Innsbruck Medical University (Austria).

Lung-targeted drug delivery, transdermal and der-

mal, pharmaceutical cell culture and radiopharma-

cy studies have been carried out. Studies regarding

development of anti-cancer medicine as part of Eu-

ronanomed project have been completed. SANTEZ

project conducted as part of a cooperation between

university and industry, and TÜBİTAK (Scientific

and Technological Research Council of Turkey) pro-

jects continue.

FACULTY of PHARMACY PHARMACEUTICAL TECHNOLOGY RESEARCH LABORATORY

30


It consists of Molecular & Analytical Toxicology, Genotoxicity and Cell Cul-ture Laboratories, and Pharmacoge-

netic Diagnosis Unit. Investigation of mechanisms that play a role in toxico-logical effects of xenobiotics (especial-ly genetic and epigenetic mechanism studies, in vitro and in vivo detection of DNA and chromosomal damages, and oxidative damages, DNA methyla-tion, histone modifications and chang-es in gene and protein expressions) is performed. Minimum toxicity and max-imum therapeutic effect, targeted de-livery of especially chronically adminis-tered drugs are intended to achieve a narrow therapeutic index in “Individual-ized Medicine” and determination of dif-ferences of gene and proteins involving in metabolism are carried out by coordi-nated studies with clinical units.

Prof. Dr. Buket Alpertunga +90 212 4400000 - [email protected]


Real time thermal cycler (RT-PCR), Thermal cy-

clers, Electrophoresis and gel visualization systems,

Microscope with fluorescence attachment, High per-

formance liquid chromatography (with diode-array

and fluorescence detection), Cell culture laboratory

equipment.


We work in collaboration with Sabancı University

(Turkey), and Boğaziçi University (Turkey), New-

castle University (England), University of Würzburg

(Germany) and University of Birmingham (Eng-

land). Two TÜBİTAK (Scientific and Technologi-

cal Research Council of Turkey) projects have been

carried out.

FACULTY of PHARMACY PHARMACEUTICAL TOXICOLOGY RESEARCH LABORATORY

31


ISTE contains a significant collec-tion of plant species comprising 70% of all plants in Turkey, including pri-

marily medicinal plants, rich in terms of plant samples from Istanbul and Thrace (90%), some of the medically most important plant species (such as Allium, Arum, Asphodeline, Cirsium, Col-chicum, Crocus, Cyclamen, Euphorbia, Ferulago, Helichrysum, Hypericum, Iris, Papaver, Rosa, Salvia, Sedum, and Tuli-pa) as well as more than 115,000 plant samples. All plant samples are scanned and input is stored in a database called “ISTE Information System” and is avail-able on ISTE website for those interest-ed. ISTE contains all endemic monotyp-ic species in flora of Turkey.

Prof. Dr. Emine Akalın+90 212 4400000 - [email protected]


It contains photographs of more than 150 types of

samples and more than 100 photographs of typus.

Stereo microscope fitted with a drawing tube and

that transmit images into digital media, Chromo-

some analysis system, Ice microtome (cryostat).


We work in collaboration with Anadolu Universi-

ty (Turkey) and Cumhuriyet University (Turkey).

Studies for identification and preservation of flora

of Turkey have been conducted in these collabora-

tions. European Union and IUCN projects regarding

conservation of biodiversity and its sustainable devel-

opment are performed. It represents Turkey in pro-

grams and databases such as “Euro-Med Plant Base”

and “Atlas Florae Europaeae”. Istanbul Development

Agency project on honey plants and KAMAG pro-

jects supported by TÜBİTAK (Scientific and Tech-

nological Research Council of Turkey) on identifi-

cation of geophytes of Turkey and chromosomes are

carried out.

FACULTY of PHARMACY ISTE (HERBARIUM)

32


Studies are conducted on freezing and long-term preservation of se-men of farm animals and pets,

development of semen freezing tech-niques as well as discovery of new ad-ditives and methods for cryopreserva-tion. Artificial vaginal mucus and a new measurement technique have been de-veloped for determination of potential fertility. Advanced analyses, as well as determination and preservation stud-ies of potential fertility are carried out on frozen semen. This laboratory also functions as a “Reference Laboratory” of the Ministry of Agriculture and pre-pares reports required for import au-thorizations of imported semen.

Prof. Dr. Alper Baran+90 212 4737070 - [email protected]

Prof. Dr. Kemal Ak+90 212 4737070 - [email protected]


Semen analysis equipment, Phase contrast micro-

scope (magnification x40 – x10000), Microscope

with fluorescence attachment (magnification x40 -

x1000), Semen freezing system.


A study involving the freezing of semen samples from

five sheep breeds and delivery thereof to National

Domestic Animal Gene Bank for establishment of

a database was conducted in collaboration with the

Ministry of Agriculture, TÜBİTAK-MAM GMBE,

Ankara University (Turkey), Uludağ University (Tur-

key), Selçuk University and Middle East Technical

University (Turkey). A study for freezing ram semen

has been carried out in collaboration with the Min-

istry of Agriculture, TÜBİTAK-MAM GMBE, Ul-

udağ University, and University of Missouri (USA)

and an appropriate freezing protocol has been devel-

oped in order to develop a DNA Analysis Laboratory

technique and a freezing technique that can be used

in TAGEM (General Directorate of Agricultural Re-

search) institutes.

FACULTY of VETERINARY MEDICINE LABORATORY of ANDROLOGY

33


Genomic and mitochondrial DNA analyses concerning pets have been carried out. Gene polymor-

phisms of pets in particular (Prion, GH, Prolactin, IGF-1, OPN, PIT-1, FASN, SCD, LEP, Milk Protein Genes, agouti genes etc.) are demonstrated both by the se-quence analysis method and the PCR-RFLP analysis method. Besides, mito-chondrial DNA analyses are performed.

Prof. Dr. Kemal Özdem Öztabak



Thermal cyclers, UV imaging device, Mini and midi

Submarine electrophoresis, Vertical electrophoresis,

Refrigerated centrifuge and mini centrifuge.


We conduct joint studies with European Science

Foundation (Austria) on genomic and mitochondrial

DNA analyses. We have collaboration protocols with

Yıldız Technical University (Turkey) and Ege Univer-

sity (Turkey).

FACULTY of VETERINARY MEDICINE LABORATORY of DNA ANALYSIS

34


Prof. Dr. Kemal Özdem Öztabak


DNA isolation is conducted on bones of pets and wild animals unearthed in archaeological exca-

vations and their mitochondrial DNAs are compared with those of living ani-mals.


Laminar flow cabinet, UV sterilizer, Electrophoresis,

Thermal Cyclers.


Goat bones unearthed in excavations of Van-Yon-

catepe castle were studied. We conduct research on

Ancient DNA Extraction Methods in collaboration

with University of York (UK).

FACULTY of VETERINARY MEDICINE FOSSIL DNA LABORATORY

35


Food Science Laboratories, with over 30 years of experience, con-ducts national and international

studies in the fields of food science and water hygiene in cooperation with in-dustry and public sector, in an enclosed area of approximately 2000 m2. It com-prises Food Microbiology Laborato-ry, Food Chemistry Laboratory, Food Technology Laboratory, Molecular Anal-ysis Laboratories, and Pilot Research Slaughterhouse. Additionally, laborato-ries support industry and public sector for routine analyses.

Prof. Dr. Gürhan Çiftcioglu+90 212 4737070 - [email protected]


Cooled and regular centrifuges, magnetic and regular mixers and shakers, Ultra centrifuge, Spectropho-tometer, Evaporator, PCR thermal cyclers, Gel elec-trophoresis, Gel screening, Laminar flows, Bio-safety cabinets, Homogenizers, ELISA reader, Automated milk analyzer, MAP, vacuum and stretch packag-ing machines, Gas analyzer, Texture analyzer and its apparatus, chromometer, Incubators, Stomacher, Blender and smashers, Aw-meter, Soxhlet, Trichino-scope, analysis equipment and kits for food microbi-ology and food technology.


Various joint studies on food safety, food security and food authenticity are conducted in cooperation with many national and international institutions, such as Ankara University (Turkey), Uludağ University (Tur-key), Adnan Menderes University (Turkey), Selçuk University (Turkey), TÜBİTAK MAM (Marmara Research Center), Pendik Veterinary Research In-stitute of Turkish Ministry of Food, Agriculture and Livestock, European Union Joint Research Centre, University of Vienna (Austria), Ludwig-Maximilians University Munich (Germany), University of Bristol (England), University of Surrey (England), Univer-sity of Thessaloniki (Greece), Joseph Fourier Uni-versity (France), University of Georgia (USA), Texas A&M University (USA), United States Department of Agriculture, Texas Agricultural Research Center (USA).

FACULTY of VETERINARY MEDICINE FOOD SCIENCE LABORATORIES

36


Pharmacological effects of new drug molecules or candidate drug molecules on healthy and cancer

cell progenies are analyzed by molecu-lar techniques for elucidation of mech-anisms of action thereof. Moreover, we conduct molecular studies on determi-nation of pharmacological effects of various plant extracts, which are raw materials of drugs. Potential genotoxic effects of compounds are determined using various genotoxicity tests (comet and micronucleus test).

Prof. Dr. Tülay Bakırel+90 212 4737070 - [email protected]


Multi-mode Reader System for Absorbance, Fluores-

cence and luminescence measurements, Cell coun-

ter, CO2 incubator, Western Blot, Thermal Cycler,

Inverted Microscope, Fluorescence microscope, Ly-

ophilizer, Spectrophotometer with Dual Beam and

Xenon Lamp, Class II Biological safety Cabinet,

protein detection device, Vertical and horizontal gel

electrophoresis, Ultrapure Water system.


We conduct research as part of TÜBİTAK (Scientific

and Technological Research Council of Turkey) and

COST projects. Studies such as molecular investiga-

tion of pharmacological effects of drug substances

on cancer cells, determination of pharmacological

properties and biological activities of plant extracts,

investigation of effect of a commonly used veterinary

antibiotic on anaerobic digestion systems producing

biogas from animal manure and determination of

outcome thereof in receiver environment, increasing

biomethane productivity in anaerobic digesters by

using specific rumen bacteria and hydrolysis enzymes

are performed in collaboration with different depart-

ments of various universities.

FACULTY of VETERINARY MEDICINE CELL CULTURE LABORATORY

37


In 2000, lambs, the first farm animals to be produced by in vitro fertilization in Turkey, were born in this laborato-

ry, in 2007 Turkey’s first animals were cloned, in 2009 the first grey bull was cloned, and in 2010 the first grey fe-male calves were cloned, in 2013 the first lambs were born by intracytoplas-mic sperm injection method, the first transgenic rabbits and the first trans-genic lambs were born. Development of estrus synchronization techniques in farm animals, oocyte yield in farm animals, pets and laboratory animals, improvement of in vitro culture envi-ronments, freezing and long-term pres-ervation of oocytes and embryos, im-provement of cloning techniques in cats and sheep, embryonic stem cells, de-velopment of gene delivery systems to produce transgenic animals, ICSI trans-genesis, sperm-mediated transgene-sis and pronuclear gene injection are in-tensely studied.

Prof. Dr. Sema Birler


Prof. Dr. Serhat Pabuccuoğlu

+90 212 4737070 [email protected]


Inverted microscope with fluorescence attachment, Micromanipulation system, Piezo microinjection, Micromanipulation system, Cell electrofusion sys-tem and oxygen and CO2 incubators.


Embryos of five sheep breeds were frozen and deliv-ered to National Domestic Animal Gene Bank, by which farm animal species specific to Anatolia are to be protected, that was established in cooperation with the Ministry of Agriculture, TÜBİTAK-MAM GMBE, Ankara University (Turkey), Uludağ Univer-sity (Turkey), Selçuk University (Turkey) and Middle East Technical University (Turkey). Embryo produc-tion studies by ICSI method, using lyophilized semen and mouse embryonic stem cell transfection studies continue in collaboration with Uludağ University (Turkey) and Fatih University (Turkey), respectively. Collaborations with University of Hawaii and mouse embryonic stem cell transfection studies jointly con-ducted with Fatih University continue. Research was conducted on control of reproduction and biology of reproduction, and a new method was developed for estrus synchronization as a consequence of the projects conducted. Moreover, a vaginal tablet which may be used for estrus synchronization was devel-oped and patent applications were made to TPI (Turkish Patent Institute) and EPO.

FACULTY of VETERINARY MEDICINE IN VITRO FERTILIZATION and EMBRYO TRANSFER LABORATORY

38


Characteristics of meat such as color, tenderness and juiciness are analyzed by reliable scientific

methods. Meat samples are evaluated in terms of parameters such as texture analysis, meat and carcass color anal-ysis, passive water loss, water-holding capacity, measurement of loss on cook-ing, and meat taste panel. Furthermore, studies on determination of quality of carcass (measurement of carcass size, determination of muscle area and com-position (meat, bone, fat ratio)) are per-formed.

Dr. Hülya Yalçıntan+90 212 4737070 - [email protected]

Prof. Dr. Bülent Ekiz+90 212 4737070 - [email protected]


Texture analyzer and a Warner-Blatzler blade com-

patible with this device, Chromometer.


Joint studies were carried out by researchers from

Uludağ University (Turkey), Kafkas University (Tur-

key), Çanakkale Onsekiz Mart University (Turkey),

Mustafa Kemal University (Turkey), and Ondokuz

Mayıs University (Turkey) to determine carcass and

meat quality traits of farm animals of various spe-

cies in different production systems used in Turkey,

which were supported by TÜBİTAK (Scientific and

Technological Research Council of Turkey) and the

Ministry of Agriculture. Joint studies were performed

with European Federation of Zootechny (Italy) on

high quality meat production.

FACULTY of VETERINARY MEDICINE CARCASS and MEAT QUALITY LABORATORY

39


Archaeological materials collect-ed from archaeological excava-tions are analyzed. Identification

of species, modifications, and patholo-gies and all traces and remains are ana-lyzed and answers are sought for many questions including, in particular, those about human-animal relationships in communities in the past.

Prof. Dr. Vedat Onar+90 212 4737070 - [email protected]


Reference collections.


National and international collaborations are es-

tablished through proposal of scientific projects on

analysis of materials from Subway and Marmaray

(Yenikapı) excavation, and excavation studies of

Kuşadası-Kadıkalesi (Anaia), Amasya-Oluz Mound,

Van Castle Mound and Yoros Castle. Excavation

analyses are performed in cooperation with Presi-

dencies of Excavations and Archaeology Museums.

Within the frame of cooperation with University of

Wroclaw (Poland), University of Trakia (Bulgaria)

and Academy of Natural Sciences (Belgium), not

only projects are carried out, but also joint studies

are conducted with foreign scientists.

FACULTY of VETERINARY MEDICINE OSTEOARCHAEOLOGY LABORATORY

40


Studies of serological diagnosis of viral diseases and viral zoonoses in animals, virus production meth-

ods, and molecular diagnosis and gene analysis are conducted. Moreover, stud-ies on methods of protection from, and control of and eradication of viral dis-eases are performed.

Prof. Dr. Hüseyin Yılmaz+90 212 4737070 - [email protected]


CO2 incubator, Inverted microscope, Shaking incu-

bator, Egg incubator, Refrigerated and normal mi-

crocentrifuges, Ultra-centrifuge, Spectrophotometer,

Real time PCR devices, Gel electrophoresis, Gel im-

aging device, Bio II safety cabinets, Homogenizers,

Thermoblocks, Western blot, ELISA reader, Lyoph-

lizer.


We conduct collaborative studies with Kansas State

College of Veterinary Medicine (USA), Liverpool

School of Veterinary Medicine (UK), Bristol School

of Veterinary Medicine (UK), Ohio College of Vet-

erinary Medicine (USA), Madrid Faculty of Veteri-

nary Medicine (Spain), Hungarian Medical School

(Hungary), Bari Faculty of Veterinary Medicine (Ita-

ly), Athens Faculty of Veterinary Medicine (Greece),

Nippon Institute of Technology (Japan), University

of Queensland (Australia), Veterinary Institute of

Wageningen (Netherlands), Friedrich Loeffler Insti-

tute (Germany). Our projects on detection of Hep-

atitis A and B in environmental samples and water

samples as part of TÜBİTAK (Scientific and Tech-

nological Research Council of Turkey) projects and

investigation of infectious bronchitis virus in poultry

as part of COST project still continue.

FACULTY of VETERINARY MEDICINE VIROLOGY RESEARCH LABORATORY

41


Presence and functions of immune system cells are determined and proteins presented on the cell

surface or inside the cell and their cell functions are demonstrated by fluores-cent-labelled mono-clonal antibodies, and specific cell populations can be pu-rified.

Prof. Dr. Günnur Deniz+90 212 4142000 - [email protected]


FACSCalibur Flow Cytometry (4 color analysis

of subcellular groups stained by 4 different color

fluorescent-labelled antibodies at the same time),

FACSAria II Flow Cytometry (10 color analysis of

cells at the same time), Refrigerated centrifuge, Lam-

inar flow cabinet.


We have collaboration protocols with University of

Giessen (Germany), Allergy and Asthma Research

Center (Switzerland), St. Anna Children’s Hospi-

tal (Austria), Uludağ University (Turkey), Medipol

University (Turkey), Marmara University (Turkey),

Bezm-i Âlem Foundation University (Turkey), Ko-

caeli University (Turkey), Ankara University (Tur-

key), Ege University (Turkey), Selçuk University

(Turkey), and Yüzüncüyıl University (Turkey).

Mechanisms involved in immunopathogenesis of

Behçet’s disease, Multiple Sclerosis, and allergy and

asthma are investigated as part of TÜBİTAK (Scien-

tific and Technological Research Council of Turkey)

projects and projects are conducted on development

of new technologies for treatment of Type 1 Diabetes

as part of the Inten-C project.

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH FLOW CYTOMETRY LABORATORY

42


Research techniques required for investigation and diagnosis of rare diseases and cerebral conditions

such as epilepsy, ataxia etc., including undiagnosed diseases frequently oc-curring in Turkey as a consequence of consanguineous marriages and tradi-tion of having more than one child, are developed and applied in our laborato-ry. We study individual cases with mul-tiple congenital anomalies and/or men-tal retardation conditions by SNP-array based molecular karyotyping approach. In familial studies, data obtained from such new generation techniques as whole genome methylation and whole genome exome sequencing based on SNP genotyping, whole genome linkage and haplotype analyses are analyzed. We have currently been constructing a DNA bank, a rich inventory to be used as reference for individuals with rare genet-ic neurological diseases. Rare Diseases Research Laboratory is Orphanet’s co-ordinator in Turkey.

Assoc. Prof. Dr. Sibel Uğur İşeri


Prof. Dr. Uğur Özbek



454 GS FLX Sequencer, GS Junior System, Confocal

microscope.


A DNA bank was constructed by collecting DNA

samples from epilepsy patients as part of an EU-fund-

ed FP6 integrated project on epilepsy (EPICURE)

and clinical characterizations of patients were jointly

conducted by specialist neurologists from İstanbul

Faculty of Medicine and Cerrahpaşa Faculty of Med-

icine of İstanbul University (Turkey). International

Inten-C project is conducted under Turkish (DE-

TAE (Institute of Experimental Medical Research),

Boğaziçi University and Sabancı University) and

German (Cologne Center for Genomics) partner-

ship, and studies are performed as part of TÜBİTAK

(Scientific and Technological Research Council of

Turkey) projects.

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH RARE DISEASES RESEARCH LABORATORY

43


We conduct studies on investi-gation of signaling pathways involved in the development

of leukemia and genes with a prognos-tic significance in acute leukemia using whole genome expression and methyl-ation array analyses and amplicon deep sequencing applications, as well as fre-quently occurring primary immune de-ficiency diseases due to high rates of consanguineous marriages in Turkey. It is the first and only center offering di-agnostic services for immune deficien-cy diseases such as SCID, CVID and XLA in Turkey and conducts gene thera-py trials in XLA mouse models. It is also a member of European Leukemia Net-work (ELN) and the sole IS-certified ref-erence laboratory in Turkey for detec-tion of BCR/ABL.

Prof. Dr. Uğur Özbek


Assoc. Prof. Dr. Müge Sayitoğlu



454 GS FLX Sequencer, GS Junior system, High se-curity cell culture laboratory and cabinets, Bacteria culture laboratory, Confocal microscope and fluo-rescence microscope and microplate luminescence reader.


We perform studies as part of IRON II and IRON III projects under European Leukemia Network and conduct deep sequencing analyses with Roche Life Sciences. Interdisciplinary projects supported by TÜBİTAK (Scientific and Technological Research Council of Turkey) and Turkish Society of Hematol-ogy Research Fund are conducted with universities such as İstanbul Faculty of Medicine (Turkey), Cer-rahpaşa Faculty of Medicine (Turkey), Marmara Uni-versity (Turkey), Hacettepe University (Turkey), Ege University (Turkey), Kocaeli University (Turkey). Furthermore, we perform joint projects with Eras-mus Faculty of Medicine (The Netherlands), Heidel-berg University (Germany) and St Jude Children’s Research Hospital (USA).

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH MOLECULAR HEMATOLOGY RESEARCH LABORATORY

44


We conduct studies on detection of DNA fingerprints of strains causing tuberculosis in İstan-

bul and surrounding areas by molecu-lar methods, and determination of in-fection dynamics of the region along with research on molecular mycobacte-riology. IP 10 levels in whole blood sam-ples stimulated with ESAT 6 and CFP 10 antigens were determined and a IG(P)RA test identifying latent TB was devel-oped. A new species of mycobacteria, “Mycobacterium celeriflavum sp. nov”, has been identified and studies for de-veloping kits for detection of rapid re-sistance to drugs and identification at the same time continue. It serves as the “Top-level Laboratory of İstanbul An-ti-tuberculosis Association” upon a pro-tocol signed between İstanbul Anti-tu-berculosis Association and Rectorate of İstanbul University.

Assoc. Prof. Dr. O. Kaya Köksalan



Light/fluorescence microscope and capillary electro-

phoresis and sequence analyzer used in DNA frag-

ment analysis and sequence analysis.


We conduct joint projects on identification of new

species of mycobacteria with San Raffaele Scientific

Institute (Italy), detection of Beijing genotype tuber-

culosis strains in our country and adaptation thereof

to regional human populations with St. Petersburg

Pasteur Institute (Russia), and genotypic diversity of

Mycobacterium caprae and characteristics of the dis-

ease it causes in human beings with Agency for Food

and Health Safety (Austria).

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH TUBERCULOSIS MOLECULAR EPIDEMIOLOGY LABORATORY

45


We conduct various research projects and protein analy-sis studies in cytogenetic, bio-

chemical and molecular fields using cell culture and tissue culture technology. We examine alterations in gene and pro-tein expression levels, cell life cycle and signaling pathways occurring in paral-lel with alterations in cells and tissues in different cancer types and such various metabolic disorders as obesity and dia-betes, in addition to conducting miRNA and protein microarray analyses. More-over, we investigate effects of many dif-ferent substances on etiology and prog-nosis of diseases. We conduct studies to determine contents, elucidate func-tions and establish structural properties of proteins in various biological materi-als.

Prof. Dr. Oğuz Öztürk+90 212 4142000 - [email protected]


Fluorescence Microscope, Optical microscope, CO2

incubator, Laminar flow cabinet, Particle counter,

Cell viability measurement device, Fluorometer,

Western Blot device and its equipment.


We conduct national and international collabora-

tive studies with University of De Montfort (UK),

Sabancı University (Turkey), and İstanbul Technical

University (Turkey). In addition, we carry out multi-

ple interdisciplinary projects funded by State Project

Organization, İstanbul Development Agency and

TÜBİTAK. We carry out joint projects with various

organizations and institutions such as BAL-DER

which is active in various industrial fields.

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH LABORATORY of TISSUE CULTURE and PROTEOMICS

46


We conduct studies for elucida-tion of pathogenesis and iden-tification of new biomarkers

for multiple Sclerosis, neuromyelitis op-tica, autoimmune encephalitis and neu-ro-Behçet’s diseases using cell culture and molecular biology methods. Vari-ous treatment methods, including mes-enchymal stem cell application, are tried using immunization-based exper-imental animal model of myasthenia gravis disease. We examine gene and protein expression levels in tissue sam-ples from different autoimmune neuro-logical diseases and alterations in sur-vival/apoptotic signaling pathways. We conduct studies for identification of new autoantibodies in autoimmune neurological diseases by primary neu-ronal culture cells, transfected cells and protein macro-array methods.

Assoc. Prof. Dr. Erdem Tüzün



Optical microscope, Laminar flow cabinet, Western

Blot, Immunohistochemistry and ELISA device.


We conduct various collaborative studies such as ex-

perimental myasthenia gravis studies with University

of Texas (USA), analysis of intestinal microbiome in

neuro-Behçet’s disease with Baylor College of Med-

icine (USA) and identification of new autoantibod-

ies in neuromyelitis optica cases with University of

Patras (Greece).

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH LABORATORY of NEUROIMMUNOLOGY

47


We conduct various projects in areas such as housing, care and production of laborato-

ry animals as well as performance of investigational trials thereon and pro-viding subsequent post-operative care thereof.

Asst. Prof. Dr. Mutlu Küçük+90 212 4400000 - [email protected]


Individually ventilated cage system, Surgical mi-

croscope, Microscope imaging system and recorder,

infusion pump, Pressurized washing machine (90

L capacity), Optical microscopes, Blood collection

containers (for rats, mice, and rabbits), Isolator.


We conduct projects in cooperation with Leibniz In-

stitute for Molecular Pharmacology (Germany) and

Karolinska Institute (Switzerland) and participate

in a COST project on gene transfer in rabbits. In

addition, we conduct a TÜBİTAK (Scientific and

Technological Research Council of Turkey) project

on investigation of neuroprotective properties of cur-

cumin coated with star block-copolymer.

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH LABORATORY for PRODUCTION, PURIFICATION and INVESTIGATION of EXPERIMENTAL ANIMALS

48


Various biological molecules and metabolites are analyzed to in-vestigate effects of etiopathogen-

esis of multifactorial diseases and indi-vidual and/or environmental variations on metabolism.

Prof. Dr. İlhan Yaylım+90 212 4142000 – [email protected]


Real time PCR, Western Blot device and its equip-

ment, Luminex, Atomic absorption device, ELISA

reader, ELISA washer, Chemiluminescence.


We work in cooperation with Casablanca Hassan II

University (Morocco), İstanbul Faculty of Medicine

(Turkey), Cerrahpaşa Faculty of Medicine (Turkey),

İstanbul University Faculty of Dentistry (Turkey),

Bezm-i Alem University (Turkey), Fatih University

(Turkey), İstanbul Technical University (Turkey),

Uludağ University (Turkey) and many other univer-

sities. Furthermore, interdisciplinary projects sup-

ported by TÜBİTAK (Scientific and Technological

Research Council of Turkey) are under way. Our col-

laborative research, as part of Technocity project with

Uludağ University, on developing a combined kit to

help perform personalized chemotherapy for cancer

patients continues.

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH MOLECULAR METABOLIC RESEARCH LABORATORY

49


It has pioneered in experimental isola-tion and transplantation of islets from experimental animals since 1990s

and is the first institution in Turkey to perform isolations of islets of Langer-hans from human pancreases, and has laid the foundation for performance of transplantation in the clinic.

Prof. Dr. M. Temel Yılmaz+90 212 4142000 - [email protected]


Class 100,000/10,000 laminar flow sterile room

at the size of 50 m2 and positive pressure, Class II

safety cabinet, Pancreas digestion chamber (Ricor-

di’s Chamber), Enzyme perfusion device, Peristaltic

pump, Dissection microscope, Islet purification de-

vice.


We continue our studies with University of Giessen

(Germany) on regenerative treatment of Type 1 dia-

betes and development of new technologies for pan-

creatic beta cell proliferation as part of a TÜBİTAK


Turkey) INTEN-C project.

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH ISOLATION and TRANSPLANTATION of ISLETS of LANGERHANS RESEARCH LABORATORY

50


We conduct projects to gain un-derstanding of altered struc-ture, of character and of func-

tions of hematopoietic stem cells that convert into cancer stem cells due to various mutations. Hematopoietic stem cell and cancer stem cell, role of en-dothelial progenitor cells and endotheli-al cells in thrombosis, myeloproliferative diseases from hematological maligni-ties and frequently occurring mutations are investigated.

Asst. Prof. Dr. Selçuk Sözer Tokdemir



Coagulometer, Laminar flow cabinet, Cell culture

laboratory, Micro-centrifuge, PCR device.


We continue joint projects with Mount Sinai School

of Medicine (USA) and Academy of Sciences (Bul-

garia). We currently conduct a TÜBİTAK (Scientific

and Technological Research Council of Turkey) pro-

ject that involves investigation of characterization

and of functional analysis of cancer-initiating cells

in myeloproliferative diseases, and a COST project

that involves “examination of effects of JAK2V617F

mutation on endothelial cell functions”.

INSTITUTE of EXPERIMENTAL MEDICAL RESEARCH HEMATOPOIETIC and STEM CELL LABORATORY

51


HUBAL is a multidisciplinary, cen-tral research laboratory with a great infrastructure and required

instruments for life sciences research, established at İstanbul University as part of a project supported by Ministry of Development of Turkey. Units active in the fields of Genomics, Neuroscience, Biotechnology, and Drug Research/Pharmaceutics have been completed in 2014 and many projects have been ini-tiated in these fields. We aim to contrib-ute to translational research in health-care with the infrastructure established. HUBAL has been structured so as to make its equipment park accessible not only for researchers from İstanbul Uni-versity, but also from other universities and research institutions.

Prof. Dr. Zeynep Çiğdem Kayacan



3.0 Tesla Magnetic Resonance Imaging (MRI) Sys-tem, Functional MR (fMRI) Attachment (visual, auditory stimulus presentation system and response buttons), MR Compatible Digital EEG System, La-ser Scanning Confocal Microscope, Ultracentrifuge, Real-time Polymerase Chain Reactor, Piezo Impact Micromanipulator, Vertical Air Flow Cabinet, Liq-uid Nitrogen Storage System, CO2 Incubator, Indi-vidually Ventilated Plexiglas Animal Cages.


We conduct projects, one of which is supported by EU (JPND), two of which are supported by COST and two of which are supported by TÜBİTAK (Sci-entific and Technological Research Council of Tur-key) ARDEB, in collaboration with Bezmialem Uni-versity (Turkey), Bilgi University (Turkey), Marmara University (Turkey) and Boğaziçi University (Tur-key). We have initiated cooperation with Max Planck Institute (Germany), Berlin Brain and Mind Institute (Germany) and Cuban Neuroscience Center (Cuba). A protocol has been signed between Drug Research/Pharmaceutics Unit and Novartis as part of Univer-sity-Industry Cooperation. We work in coordination with Life Sciences and Technologies Application and Research Center of Boğaziçi University.

HULUSİ BEHÇET LIFE SCIENCES RESEARCH LABORATORY

52

53

NATURAL SCIENCES and ENGINEERING RESEARCH LABORATORIES


We perform photometric obser-vations of binary stars, aster-oids and planets orbiting oth-

er stars (exoplanets) and determination of both positions and orbital elements thereof. This observatory contributes to international campaign observations organized for identification of planets that are in exoplanetary systems, but cannot be identified by direct observa-tions. Furthermore, it also contributes to projects aimed to discover asteroids that may pose a threat to the Earth and determine whether there are any chang-es in their orbits compared to previous ones. In addition, we follow changes in orbital periods of binary star systems which account for a significant part of our astrophysical knowledge.

Prof. Dr. A. Talat Saygaç+90 212 4440000 - [email protected]

Prof. Dr. Adnan Ökten+90 212 4440000 - [email protected]


A Ritchey-Chrétien optical telescope with a main

mirror of 60 cm aperture, Alta U42 model CCD

camera with E2V series (CCD42-10) chip, 13.5 x

13.5 microns 2048 x 2048 array pixels, 9-slot filter

wheel, Bessel UBVRI and Strömgren uvby-Hβ filter

sets, meteorology station.


This observatory was founded on premises of Çanak-

kale Onsekiz Mart University Astrophysics Research

Center and Ulupınar Observatory (Turkey) by a

protocol based on shared observation time using our

university’s resources. Additionally, it contributes to

TÜBİTAK (Scientific and Technological Research

Council of Turkey) projects. A 5-year research pro-

tocol encompassing subjects such as extra-galactic

astronomy, cosmology, analyses of images and astro-

nomical catalogues and stellar astrophysics has been

signed with Cote d’Azur Observatory (France) as of

June 2014.

FACULTY of SCIENCE OBSERVATORY IST60 TELESCOPE

56


Solar observations are made on a daily basis using a mechanism of two separate telescopes attached

to an astrograph which forms the main body. The solar activity is monitored based on sunspots and solar flares. One of the observation mechanisms is used to draw the projection disc of the photosphere (light sphere). Second mechanism is used for Hα CCD imag-ing and monitoring of chromosphere (color sphere). Obtained data are ar-chived both digitally and physically.

Asst. Prof. Dr. Mevlânâ Başal


Assoc. Prof. Dr. Nurol Al



Astrograph with a 30 cm aperture and 150 cm focal

length, Photospheric telescope with a 13 cm aperture

and 200 cm focal length, Chromospheric telescope

with a 12 cm aperture and 232 cm focal length, In-

terference filter with a wavelength of 6562.8 Å and

a bandwidth of 0.3 Å, A flip-mirror system and an

eyepiece, An SBIG-STL series (11000M) astronomi-

cal CCD camera with a 4008 x 2672 pixel chip, Me-

teorology station.


Photospheric data obtained are shared with Solar In-

fluences Data Analysis Center (Belgium). We have

initiated a 5-year research protocol with Instituto

Ricerche Solari Locarno (Switzerland) as of March

2014 covering solar physics subjects.

FACULTY of SCIENCE SOLAR OBSERVATORY

57


Effects of environmental factors on male reproductive system and de-velopment are examined in vitro.

Various studies are conducted on devel-opment and health of male reproduc-tive system. For instance, agonist and antagonist impacts of substances as arsenic and flouride consumed via diet on reproductive cells. The metabolic products of substances are investigat-ed on receptor binding levels as well as hormone inhibition and induction path-ways. Studies conducted in this labora-tory with cell lines such as TM3 (Leydig) and TM4 (Sertoli) of male reproductive system reveal that environmental fac-tors affect the metabolic pathways dur-ing development of male reproductive system. Moreover, embryonic develop-ment of various living organisms is ex-amined.

Prof. Dr. Melike Erkan+90 212 4555700 - [email protected]


Laminar flow cabinet, Fluorescence inverted micro-

scope and imaging system, Deep freezer (-80°C),

Ultrasonicator, Multi-scan spectrum, Homogenizer.


We conduct collaborations and projects on xenobiot-

ics, infertility and production of mature sperm from

stem cells with Çanakkale Onsekiz Mart University

(Turkey), Yeni Yüzyıl University (Turkey), Technical

University of Dresden (Germany), University of Por-

to (Portugal) and Joint Research Centre of Institute

for Health and Consumer Protection (Italy).

FACULTY of SCIENCE CELL and TISSUE CULTURE LABORATORY

58


We investigate cell death, dam-age and repair mechanisms in various in vivo and in vitro ex-

perimental disease models and human diseases at a molecular level. Molecu-lar studies are conducted on apoptosis, necrosis, autophagy, cell growth, tissue regeneration, fibrosis, various growth factors and cytokines-related signal-ing pathways, glycobiology: lectine-car-bohydrate interactions and anti-can-cer activities of some molecules. DNA and RNA isolation, analysis and imag-ing, gene expression analyses: RT-PCR, in-situ hybridization, various glycan de-termination and analysis methods, sin-gle and multiple immunohistochemical and immunofluorescence methods, im-munoprecipitation, 1D and 2D protein electrophoresis and western blotting methods are applied.

Prof. Dr. Şehnaz Bolkent+90 212 4555700 - [email protected]


Laminar flow cabinet, Ultrasonic water bath, PCR

system, Fluorimeter, Refrigerated centrifuge, Ho-

mogenizer, Vertical and horizontal electrophoresis

systems, IEF system, Gel imaging device, Inverted

microscope with fluorescence attachment.


We conduct collaborative studies with İstanbul

Technical University (Turkey), Marmara University

(Turkey), Helmholtz Zentrum München - German

Research (Germany), Universidad Nacional Autono-

ma de Mexico (Mexico), and University of Maryland

(USA). TÜBİTAK (Scientific and Technological Re-

search Council of Turkey) funded research and devel-

opment projects are being conducted.

FACULTY OF SCIENCE MOLECULAR CELL BIOLOGY RESEARCH LABORATORY

59


Cell death, damage and tissue re-pair mechanisms are investigated biochemically. Also, biological ac-

tivities of new molecules are examined therapeutically in various experimental disease models and human diseases. Protein isolation and purification, pro-tein assays, determination of enzyme activities, oxidant/antioxidant param-eters, apoptotic and necrotic markers, inflammatory and anti-inflammatory agents, and various growth factors and cytokines are analyzed by ELISA, spec-trophotometric, colorimetric and elec-trophoretic methods in animal tissue homogenates, cell lysates, blood, se-rum, plasma and bronchoalveolar flu-ids.

Asst. Prof. Dr. Pelin Arda Pirinççi


Assoc. Prof. Dr. Füsun Öztay



Spectrophotometer, ELISA reader, Refrigerated cen-

trifuge, Homogenizer, Horizontal and vertical elec-

trophoresis systems, Transilluminator, Ultrapure wa-

ter system, Deep freezer -86°C, Vortex.


We conduct TÜBİTAK (Scientific and Technolog-

ical Research Council of Turkey) funded research

and development projects on activity mechanisms of

therapeutic new molecules in various disease models.

Furthermore we have completed national and inter-

national patent applications about a new molecule

proposed to be used in treatment of some pulmonary

diseases. We have collaborations with Department

of Chemistry from Faculty of Engineering, Depart-

ment of Chest Medicine from Cerrahpasa Medical

Faculty (Turkey), Marmara University (Turkey),

Helmholtz Zentrum München - German Research

Center (Germany), University of Antwerp (Bel-

gium), and University of Maryland (USA).

FACULTY of SCIENCE BIOCHEMISTRY RESEARCH LABORATORY

60


This laboratory consists of Primary and Stem Cell Culture Research Laboratory, and Cancer Cell Cul-

ture Research Laboratory. In Prima-ry-Stem Cell Culture Research Labora-tory, pancreatic beta cells were isolated for the first time in Turkey and single cell studies were conducted by long-term culture applications. Molecular mech-anisms affecting beta cells in diabe-tes are investigated by trying to unveil mechanisms of cell death, damage and repair in diabetes. Our research group, studying primary pancreatic beta cells isolated from in vivo experimental hy-perglycemic and diabetic animals and islet-derived mesenchymal stem cells, aim to make a fundamental contribu-tion to therapeutic approaches to hu-man health, and ensure implementation of studies by building a bridge be-tween fundamental sciences and clin-ical sciences. In addition, mechanisms that may contribute to process of fibro-sis in cGRP and GRP-stimulated human

Assoc. Prof. Dr. Engin Kaptan

+90 212 4555700 - 15089 [email protected]

Assoc. Prof. Dr. Selda Gezginci Oktayoğlu

+90 21 2 4555700 - [email protected]


Laminar flow cabinet, Ultrasonic water bath, Invert-

ed microscope, Autoclave, UV cabinet, Deep freezer

-152°C, Flow cytometry.


We conduct international collaborative studies with

Helmholtz Zentrum München - German Research

Center (Germany), Universidad Nacional Autono-

ma de Mexico (Mexico) and University of Maryland

(USA) as well as TÜBİTAK (Scientific and Techno-

logical Research Council of Turkey) funded research

and development projects.

pulmonary primary fibroblast cells and mouse primary type II pneumocyte are investigated. In Cancer Cell Culture Re-search Laboratory, researches on Insuli-noma cell line (INS-1), pancreatic ductal cell line ARIP, pancreatic acinar cell line AR42J, breast cancer cell lines (MCF-7 and MDA- MB 231), C6 glioma cell line, follicular, papillary and anaplastic thy-roid carcinoma lines are conducted.

FACULTY of SCIENCE PRIMARY-STEM CELL and CANCER RESEARCH LABORATORY

61


Qualitative and quantitative anal-yses of gamma (137Cs, 40K, 232Th and 238U series) and alpha-emit-

ting (210Po) radionuclides in terrestri-al and marine samples are performed using gamma spectrometry equipped with a high-purity Ge detector and alpha spectrometry. Sediment core, sediment trap and mussel transplantation meth-ods are used in biomonitoring studies. Furthermore bioaccumulation kinetics of radionuclides and metals in marine invertebrates is studied.

Assoc. Prof. Dr. Önder Kılıç


Assoc. Prof. Dr. Murat Belivermiş



Gamma spectrometer (with a high-purity Ge detec-

tor), Alpha spectrometer (with eight ion-implanted

silicon alpha detectors with an active area of 300

mm2).


We conduct collaborative studies with İstanbul

Technical University Faculty of Mines Department

of Geology (Turkey) within the scope of TÜBİTAK


Turkey) project and with Kocaeli University Faculty

of Sciences Department of Biology (Turkey) in deter-

mination of contaminants (radionuclide, metal and

organic) in Golden Horn by active bio-monitoring

methods. We work in collaboration with University

of La Rochelle (France) and Environmental Labora-

tory of Monaco (Monaco) on accumulation of radi-

onuclides in marine invertebrates under high CO2

conditions, and with University of Lisbon Institute

of Technical Sciences (Portugal) on 226Ra, 238U, 232Th, 238+239Pu, 210Po measurements in marine organisms.

FACULTY of SCIENCE RADIOECOLOGY LABORATORY

62


Studies on routine cellular passag-es of normal and tumoral cell lines, and cellular and molecular analy-

ses are conducted. Moreover, cytotox-icity analyses of various antineoplas-tic agents and plant extracts in cell and tissue culture, cell kinetics parameters (Mitotic Index, Labelling Index and Ap-optotic Index), DNA damage and repair pathways, cell cycle and expressions of genes involved in cell death types as well as radiosensitivity and chemosen-sitivity studies are conducted.

Assoc. Prof. Dr. Gül Özcan Arıcan

+90 212 455 57 00 - [email protected]


Optical microscope (phase-contrast and fluores-

cence), Laminar flow cabinet, CO2 incubator, Re-

frigerated centrifuge, PCR system, Electrophoresis

system, Qiaxcel imaging device (As many as 96 sam-

ples can be analyzed at as low concentrations as 3-5

base pair).


We conduct joint studies with American Association

for Advancement of Science (USA), European Asso-

ciation for Cancer Research (UK) and Migal-Galilee

Research Center (Israel).

FACULTY of SCIENCE MOLECULAR CANCER BIOLOGY LABORATORY

63


Various studies are conducted us-ing TUNEL method where apop-totic cells are exhibited by immu-

nohistochemical labeling of enzymes and hormones in appropriate tissues in different experimental models, includ-ing primarily diabetes, sepsis, epilepsy and cancer induced in mice and rats.

Prof. Dr. Cihan Demirci Tansel

+90 212 4555700 – [email protected]

Prof. Dr. Kadriye Akgün Dar

+90 212 4555700 – 15101

[email protected]


Rotary microtome, Microscopic image analysis sys-

tem.


We work in collaboration with University of Am-

sterdam Academic Medical Center (The Nether-

lands), Bezmialem Foundation University (Turkey)

and Giresun University (Turkey). We also conduct

projects where immunohistochemical methods are

used in various tissues sampled from different exper-

imental models as part of TÜBİTAK (Scientific and

Technological Research Council of Turkey) projects.

FACULTY OF SCIENCE IMMUNOHISTOCHEMISTRY RESEARCH LABORATORY

64


We perform physiological stud-ies, circulatory and nervous system applications, microcir-

culation studies, investigation of effects of various endogenous and exogenous agents against acute and/or chronic is-chemia/reperfusion injury and studies on determination of cardiac parameters in Langendorff Isolated Heart System, and various studies regarding neurode-generative diseases on different animal models (sepsis, diabetes, hypertension, hyperglycemia, epilepsy, hemorrhagic shock etc.) by real time measurements under anesthesia.

Prof. Dr. Cihan Demirci Tansel



Langendorff isolated heart system, Homogenizer,

ultra-pure water purification system, Powerlab 8Sp

chart recorder and scope software, Bio amplifier,

bridge amplifier, Blood pressure transducer, Blood

flowmeter, Fine needle probe, Infusion pump, Venti-

lator, Stereotactic surgery system.


We conduct collaborative studies with University of

Amsterdam Academic Medical Center (The Nether-

lands), Bezmialem Foundation University (Turkey),

Giresun University (Turkey) and Karadeniz Tech-

nical University (Turkey). We also conduct projects

on effects of various agents in Langerdorff Isolated

Heart System and septic shock in vivo electrophysi-

ological data acquisition system and circulatory and

renal functions in different experimental models as

part of TÜBİTAK (Scientific and Technological Re-

search Council of Turkey) projects.

FACULTY of SCIENCE PHYSIOLOGY RESEARCH LABORATORY

65


In preclinical cancer research, besides treatment of cancer by chemother-apeutic agents and various extracts,

regulation of treatment of cancer by cellular aging, aromatase inhibitors, na-notechnological drugs and hyperther-mia are investigated as well. Studies on subjects such as Labelling Index, Mitot-ic Index, Apoptotic Index, and Cell Index, Mitochondrial dehydrogenase activity assay, tyrosine kinase activity assay, hy-perthermia applications and evaluation continue.

Asst. Prof. Dr. Mehmet R. Topçul



Laminar flow cabinet, Inverted microscope, Optical

microscope, Centrifuge, Deep freezer -20oC, Deep

freezer -70oC, Precision scales, Distilled water sys-

tem, xCELLigence Real Time Cell analysis system,

CO2 incubator, Shaker incubator, MagCellect devic-

es.


We conduct joint studies with Marmara University

Faculty of Pharmacy (Turkey), İstanbul Faculty of

Medicine (Turkey), İstanbul University Cerrahpasa

Faculty of Medicine (Turkey), İstanbul University

Faculty of Pharmacy (Turkey) and American Associa-

tion for the Advancement of Science (AAAS), Amer-

ican Society Therapeutcal Radiology and Oncology

(ASTRO) and European Society Therapeutical Radi-

ology and Oncology (ESTRO).

FACULTY of SCIENCE MOLECULAR RADIOBIOLOGY and BIOMOLECULAR TECHNOLOGY RESEARCH LABORATORY

66


Qualitative and quantitative anal-ysis of genetically modified or-ganisms (GMO), reproduction of

certain gene regions, quantitative deter-mination of functional genes, determi-nation of gene expression and analysis of specific genes are performed using RT-PCR. In addition, studies such as DNA, RNA, protein isolations, Southern, Northern and Western blotting, gel elec-trophoreses and imaging of protein and nucleic acids, microproduction of en-demic or endangered plants by tissue culture, and determination of polymor-phism and phylogenetic relationships between species by molecular marker techniques are conducted.

Prof. Dr. Mahmut Çalışkan+90 212 4555700 - [email protected]

Prof. Dr. Gül Cevahir Öz+90 212 4555700 – [email protected]


Real-time PCR, Nanodrop 2000 spectrophotometer,

Geliance 200 imaging system, 3 - 30 K ultracentri-

fuge.



Council of Turkey) funded projects and COST pro-

jects as well as other EU-supported collaborative

studies on molecular approaches for increasing starch

synthesis of plants which is of nutritional, industrial

and economic importance with Koç University (Tur-

key), “Taxonomic Revision of Campanula: Sections

Symphyandriformes, Rupestres, Scapiflorae, Saxico-

lae, Tracheliopsis, Dictyocalyx and Platysperma and

their Phylogenetic relationships in Turkey and 2012-

COST ACTION: Omics Technologies for Crop Im-

provement, Traceability, Determination of Authen-

ticity, Adulteration and Origin in Saffron continues.

This laboratory has a potential to conduct routine

GMO analyses. We conduct collaborative studies

with National Institute for Scientific Agricultural

Research (France) for development of new GMO

analysis methods.

FACULTY of SCIENCE PLANT BIOTECHNOLOGY and GENETICALLY MODIFIED ORGANISMS LABORATORY

67


Determination of elemental con-tents of plants, soil, water and sediment samples, purifications,

characterization of peptides and pro-teins, fractionation of such molecules as amino acids, vitamins, such con-taminants as pesticides and polycyclic aromatic compounds have been con-ducted and detection studies for such various chemical compounds as vola-tile oils and fatty acids in samples and high molecular weight biopolymers are performed.

Assoc. Prof. Dr. Gülriz Bayçu Kahyaoğlu


Prof. Dr. Gül Cevahir Öz+90 212 4555700 – [email protected]


ICP-optical emission spectrometer, Ultrahigh per-

formance liquid chromatography, Gas chromatogra-

phy-mass spectrometry, Microwave oven system, Fat

extractor.


We conduct collaborative studies with Yıldız Tech-

nical University (Turkey), University of Orleans

(France), Bielefeld University (Germany), Univer-

sity of Oslo (Norway) and University of Debrecen

(Hungary). TÜBİTAK (Scientific and Technological

Research Council of Turkey) funded projects and re-

search and development projects within the scope of

University-Industry Cooperation are being conduct-

ed and the laboratory has a potential and capacity to

perform routine analyses.

FACULTY of SCIENCE ENVIRONMENTAL and INSTRUMENTAL ANALYSIS LABORATORY

68


We conduct studies on isolation and identification of Legionel-la, sulphate-reducing bacteria

and sulphur-oxidating bacteria, free liv-ing amoeba, microbiological corrosion, determination of antibacterial activity, disinfectant effectiveness studies (sus-pension, biofilm), microbiological food analysis, isolation of bacteria reduc-ing sulphur from petroleum and meth-ane-producing bacteria, biological qual-ity determination of various products, mycology, aerobiology, determination of internal and external air quality, water pollution, quorum sensing, biofilm tests and characterization in man-made wa-ter systems.

Prof. Dr. Ayşın Çotuk+90 212 [email protected]


Identification of bacteria (Epifluorescence micro-scope, Gradient PCR), Community analysis (Dena-tured gradient gel electrophoresis), Anaerobic culture methods (Glovebox), Electrochemical microbiologi-cal corrosion trials (Potentiostat-Galvanostat device), Environmental molecular microbiology studies (Na-nodrop-ELISA reader), Microbiological air quality (Air sampler).


We have academic collaborations with Yıldız Tech-nical University (Turkey), Boğaziçi University (Tur-key), Trakya University (Turkey), Delft University of Technology (The Netherlands), Flinders Univer-sity (Australia), and Turkish Petroleum Corporation (TPAO). We conduct projects on microbiological characterization of petroleum produced in Turkey, microbiological corrosion of metals in cooling tow-ers within the scope of project funded by TÜBİTAK (Scientific and Technological Research Council of Turkey) and make preparations for commercializa-tion and patent applications for anti-biofilm nano-technological coatings.

FACULTY of SCIENCE FUNDAMENTAL and INDUSTRIAL MICROBIOLOGY RESEARCH LABORATORY

69


Putative-mutant plants, with tol-erance to various abiotic stress-es, including drought, salinity and

herbicides have been produced in vari-ous plants, including sugar beet, pota-to, wheat and soybean by using a com-bination of Plant Mutation Breeding and Molecular Biology techniques. Gamma irradiation of in vitro and in vivo samples has been used to improve these target traits. Desired mutants are screened using molecular and biochemical tech-niques. Various plant species, which have agricultural and economic impor-tance, are propagated by plant tissue culture techniques.

Asst. Prof. Dr. Sema Alikamanoğlu

+90 212 455 57 00 - [email protected]


Laminar flow cabinet, Incubator, Precision scales,

PCR cycler, Nanophotometer, Growth cabinet

(Nuve), Plant growth cabinet (Sanyo), Centrifuge,

Gel running vertical and horizontal electrophoresis

tanks.


We have an ongoing collaboration with Join FAO/

IAEA Nuclear Techniques in Food and Agriculture,

Plant Breeding and Genetics Laboratory (Austria).

FACULTY of SCIENCE MOLECULAR RADIOBIOLOGY and PLANT BIOTECHNOLOGY RESEARCH LABORATORY

70


We conduct studies on diagno-sis and production of dinoflag-ellate cysts found particularly

in sea sediment within the frame of pro-duction and culturing of microscopic or-ganisms found in our waters in labora-tory environment.

Asst. Prof. Dr. Benin Toklu Alıçlı

+90 212 455 57 00 - [email protected]

Prof. Dr. Neslihan Balkıs

+90 212 455 57 00 - [email protected]


Incubator, autoclave, Ultrasonic bath, Precision

scales, Photometer, Optical microscope and imaging

system.


International bilateral collaboration project “Mi-

croalgae resting cysts in recent marine sediments and

their role in establishment of Harmful Algal Blooms

(HABs) in three eutrophicated bays in Greece and

Turkey” supported by TUBITAK (Scientific and

Technological Research Council of Turkey) -GSRT

(Greece) partnership has been conducted.

FACULTY of SCIENCE PLANKTON CULTURE LABORATORY

71


It is an international herbarium reg-istered in Index Herbariorum since 1956. Every year, national and inter-

national researchers visit herbarium to conduct studies on more than 40000 plants including samples of a high his-torical and scientific value.

Assoc. Prof. Dr. Osman Erol



Scanning Electron Microscope (Jeol JCM 5000 Ne-

oscope Benchtop), Photomicroscope and Stereomi-

croscope (Olympus SZX16)/Photography and meas-

urement, Optical microscopes and stereomicroscopes

for dissection


It is in contact with all formal and registered herbar-

iums in the world and admits visitors.

FACULTY of SCIENCE ISTF (HERBARIUM)

72


Optical and electrical characteri-zation of novel semiconductor materials and electronic/opto-

electronic devices based on semicon-ductors at a wide range of tempera-ture (2 – 300 K), investigation of charge transport phenomena in solid materials by magneto-transport, detection of de-fect levels, synthesis and characteriza-tion of nanostructures and investigation of magnetic properties of semiconduc-tors are the main research activities.

Prof. Dr. Ayşe Erol



Optical characterization (spectral photoconductivity,

spectral photovoltage, reflection, modulation spec-

troscopy, photoluminescence) from UV (200 nm) to

IR (10 µm) region between 2 and 300 K, Electrical

characterization (a.c. and d.c. Current-Voltage Meas-

urements), Hall Effect measurement system (2.3 T,

10 - 300 K), Magneto-transport set-up (7 T, 4 - 300

K), Defect spectroscopy (PITS), Liquid nitrogen

generator with a production capacity of 40 l/day.


We conduct collaborative studies with Anadolu Uni-

versity (Turkey), Cumhuriyet University (Turkey),

Sakarya University (Turkey), Akdeniz University

(Turkey), University of Essex (UK), Tampere Uni-

versity of Technology (Finland), LAAS (France),

and Victoria University (Canada). We conduct


Council of Turkey) funded projects on electrical/op-

tical properties of novel semiconductor alloys, design

and characterization of photodetectors for optical

communication and COST projects on development

of novel gain materials/devices based on semiconduc-

tors alloys and devices operating in THz region.

FACULTY of SCIENCE NANO and OPTOELECTRONIC RESEARCH LABORATORY

73


Advanced Lithographic Methods Laboratory has been established in 2014 as an outcome of Minis-

try of Development-funded infrastruc-ture project and comprises of a clean room area of 100 m2 with Class 10, 100 and 1000 sections. The laborato-ry facilities are suitably equipped to ena-ble studies on fabrication of electronic/optoelectronic devices by photolithog-raphy and dry etching techniques at a nano/micro scale, imaging of surfaces and cross-sections of solids and deter-mination of elemental composition of materials.




Wet bench equipped with spin coater, Hot plate,

Ultrasonic cleaner, Chemical bench, Mask aligner

(SUSS MJB4), Thermal evaporator (VAKSIS), Pro-

filometer (KLA Tencor P6), Wire bonder (Kulicke

&Soffa), Dry etching equipment (FEI Versa 3D

Dual Beam Focused Ion Beam / RAITH Electron

beam system), SEM (FEI), AFM (Park Systems),

EDS (FEI).


It is aimed to initiate and conduct collaborative re-

search with Anadolu University (Turkey), Cumhuri-

yet University (Turkey), Sakarya University (Turkey),

Akdeniz University (Turkey), University of Essex

University (UK), Tampere University of Technolo-

gy (Finland), LAAS (France) and Victoria Univer-

sity (Canada) on fabrication and characterization of

novel semiconductor structures and optoelectronic/

electronic devices.

FACULTY of SCIENCE ADVANCED LITHOGRAPHIC METHODS LABORATORY

74


High Magnetic Field and Low Tem-perature Laboratory, founded in 2012 as an outcome of a Istan-

bul University-funded project, is suitably equipped to enable studies on investi-gation of charge transport mechanisms in solid materials and semiconductor devices at a variable magnetic field and low temperatures, magnetic field-de-pendent conductivity, classical Hall Ef-fect and quantum Hall Effect, electri-cal characterization and investigation of magnetic properties of solids.

Asst. Prof. Dr. Saffettin Yıldırım





18/20 T Superconducting magnet system with a di-

lution refrigerator (10 mK), Superconducting mag-

net system (7 T, 4.2 - 300 K), Helium recycling sys-

tem and helium liquefier system (18 l/day).


It is proposed to conduct collaborative studies and

projects with University of Essex (UK), Tampere

University of Technology (Finland), LAAS (France),

INSA (France) and Victoria University (Canada)

based on investigation of magneto-transport proper-

ties of semiconductor materials, classical and quan-

tum Hall Effects, charge transport in solids.

FACULTY of SCIENCE HIGH MAGNETIC FIELD and LOW TEMPERATURE LABORATORY

75


Characterization of molecular structures, identification of func-tional groups and determination

of crystallinity are among the main ac-tivities of this laboratory. The structural analysis of the drugs used in the treat-ment of important diseases and their interactions with the media are being studied spectroscopically. Detection of the effects of various diseases at mo-lecular level is also aimed (identification of cancerous tissues, studies on osteo-porosis etc.). In addition, the structural analysis of archaeological findings and determination of the chemical compo-sitions of semiconductor alloys are in-cluded in its range of activities. All of these experimental studies are further supported by molecular simulation cal-culations.

Prof. Dr. Ayşen E. Özel+90 212 [email protected]

Prof. Dr. Elif Akalın+90 212 4555700 - [email protected]


Fourier Transform Infrared Spectrometer (Medium

and near-IR), Fourier Transform Raman Spectrom-

eter (50 – 3600 cm-1 spectral range, 1064 nm wave-

length and 1 W laser source), Micro Raman disper-

sive spectrometer (50 – 8000 cm-1 spectral range,

785 nm and 532 nm wavelength and 100 mW laser

sources).


We have collaborative studies with University of

Potsdam (Germany), Oral Roberts University (USA),

Uzhgorod University (Ukraine) and Politechnico di

Milano (Italy). Molecular structure and vibrational

analysis studies as part of TÜBİTAK (Scientific and

Technological Research Council of Turkey) projects,

and structural analysis and electronic band gap stud-

ies of amorphous solids as part of a TÜBİTAK Inter-

national Bilateral Cooperation project are among he

conducted projects.

FACULTY of SCIENCE MOLECULAR SPECTROSCOPY LABORATORY

76


Laser Spectroscopy Laboratory, es-tablished in 2012 with the sup-port of Istanbul University, current-

ly deals with determination of hyperfine structure constants from atomic spec-tra of elements, and determination of unknown spectral lines of atoms. Hy-perfine structure constants are also used in astrophysics. Accordingly, it is an area befitting interdisciplinary stud-ies.

Prof. Dr. Gönül Başar+90 212 [email protected]


In order to examine the hyperfine structure of atoms

and to find new energy levels, Laser Induced Fluo-

rescence Spectroscopy (LIF), Saturated Absorption

Spectroscopy (SAS) and Opto-galvanic Spectroscopy

(OGS) methods are applied by using a tunable cw Ti-

tan Sapphire laser pumped by an 18 W optical pow-

er, 532 nm wavelength, Cw solid-state laser (having

an optical power of 4 W operating within 700 and

1100 nm range, Continuously tunable at 30 GHz).


We have bilateral collaborative projects and studies

with HTW Berlin (Germany), Latvia University

(Latvia), Graz Technical University (Austria) and

Poznan Technology University (Poland), aimed at

experimental and theoretical identification of fine

structure parameters and hyperfine structure con-

stants of atoms, and determination of new energies

of atoms.

FACULTY of SCIENCE LASER SPECTROSCOPY LABORATORY

77


Dielectric Spectroscopy Laboratory, established in 2012 with the sup-port of Istanbul University, is ca-

pable of producing oxide and polymer materials by using different techniques such as electron beam, thermal evapo-ration, rf and magnetron sputtering. Di-electric characteristics (capacity, die-lectric loss, AC conductivity, relaxation time, etc.) of bulk and powder materi-als, thin films, polymers and liquid sam-ples within 3 µHz – 20 MHz frequency and 173 K – 373 K temperature rang-es, and DC conductivity of bulk and thin films are studied.

Prof. Dr. Deniz Değer Ulutaş



A vacuum system (10-6 Torr with a thickness mon-

itor) and Dielectric Conductivity and Impedance

Measurement System operating within 3 µHz – 20

MHz frequency and 173 K – 373 K temperature

ranges and ELGA Purelab Options-S7/15 water pu-

rification system.


We have collaborative projects and studies with Mar-

mara University (Turkey) and Bahçeşehir University

(Turkey) on growth and characterization of mate-

rials for industrial needs, biological liquids, and an

international collaboration with Charles University

(Czech Republic).

FACULTY of SCIENCE DIELECTRIC SPECTROSCOPY LABORATORY

78


Nuclear Physics Research Labora-tory was established in 2014 with the support of Istanbul Universi-

ty. Nuclear Physics Laboratory consists of Gamma Spectroscopy and Radon Measurement Laboratories. Gamma Spectroscopy Laboratory can handle vast variety of samples including food (tea, hazelnuts, etc.), drink, industrial materials and products (fertilizers, coal, cement, ceramic, marble, granite, etc.) for preparation and measurements. Radon Measurement Laboratory is ca-pable of performing active and passive radon concentration measurements in soil, water and air samples and carries out research activities related with envi-ronmental radiation safety, earthquake – radon relation.

Assoc. Prof. Dr. Latife Şahin Yalçın



A high resolution Gamma Spectroscopy System com-

posed of a p-type Co-axial Ge (HPGe) detector with

35% efficiency for gamma energies between 40 keV

to 10 MeV, Solid state nuclear alpha track detectors

for passive radon measurements and an AlphaGuard

for active radon concentration measurements in soil,

water and air.


This laboratory is suitably equipped for future col-

laborations.

FACULTY of SCIENCE NUCLEAR PHYSICS RESEARCH LABORATORY

79


DNA isolations from fossils (hu-man, animal, plant, etc.) found in archeological sites, and at later

stages, sex-determination and analyses of mitochondrial, X and Y chromosome series are carried out. The resulting se-ries information is bioinformatically as-sessed, and Haplo-group studies are conducted.

Assoc. Prof. Dr. Ercan Arıcan



Gradient PCR and classical PCR systems, Comput-

ers and bioinformatics softwares.


We have collaborative studies and projects with Trak-

ya University (Turkey), Süleyman Demirel Universi-

ty (Turkey), International Society for Computational

Biology (Italy) and International Center for Genetic

Engineering and Biotechnology (Italy), and ongoing

projects with the Ministry of Science, Industry and

Technology.

FACULTY of SCIENCE ANCIENT DNA RESEARCH LABORATORY

80


Cultivation studies are being con-ducted on barley (Hordeum vul-gare L.), bread wheat (Triticum

aestivum L.), rice (Oryza sativa L.), to-bacco (Nicotiana tabaccum L.) and sun-flower (Avena sativa L.), as model organ-isms for plants. Somatic variations are studied on barley under tissue culture conditions and especially at transposon level, and gene expression analyses and transposon analyses are conducted on transgenic tobacco plants, and pheno-logical, physiological and genomic re-sponses are analyzed and correction of these responses by plant hormones is studied on barley, wheat and sunflow-er under abiotic stress circumstances (salinity and heavy metals, etc.), and ge-netic and epigenetic methods are used therein for. GMO analyses are carried out on rice plant. Our Laboratory further uses its expertise on molecular mark-ers in genetic and epigenetic analyses of geriatric genes in human.

Prof. Dr. Nermin Gözükırmızı



Plant growth cabinets, Horizontal electrophoresis

systems, PCR systems (classical and real-time), Auto-

claves, Optical microscopes, Fluorescent microscope,

Confocal microscope.


We have collaborative studies and projects with In-

stitute for Biotechnology and Genetic Engineering

(Bosnia-Herzegovina), Sofia University (Bulgaria)

and Marmara University (Turkey).

FACULTY of SCIENCE PLANT BIOTECHNOLOGY LABORATORY

81


Proteomic analyses (1D, 2D Elec-trophoresis and MS analyses) are conducted on various biological

materials (plants, yeasts, animal cells, stem cells, etc.) and on clinical sam-ples. Bioactivities of proteins and pep-tides (especially HSPs, allergenic pollen proteins, milk proteins and hydrolysis products) are determined, and electro-phoretic / chromatographic separation techniques and Western-blot analysis are carried out. Activities of various en-zymes such as SOD, catalase, peroxi-dase, IMPDH and caspases are meas-ured. In recombinant cells and clinical samples developed by genetic engineer-ing techniques, expression of oxidative stress and apoptosis-related genes is examined, and their protein profiles are compared.

Asst. Prof. Dr. Evren Önay Uçar


Prof. Dr. Nazlı Arda



Vertical and horizontal electrophoresis systems,

HPLC, Isoelectric focusing device, Micro-rota-

tor fractionation device, Gel imaging systems, Gel

drying system, Automated electrophoresis system

(Experion), Protein purification system (Profinia),

Spectrofluorometer, Quibit Spectrofluorometer, Re-

frigerated centrifuge, Transblotter, Western-Blot Sys-

tem, Digital PCR system, Fluorescent microscope,

Freeze dryer.


We have international collaborative studies and pro-

jects with Edinburgh University (UK), Joseph Fou-

rier University and Promethee Proteomic Platform

(France), Cologne University (Germany), Marma-

ra University (Turkey), Ege University (Turkey),

Adıyaman University (Turkey), Kocaeli University

KABI Proteomics Laboratory (Turkey), TÜBİTAK


Turkey) – Marmara Research Center Genetic Engi-

neering and Biotechnology Institute.

FACULTY of SCIENCE PROTEOMICS LABORATORY

82


Our laboratory is engaged in in-tensive research on prenatal di-agnosis by fetal genomic anal-

ysis methods, and is trying to clarify fetal physiology. Genetic diseases that can be diagnosed by non-invasive pre-natal diagnosis methods with microar-ray technology are researched, in addi-tion to molecular genetic analyses for diagnosis and treatment of genetic or-igin diseases. Studies aimed at finding a new molecular marker that can be used for diagnosis of pregnancy com-plications such as pre-eclampsia are ongoing. Blood group of fetus is deter-mined through amniotic fluid, and exist-ence of RHD gene (blood incompatibili-ty) of baby can be detected in maternal blood. In cooperation with specialized doctors, gonadic and sex-linked diseas-es can be diagnosed respectively from amniotic fluid and maternal blood. Fur-thermore, through analysis of polymor-phisms and sports-susceptibility genes in genome, we are trying to make contri-

Assoc. Prof. Dr. Tuba Günel



Real-time PCR systems, Microcentrifuge, Hybridiza-

tion oven, Pikofuge, Microarray scanner, Bioanalyz-

er, DNA/RNA extraction device.


We have international collaborative studies and pro-

jects with Sweden Genome Center (Sweden), in ad-

dition to TÜBİTAK -supported projects, and collab-

orations with some private clinics and SMEs.

bution to sports and exercising.

FACULTY of SCIENCE MOLECULAR DIAGNOSIS in HUMAN DISEASES LABORATORY

83


This laboratory conducts studies on Hordeum spontaneum and Brachypodium types of barley

(Hordeum vulgare L.), a model organ-ism for plants. Phenological, physiolog-ical and genomic responses of plants under stress conditions are studied by molecular methods. Expressions and allelic variations of genes of different pathways under conditions of drought, salinity and combined stress are exam-ined. The studies aimed at increasing transformation frequency in monocot cells through Agrobacterium tumefa-ciens-mediated gene transfer are also carried out. Polymorphism studies based on IGS-RFLP and SSR mark-ers are conducted on our country-ori-gin pathogen and endophyte Fusarium types, and distribution, pathogenicity levels and use of endophytes in agricul-ture are researched. Changes caused by Fusarium infection in barley roots are examined by physiological and genom-ic tools.

Prof. Dr. Filiz Gürel+90 212 4555700 - [email protected]


Plant growth cabinets, Electroporator system, Os-

mometer, Conductivity meter, Incubator, Micro-

scope.


We have COST projects and collaborative studies

with Perugia University (Italy), Ondokuz Mayıs Uni-

versity (Turkey), and Ebittek Biotechnology R&D

Ltd. company.

FACULTY of SCIENCE PLANT GENOMIC RESEARCH LABORATORY

84


Bioinformatics laboratory carries out research on various different DNA structures (Z-DNA, G-Quad-

ruplex, etc.) in Yeast (S. cerevisiae and S. pombe) genome, and determines in-teractions between the relevant struc-tures and gene functions, and com-pares mitochondrial genome X and Y chromosome series, and in the light of the resulting information, assesses phy-logenetic information. The studies on identification of bioinformatics-support-ed molecular markers in plants are also carried out.

Assoc. Prof. Dr. Ercan Arıcan



Gradient PCR and classical PCR systems, Comput-

ers and bioinformatics softwares.



ternational Society for Computational Biology (Ita-

ly) and International Center for Genetic Engineer-

ing and Biotechnology (Italy), and some ongoing

projects with the Ministry of Science, Industry and

Technology.

FACULTY of SCIENCE BIOINFORMATICS LABORATORY

85


Molecular studies are conduct-ed on foreign genes in micro-organisms, in addition to plants

among the genetically modified organ-isms. For the purpose of GMO diagno-sis in plant systems, DNA isolation from processed and unprocessed food stuff, and foreign gene screening by qualita-tive and quantitative PCR, and quanti-fication of foreign genes, and typology of foreign genes continue. Furthermore, studies are carried out for genomic level determination of manipulations, which are aimed at the change of gene ex-pression in plants and plant products. As part of biosafety, transformation fre-quency determination studies are car-ried out in microbial system models for horizontal gene passage from plant or-ganisms to animals and to soil microor-ganisms.

Dr. Özgür Çakır+90 212 4555700 - [email protected]

Prof. Dr. Şule Arı+90 212 4555700 - [email protected]


PCR system, Vertical and horizontal gel electropho-

resis systems.


We have collaborative studies and projects with Eu-

ropean Union Joint Research Center (Italy), Biosafe-

ty Board (Turkey), Union of Seed Raisers (Turkey),

Crop Central Research Institute (Turkey), in addition

to TÜBİTAK (Scientific and Technological Research

Council of Turkey) supported ongoing projects.

FACULTY of SCIENCE GENETICALLY MODIFIED ORGANISMS LABORATORY

86


Research is conducted on more than 70 isolates of 4 types of Fusarium fungi leading to Fusar-

ium culmorum (WG Smith) Sacc. and Pc / Phyphtora capsici in barley, wheat and corn plants of different geograph-ical regions. Also, ongoing are geno-typing of (chromosomal and mitochon-drial) isolates by using RAPD, CAPS, PCR-RFLP, SCAR, ISSR and SSR mo-lecular marker techniques. As part of chemotyping of fungi, mycotoxin gener-ation potentials of fungi are analyzed on genomic (PCR-based) and transcrypto-mic (RT-PCR and real time-PCR) levels, and existence of generated mycotoxins is identified by thin layer chromatogra-phy analysis. As a part of gene-silenc-ing studies on Fusarium types, syn-thetic siRNA molecules are designed specifically for genes related to tox-in generation, and furthermore, silenc-ing vectors carrying the copies of these genes are developed. Genetic manipula-tions in Fusarium types are carried out

Assoc. Prof. Dr. Gülruh Albayrak



Laminar flow cabinet, Temperature and light con-

trolled plant growth cabinet, Shaker incubator, PCR

system, Electroporation system, Optical microscope.


We have an ongoing collaboration with Isfahan Uni-

versity of Technology (Iran).

at co-transformation level, and trans-formants are examined at morpholog-ical, genomic, transcryptomic, metabo-lomic and spectrofluorimetric levels.

FACULTY of SCIENCE PLANT PATHOLOGY LABORATORY

87


For overproduction of plant second-ary metabolites characterized as biological active drug substanc-

es, callus, cell suspension and hairy root cultivations and genetic transfor-mation studies (Agrobacterium mediat-ed and electroporation) are conducted. For production of phenolic substances at pilot level, actions are taken for opti-mization of physicochemical cultivation conditions and for biotechnological pro-duction by elicitation. For identification of antioxidant and cytotoxic, etc. activi-ties of plant secondary metabolites, not only enzyme activity tests and molecu-lar analyses, but also analyses for sec-ondary metabolite identification are car-ried out together with project partners. Furthermore, metabolism of selenium where anti-cancer ingredients are gen-erated is also examined at physiologi-cal, genetic (identification and cloning of genes operating at selenium meta-bolic pathway), genomic and bioinfor-matics levels.

Asst. Prof. Dr. Neslihan T. Kara


Prof. Dr. Şule Arı



PCR system, Ultra-purified water device, Nanodrop

spectrophotometer, Shaker incubator.


Projects supported by East Carolina University

(USA), TÜBİTAK (Scientific and Technological Re-

search Council of Turkey) and the Ministry of Sci-

ence, Industry and Technology are being conducted.

We have collaborative studies and projects with Ege

University (Turkey), Koç University (Turkey), Sa-

bancı University (Turkey) and Istanbul University

Teknokent NGS Biotechnology and Sativa Biotech-

nology companies (Turkey).

FACULTY of SCIENCE PLANT SECONDARY METABOLISM ENGINEERING LABORATORY

88


It is inquired how eucaryotic cells per-ceive their environment, and how they regulate their biological processes in

response thereto. Accordingly, such metabolic pathways as glucose sens-ing, transportation into cell, signal trans-mission, stress response pathways, synthesis and destruction of depot car-bohydrates, and thiamine and purine metabolisms are researched and stud-ied at gene, genome and biochemi-cal levels by a combination of classical yeast genetic methods and molecular techniques. In addition, studies are con-ducted for optimization of enzymes to be used in textile industry for production by fermentation and chronological aging processes at cellular metabolism levels. Studies are ongoing for creation of a S. pombe deletion racial library in terms of various different genes. Furthermore, they are also used as host in clarifica-tion of various metabolic pathways and in heterologous gene expression stud-

Asst. Prof. Dr. Semian Karaer Uzuner

+90 212 4555700 [email protected]

Assoc. Prof. Dr. Bedia Palabıyık



Eukaryotic cell counter, Real Time and classical PCR

systems, Fermenter, Cell fractionation tools, Gel im-

aging systems, UV sterilization cabinet.



ternational Society for Computational Biology (Ita-

ly) and International Genetic Engineering and Bio-

technology Center (Italy), and ongoing TÜBİTAK


Turkey) supported projects and projects with SMEs.

ies for determination of functions of an-imal and plant origin genes.

FACULTY of SCIENCE YEAST GENETICS, TECHNOLOGY and GENOMIC RESEARCH LABORATORY

89


Studies are conducted for safe and stable storage of mine tail-ings above ground and under-

ground. Included among the analyses and studies carried out in our labora-tory are particle size distribution anal-ysis of waste materials, chemical ele-ment content analysis, determination of particle shape, compaction curves and optimum intensity analysis, liquid limit analysis, porosity, permeability, slump and water contents, sedimenta-tion and filtration, pipe flow tests, chan-nel flow tests, yield stress, compressive strength, shearing stress, process water quality analysis, viscosity, liquefaction, consolidation, desiccation cracks inten-sity analysis, and water holding (reten-tion) curves analysis. At the same time, for simulation of behavior of pasty ma-terials at storage site, laboratory meas-urements and analyses are effected under field conditions simulated in lab-oratory waste cabinets.

Prof. Dr. Ataç Başçetin+90 212 4737070 - [email protected]


Tension/compression resistance testing machine,

Ground compactor device, Ground sampling set,

Atterberg consistency limits experiment set, Fall-

ing-head permeability experiment set, Shear box

test device, Consolidation experiment set, CBR

test device, Waste cabinets of various different siz-

es, Temperature – volumetric water content sensors,

Water absorption potential sensors, oxygen sensors,

Elemental analysis (XRF) device, Rheometer device,

Cure cabinet, Laboratory-type mixer, Slump experi-

ment set.


We have collaborative studies and projects with Que-

bec University (Canada).

FACULTY of ENGINEERING WASTE TECHNOLOGY RESEARCH LABORATORY

90


Reactions of polyhalogenic com-pounds and haloquinones with amines, alcohols and thiols in var-

ious different solvents (protic, aprotic, etc.) in presence of acid or base are ex-amined, and new organic compounds are synthesized, and chromatographic chemical and physical characteristics of synthesized compounds and com-plexes are determined, and structural clarification studies are conducted.

Prof. Dr. F. Serpil Göksel+90 212 4737070 – [email protected]


FTIR (400 – 4000 cm-1), Potentiostat / galvanostat /

ZRA System (60 pA – 600 mA), UV-Vis spectrome-

ter (200 – 900 nm), Fluorescence spectrophotometer

(200 – 900 nm), Polarimeter, Horizontal or vertical

condenser rotating evaporation systems, Microdistil-

lation unit, Platform purification device.


We have completed a project for synthesis, character-

ization and activity qualification of new biologically

active substances together with Lviv Polytechnical

University (Ukraine) as a part of an international-

ly funded TÜBİTAK (Scientific and Technological

Research Council of Turkey) project. Furthermore,

Ministry of Development projects have also been

completed in connection therewith.

FACULTY of ENGINEERING ORGANIC CHEMISTRY RESEARCH LABORATORY

91


Reporting of total antioxidant ca-pacity values of food stuffs (all kinds of solid and liquid foods)

produced and processed in our country, and labeling according to the Turkish Food Codex Regulation, and scaveng-ing activity assay of food antioxidants towards reactive oxygen types are among the activities of our laboratory. Antioxidant contents of food stuffs are reported and labeled by means of CU-PRAC antioxidant capacity / activity as-say method. Through identification and separation of antioxidant-rich fractions of foods, new diet and nutrition sugges-tions abundantly containing these com-pounds are formulated.

Prof. Dr. Reşat Apak+90 212 [email protected]


HPLC (UV-Vis, luorescence and PDA detector and

post-column derivatization system), Electrochemical

potentiostat/galvanostat, Mercury drop electrode cel-

lular set, Rotary disk electrode cellular set, UPLC/

MS/MS (Mass-Mass triple quadropole) (with Elec-

trospray [ESI] ion source with a mass measurement

range of 2-2000 a.m.u. and a scanning rate of 10000

a.m.u./sec and an ion source capable of Multimode

[ESI and APcI) ionization and an automatic sampler

and PDA detector), UV-Spectrometer (190 – 900

nm, double beam line).


We have collaborative studies and projects with Min-

istry of Food and Agriculture, General Directorate of

Agricultural Researches and Policies, Istanbul Tech-

nical University (Turkey), some leading companies

(Turkey). A TÜBİTAK (Scientific and Technological

Research Council of Turkey) project aimed at devel-

opment of a new spectrofluorometric method with

resorcinol probe for measurement of hypochlorous

acid scavenging activity of polyphenols is ongoing.

Also, ongoing studies are classification and assess-

ment of food stuffs according to their antioxidant

contents, and development of sensors for antioxidant

enzyme activity measurement.

FACULTY of ENGINEERING FOOD ANTIOXIDANTS MEASUREMENT APPLICATION and RESEARCH CENTER

92


Our laboratory investigates en-zyme activity assays and various biochemical parameters assays

in animal tissue and serum samples, and enzyme inhibition tests, antioxidant activity assays in various plant extracts and chemicals, enzyme purification, enzyme immobilization, effects of vari-ous synthesized inorganic and organic substances on enzyme activities, exper-imental diabetes, examination of pro-tective effects of various chemicals and plant extracts in experimentally creat-ed toxicity models, hyperlipidemia, and determination of contents of plant ex-tracts.

Prof. Dr. Refiye Yanardağ +90 212 4737037 - [email protected]


HPLC, Spectrophotometer, Spectrofluorometer,

Electrophoresis device, Gel imaging device, Frigorif-

ic centrifuge, -80°C refrigerator, Freeze dryer, ELISA

device.


We have collaborative studies and projects with Mar-

mara University (Turkey), Yıldız Technical Univer-

sity (Turkey), Giresun University (Turkey), İnönü

University (Turkey) and İstanbul Aydın University

(Turkey).

FACULTY of ENGINEERING BIOCHEMISTRY RESEARCH LABORATORY

93


Included among the activities of our laboratory are production of catalytic hydrogen from natural gas, dehydro-

genation of oxidative propane, catalyt-ic reactions such as methane pairing, development of catalysts, such fuel cell technologies as polymer electrolyte fuel cells and solid oxide fuel cells, as well as membrane syntheses, and technol-ogies for preparation of different cata-lysts.

Prof. Dr. M. Ali Gürkaynak

+90 212 4737070- [email protected]


Gas chromatography, micro reactor-mass spectrom-

eter combined system, Electrochemical impedance

spectroscopy (30 MHz – 1 mHz), Scanning electron

microscope (SEM), UV spectrophotometer, Test sta-

tions for solid oxide fuel cells and polymer electrolyte

fuel cells (PEMFC), Thermogravimetric analysis –

differential thermal analysis simultaneous measure-

ment device (maximum temperature 1200°C), Con-

tact angle measurement device, Ultrasound provider,

limited high temperature ovens (maximum temper-

atures 1750°C, 1300°C and 1000°C) and drying

ovens, BET Surface Area device, Ultrasound Device

(40 kHz).


The laboratory took part in the project titled “Elec-

trical Neuronal Oscillations and Cognition” within

the scope of the COST program by European Union.

A joint project has been conducted with Macedonian

Academy of Sciences on EEG-Neurofeedback within

the scope of TÜBİTAK’s (Scientific and Technolog-

ical Research Council of Turkey) Macedonia-Turkey

bilateral research support.

FACULTY of ENGINEERING PROCESS and REACTOR DESIGN RESEARCH LABORATORY

94


Our laboratory is engaged in ap-plication of processes such as mineral separation and enrich-

ment of rock samples for radiochrono-logical analyses, and separation of zir-con, xenothyme, amphibole, lawsonite, granitite, monazite, mica, etc. minerals used for age determination, and making them ready for analyses.

Asst. Prof. Dr. Namık Aysal



Magnetic separator, Heavy liquids and minerals flo-

tation – sedimentation systems.


We have collaborative studies with Çukurova Uni-

versity (Turkey), Fırat University (Turkey), Istanbul

Technical University (Turkey), and Bulgarian Sci-

ence Academy (Bulgaria), in addition to ongoing


Council of Turkey) projects.

FACULTY of ENGINEERING GEOCHRONOLOGICAL SAMPLE PREPARATION and MINERAL SEPARATION LABORATORY

95


Our laboratory is engaged in pH, electrical conductivity, carbon, ni-trogen and other elemental analy-

ses in plant, turf, soil and water samples, and such analyses as texture, calcium carbonate and water holding (retention) capacity in soil, and studies for identi-fication of forest ecosystems. In addi-tion, projects are ongoing on monitor-ing of forest ecosystems, mapping of forest soils, plant nutrition, rehabilitation of mineral sites, soil pollution, phytore-mediation, determination of effects of air pollution on forests.

Asst. Prof. Dr. Serdar Akburak



C/N elemental analysis device, ICP-OES, microwave

sample granulator, UV spectrometer, Flow injection

device, Nitrogen/protein device, Centrifuge device,

Frigorific incubator, Stereo microscope, pH-meter

and EC-meter.


We have collaborative studies and projects with Ko-

rean University (Korea), Debrecen University (Hun-

gary) and Istanbul Technical University (Turkey),

Dokuz Eylül University (Turkey), Süleyman Demirel

University (Turkey) and many other universities, in

addition to ongoing joint projects with Forestry Re-

search Institutes of the Ministry of Forest and Hy-

draulic Works. There are also pending TÜBİTAK


Turkey) projects pertaining to the quantity of carbon

stored in soil and plant masses in forest ecosystems in

tandem with climatic changes.

FACULTY of FORESTRY SOIL SCIENCE (AGROLOGY) and ECOLOGY LABORATORY

96


It is the first Nanotechnology Labora-tory and Thermal Analysis Laboratory in forest industry field (wood, wooden

composite materials, biomaterials, ther-moset/thermoplastic glues, furniture) in Turkey. It deals with research and devel-opment and innovation studies on ap-plications of nanoscience and nano-technology in wood industry, and with thermal characterization of materials. Also, ongoing are scientific and indus-trial projects related to development of new generation of environmental-friend-ly wooden composites, development of composites with reduced formaldehyde emission, development of composites with enhanced resistance and thermal stability, and development and charac-terization of biomaterials, biocompos-ites and nanocomposites.

Prof. Dr. Nusret As+90 212 3382400 - [email protected]


Thermogravimetric Analysis/Differential Thermal

Analysis (TGA/DTA) system, Dynamic Mechan-

ical Thermal Analysis/Thermomechanic Analysis

(DMTA/TMA) system, Vacuum oven, Ultrasonic

homogenizator, Viscosimeter.


We have collaborative studies and projects with

Maine University (USA), Louisiana State University

(USA), Tennessee University (USA), Bangor Univer-

sity (United Kingdom), and Beijing Forestry Uni-

versity (People’s Republic of China), in addition to

ongoing joint research and development projects. We

also have memberships in European Union COST

actions regarding nanotechnology and composite

materials. We have also pending joint projects and

collaborations with Sabancı University (Turkey),

Istanbul Technical University (Turkey) and Bursa

Technical University (Turkey) and many other uni-

versities and non-governmental organizations.

FACULTY of FORESTRY NANOTECHNOLOGY LABORATORY and THERMAL ANALYSIS LABORATORY

97


Our laboratory is engaged in meas-urement of mass loss and con-vection speed occurring in wood-

en materials during combustion, and combustion tests, thermal analyses of wooden materials, and anti-fire perfor-mances of wood and wooden-based products and non-wood constructional materials.

Research Assistant Evren Terzi


Prof. Dr. S. Nami Kartal+90 212 3382400 - [email protected]


Mass loss calorimeter, Single-flame source ignitabili-

ty analyzer, Fourier Transform Infrared Spectrometer

(FT-IR).


We have collaborative studies and projects with For-

estry Service, Forest Products Laboratory (USA) and

Yıldız Technical University (Turkey), on various bo-

ron products which have not yet been introduced to

forestry industry, and on synthesis of boron products

as a fire-retardant additive.

FACULTY of FORESTRY PROF. DR. A. YILMAZ BOZKURT WOODEN MATERIALS COMBUSTION TEST and ANALYSIS LABORATORY

98


It is the first and single laboratory deal-ing with annual ring research in Tur-key. Accordingly, it generates data for

various disciplines such as forestry, cli-mate sciences, geography, archeology, history of art, architecture, etc. The lab-oratory conducts its “wood annual ring” and “wood anatomy” studies togeth-er. The history of climate in Anatolia is studied, and annual ring data sets are created for our natural tree species. Fur-thermore, wood materials found in his-torical buildings and archeological sites are diagnosed, and their period of use, and building construction and/or repair dates are determined in reliance upon annual ring analyses. In addition, den-drogeomorphological studies are con-ducted for determination of frequency and limits of such events as avalanche, landslide, etc. Operating as a part of ISTO Herbarium, this laboratory is en-gaged not only in ecological wood anat-omy researches, but also in wood anat-omy leg of taxonomic revision studies

Assoc. Prof. Dr. Nesibe Köse


of wood-like plants, and holds an im-portant collection of contemporary and petrified woods.


Linear-tray and computer-aided Annual Ring Meas-

urement Systems, Microscopes, Microtomes, Incre-

ment borers and cleaning sets of different sizes.


We have collaborative studies and projects on den-

drochronology, dendroclimatology, dendroarcheolo-

gy, dendroecology and dendrogeomorphology with

Arizona University (USA), Columbia University

(USA) and Purdue University (USA), in addition to

collaborative projects ongoing with various local uni-

versities such as Istanbul Technical University (Tur-

key), Ege University (Turkey) and Bartın University

(Turkey), and with Forestry Research Institutes.

FACULTY of FORESTRY ANNUAL RING RESEARCHES and WOOD ANATOMY LABORATORY

99


Our laboratory is engaged in detec-tion of local and exotic tree spe-cies in the merchandized raw

materials, semi-finished and finished products, and determination of tree species in restoration / conservation projects and in archeological wooden objects, and determination of desired quality specifications of raw material wood at the place of use in tandem with anatomic composition, and identifica-tion of material-based problems emerg-ing as a result of anatomic composition and development of resolution sugges-tions in Forestry Products Industry, and determination of quality losses in wood-en materials through examination of an-atomic composition, and assessment of the degree of success of industrial processes on woods in line with chang-es caused thereby in anatomic compo-sition. Furthermore, it covers Prof. Dr. Adnan BERKEL Xylarium (ISTUFw Xy-larium), being the first and single collec-tion accepted to International Xylariums

Research Assistant F. Diğdem Tuncer


Assoc. Prof. Dr. Ayşe Dilek Doğu


(INDEX XYLARIUM) used for education, scientific research, wood diagnosis and industrial service purposes.


Stereo microscope, Optical microscope with digi-tal imaging system with polarized and fluorescence equipment and slide microtome.


We have collaborative studies and projects with Min-istry of Culture and Tourism, Istanbul Restoration and Conservation Central Laboratory Directorate, National Union of Wood, Istanbul Metropolitan Municipality, Protection Application and Super-vision Directorate, National Research Institute on Cultural Features (Japan), and Natural Resources and Applied Life Science University (Austria). In ad-dition to a TÜBİTAK (Scientific and Technological Research Council of Turkey) project focused on an-atomic and microbiological specifications of archeo-logical wooden materials found in Marmaray Project excavations (Turkey), and effects of thermal process on anatomic composition of wood, we have carried out projects for diagnosis of tree species in archeolog-ical wood finds of Aegean Region.

FACULTY of FORESTRY PROF. DR. A. YILMAZ BOZKURT WOOD ANATOMY LABORATORY

100


Included among its activities are clar-ification of chemical composition of wood-based and non-wood lignocel-

luloses-based materials, and determi-nation of structures and specifications of new products produced as a result of chemical transformation of these mate-rials, and identification of places of use of them, as well as analyses relating to processes from cellulose production to final area of use of paper, and structur-al analyses of woods and wood-based materials, as a part of industrial servic-es.

Prof. Dr. Celil Atik+90 212 3382400 - [email protected]


HPLC, UV-Vis spectrometer, GC-MS, Fourier

Transform Infrared Spectrometer (FT-IR), Viscos-

imeter, Rheometer, TMA, Universal tester (for pa-

per products), Spectrophotometer (Elrepho), Glossy

paper coating device, Manual paper manufacturing

devices fit to various different standards.


We have collaborative studies and projects with Yıldız

Technical University (Turkey), Kastamonu Universi-

ty (Turkey), Gebze High Technology Institute (Tur-

key), Dokuz Eylül University (Turkey), İzmit Poplar

Industry Research Institute (Turkey), Western Mich-

igan University (USA), and North Carolina Univer-

sity (USA), in addition to joint projects with private

sector entities, and TÜBİTAK (Scientific and Tech-

nological Research Council of Turkey) projects.

FACULTY of FORESTRY – FORESTRY PRODUCTS CHEMISTRY and TECHNOLOGY RESEARCH LABORATORY and CELLULOSE, PAPER and CARDBOARD ANALYSIS LABORATORY

101


It consists of two separate laborato-ries where water and soil analyses are conducted. These laboratories offer

services on basin, hydrology, hydroeco-logy, soil, etc. research by international methods and through new generation detailed analyses in line with needs and demands of public and private sectors.

Prof. Dr. Kamil Şengönül+90 212 3382400 - [email protected]


Kjeldahl semi-automatic nitrogen tester, Centri-

fuge, Turbidimeter, Ion-meter, Spectrophotometer,

pH-meter and EC-meter, Dissolved oxygen tester,

water turbidity meter, Soil moisture tester, Permea-

bility device, Penetrometer, Lysimeter.


We have collaborative studies and pending projects

with Massachusetts University (USA), Department

of Agriculture, South Research Station (USA),

Çankırı Karatekin University, Süleyman Demirel

University (Turkey) and Forestry Research Institutes,

focused on basin management, semi-arid areas as a

part of climatic changes, pasture improvement.

FACULTY of FORESTRY BASIN MANAGEMENT LABORATORY

102


It deals with quality control, hygiene and sanitation of aquacultural prod-ucts from fishing to consumption,

and aquacultural toxicology, food safety and product development. This labora-tory conducts analyses for determina-tion of fatty acid, amino acid, trimethyl-amine nitrogen and thiobarbituric acid indices, and quantification of 4-hexylre-sorcinol and biogenic amine, and color measurement and texture measure-ment analysis in aquacultural products.

Prof. Dr. Özkan Özden+90 212 4555700 - [email protected]


Gas chromatography, High pressure liquid chroma-

tography, UV-Vis spectrometer, Ultrasonic water

bath, Texture measurement device, Color measure-

ment device, Frigorific centrifuge.


As a part of TÜBİTAK (Scientific and Technologi-

cal Research Council of Turkey) supported and oth-

er internationally funded projects, various projects

focused on protection of aquacultural products and

prolongation of their shelf lives have been complet-

ed, and a European Union project is continuing for

formation of monitoring systems for food safety in

aquaculture.

FACULTY of AQUACULTURE INSTRUMENTAL ANALYSIS LABORATORY

103


Accumulation of cyanotoxins pro-duced by cyanobacteria in aquat-ic biota, and determination of

genes producing cyanotoxins, and ef-fects of environmental factors on cy-anotoxin production, and accumulation and convection of heavy metals in food chain, and lethal dose studies for or-ganism groups, and pesticide accumu-lation in living creatures and water, and PAH analyses are conducted.

Assoc. Prof. Dr. Reyhan Akçaalan Albay



HPLC, ICP-MS, GS-MS, Real time PCR, Imaging

device, Freeze dryer, Cyanobacteria cultivation room,

TOC-meter, Laminar flow cabin, Ultrasonicator,

Spectrophotometer, Filtration system and micro-

scopes.


Three European Union projects are continuing on

examination of cyanotoxins in our internal waters

and seas, and determination of their effects.

FACULTY of AQUACULTURE ECOTOXICOLOGY and CYANOTOXIN LABORATORY

104


It is founded for analyses in line with demands of both Istanbul University organization units and other public and private entities. Clarifica-

tion of composition of organic ingredients (syn-thetic organic ingredients, natural organic ingre-dients, organometric ingredients, organic metal complexes, polymers, etc.), trace element as-says, identification of organic ingredients, deter-mination of elemental percentages of solid or liquid organic ingredients by combustion, quali-tative and quantitative assay of inorganic com-plexes and organic ingredients, quantitative and qualitative analyses of elements contained in solid, powder and liquid samples, examination of single crystalline – powder crystalline struc-tures, molecule structures and molecule mod-eling of small molecules, and qualitative miner-al analyses.

Assoc. Prof. Dr. Hasret Demircan Yardibi


Research Infrastructure of the Laboratory• Nuclear Magnetic Resonance Spectrometer (Var-

ian UNITY INOVA 500 MHz, 1D and 2D NMR,

APT, DEPT)

• Elemental Analyzer (Thermo Finnigan Flash EA

1112 Series)

• Inductive Coupling Plasma – Mass Spectrometer

(Thermo Elemental X Series 2)

• FT-IR Spectrometer (Perkin Elmer, 450 - 4000

cm-1, with ATR unit)

• X-Ray Powder Crystal Diffraction (Rigaku D, with high temperature oven unit, Cu source, and graphite monochromator)

• X-Ray Single Crystal Diffractometer (Rigaku R-Axis Rapid-S)

• X-Ray Fluorescence Spectrometer

• Liquid Chromatography – Mass Spectrometer

• Gas Chromatography (Thermo Finnigan Trace GC Ultra) – Mass Spectrometer (Thermo Finnigan Trace DSQ)

• Mass Spectrometer (Thermo Finnigan Trace LCQ)

• Ultraviolet Visible Spectrometer (190 – 600 nm)

• Atomic Absorption Spectrophotometer (Analyst 200 flame, Analyst 600 Graphite oven and Perkin

Elmer Hydride Systems).


Contemporary method studies are continuing on X-ray diffraction with Max Planck Institute (Germany) and Rikagu/MSC Woodland Texas Laboratory (USA). In addition, contemporary NMR and Elemental Analysis method studies are carried out with Varian Application Labora-tory (Germany).

TECHNOLOGY TRANSFER APPLICATION AND RESEARCH CENTER CENTRAL RESEARCH LABORATORY (MERLAB)

105

SOCIAL SCIENCES RESEARCH LABORATORIES


This laboratory owns all generally accepted professional software programs used for editing, com-

positing and color grading works for dig-ital videos. It is composed of 6 rooms, four of which are offline editing rooms, one is sound recording room, and one is “Da Vinci Resolve” room used for fi-nal mixing. The laboratory has a world standard infrastructure for work flow after a healthy and reliable shooting. It is technically satisfactory, reassuring, quick and creative for users.

Asst. Prof. Dr. İlkay Nişancı+90 212 4400000 - [email protected]


Tangent Device - DA VINCI Control Interface,

LYNX HILO - Analog Digital, Digital Analog Sound

Converter, BON 24 inch Grade 1 Monitor, MAC

OS Workstation-based montage and cutting system,

FCP X, AVID, ADOBE, DA VINCI, WINDOWS

Workstation-based montage and cutting system,

EDIUS and ADOSE, Main Storage Unit (50 TB),

SAS Storage Unit (16 TB), data speed above 1 GB

per second, Real Time H.264 Converter, FOCAL

CMS 65 Reference Monitors, ART TPS II – Micro-

phone Preamp.


Montage, cutting, color arrangement and sound mix

of short documentary film named Kamilet - 2014

Trento Mountain Films Festival (Italy); montage,

cutting, color arrangement and sound mix of medi-

um-length documentary film named Antigoni – Fi-

nalist in 2013 Antalya Film Festival; vocal records

and mix of new album of famous Rock musician

named Umut Kaya; Nursing Faculty Skill Vide-

os; montage and cutting of around 200 skill videos

sponsored by Florence Nightingale Foundation; and

montage and cutting of “Democracy” project spon-

sored by YEKÜV and handled by a project of Istan-

bul University Scientific Research Projects Unit.

FACULTY of COMMUNICATION PRODUCTION and POST-PRODUCTION LABORATORY

108


Earthenware, stones, bones and clay findings of different regions and pe-riods are examined and analyzed in

typological, technological and function-al terms. This laboratory has the most comprehensive archaeological materi-als archive of Turkey. The archaeologi-cal archive, standing as a reference cat-alogue, contains materials coming from 1645 mounds, ruins and sites, and sys-tematic – layered – samples of around one hundred archaeological sites, and material samples of prehistoric cultures of Near East and Balkans, and West Eu-ropean Paleolithic Era finds, and mate-rial samples coming from all obsidian sources in Turkey, Aegean and Mediter-ranean regions.

Asst. Prof. Dr. Eylem Özdoğan



Multi-enlargement metallurgic microscopes, Stereo

microscopes.


Connecticut University (USA), Arizona Universi-

ty (USA), Cornell University (USA), Paris Univer-

sity (France), National Natural History Museum

(France), National France Scientific Research Center

(France), Lyon University (France), Eberhard Karls

Tubingen University (Germany), Ludwig-Maximil-

ian University (Germany), Munich Archaeology

Museum (Germany), German Archaeology Insti-

tute, Bergbau German Mining Museum (Germany),

Karlsruhe University (Germany), Cologne Universi-

ty (Germany), Austrian Science Academy (Austria),

Vienna University (Austria), New Bulgarian Uni-

versity (Bulgaria), Sozopol Underwater Archaeology

Center (Bulgaria), Czech Republic Science Academy

(Czech Republic), Prague University (Czech Repub-

lic), Natural History Museum (United Kingdom),

Groningen University (Netherlands), Athens Clas-

sical Studies American School (Greece), Istanbul

Technical University (Turkey), Hacettepe Universi-

ty (Turkey), Koç University (Turkey) and Eskişehir

Anatolian University (Turkey).

FACULTY of LETTERS PREHISTORY LABORATORY

109


Various chemical experiments that may be needed in mortar and plaster analyses, ship models,

conservation and restoration works are conducted. Underwater artworks are subject to conservation and restoration works.

Research Assistant Taner Güler

+90 212 4555700 - 16017 [email protected]


Heating system stainless steel PEG impregnating

tank, Fume hoods, Drying oven, Microscopes and

ship modeling tools.


We conduct joint projects with Byzantine and

Post-Byzantine Monuments Research Center

(Greece) and Presidency of the Republic of Turkey.

FACULTY of LETTERS SHIP CONSERVATION and RECONSTRUCTION LABORATORY

110


Conservation, restoration, three di-mensional drawing, photograph-ing and photomosaic works of

sunken ships are performed.

Research Assistant Namık Kılıç

+90 212 [email protected]


FaroArm 3D digitizer, Photograph mechanism with

paraflash system, Water purification system, Large-

scale oven and freeze dryer.


We conduct joint projects with Byzantine and

Post-Byzantine Monuments Research Center

(Greece) and Presidency of the Republic of Turkey

and Roskilde Museum (Denmark).

FACULTY of LETTERS YENİKAPI SUNKEN WRECKS RESEARCH CENTER LABORATORY

111

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ISTANBUL UNIVERSITY · İstanbul University is the first university in Turkey and among the first ten universities founded in Europe, directing the society in areas of health, social