Departments and Programmes


Our Programmes:


Council of Higher Education, Graduate Training Regulation



IZMIR INTERNATIONAL BIOMEDICINE  AND GENOME INSTITUTE ACADEMIC AND ADMINISTRATIVE STAFF NUMBERS

  • 7 Faculty Members
  • 3 Foreign Faculty Members
  • 1 Foreign Visiting Professor
  • 3 Foreign Specialist
  • 1 Instructor
  • 13 Administrative Staff

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ ÖĞRENCİ SAYILARI ( SON 2 YIL)

 AKADEMIC YEAR MSc PhD Total
2016-2017 24 16 40
2017-2018 21 37 58

 



  1. Tez Yazım Kılavuzu

  2. Tez Önerisi Formu

  3. Danışman Atama Formu

  4. 2. Danışman Atama Formu

  5. Danışman Değişikliği Formu

  6. Tez Önerisi Değişikliği/Tez Başlık /Tez İçerik Değişikliği Formu
  7. Yüksek Lisans Tez Savunma Başvuru Formu

  8. Doktora Yeterlilik Başvuru Formu

  9. Tez İzleme Komitesi Oluşturma Formu

  10. Tez Teslim İşlemleri

  11. İntihal Raporu Beyan Belgesi

  12. DEÜ TURNITIN İntihal Programı Kullanma Kılavuzu

  13. Tez İntihal Analiz Programı 


http://biyotip.deu.edu.tr/wp-content/uploads/2018/07/yonetim-semasi.pdf


DEÜ Bilimsel Araştırma Projeleri


YÖK Bilimsel Araştırma ve Yayın Etiği Yönergesi


Yurtdışı Yükseköğretim Diploma ve Denkliği Yönetmeliği


YÖK 100/2000 Doktora Bursu


YÖK Lisansüstü ve Öğretim Yönetmeliği


DEÜ Yatay Geçiş Yönergesi


DEÜ Muafiyet ve İntibak Yönergesi


DEÜ Akademik Danışmanlık Yönergesi


DEÜ Lisansüstü Eğitim ve Öğretim Yönetmeliği




Column content

+90 (232) 412 67 04
+90 (232) 412 63 53




Misyonumuz, sağlık alanında uluslararası camiada etkin olabilecek seçkin, yetenekli bilim insanları ve akademisyenler yetiştirmek, insanlığın refah düzeyini arttırmak ve küresel sağlık sorunlarını azaltmaya yönelik bilgi, deneyim, teknoloji ve araç geliştirmeye yönelik eğitim faaliyetleri düzenlemek, ulusal ve küresel düzeyde eğitim ve araştırma paydaşları ile ortaklıklar oluşturarak inovatif bir eğitim merkezi olmaktır.

Vizyon

Ülkemizde en çok tercih edilen, dünya çapında saygın, uluslararası standartta, yaşam bilimlerindeki yeni bilimsel bilgiyi toplumun sağlık ve refahı için kullanılabilir hale dönüştüren, yaptığı bilimsel keşifler ile dünya çapında sağlık ve bilim politikalarına yön veren bir eğitim ve araştırma kurumu olmaktır.



 

İzmir Uluslararası Biyotıp ve Genom Enstitüsü (iBG-izmir)
Dokuz Eylül Üniversitesi Sağlık Yerleşkesi
Balçova 35340 İzmir
Telefon: 0(232) 412 67 04
Faks: 0(232) 277 63 53
E-posta: ibg@deu.edu.tr
Izmir International Biomedicine and Genome Institute (iBG-izmir)
Dokuz Eylül University Saglik Yerleskesi
Balcova 35340 Izmir/TURKEY
Phone: 0(232) 412 67 04
Fax: 0(232) 277 63 53
E-mail: ibg@deu.edu.tr

 

INSTITUTE SECRETARY

       ALKAN DURMUŞ  ( Institute Secretary )

       TEL: +90 232 412 8654 

       E-mail:  alkan.durmus@deu.edu.tr

STUDENT AFFAIRS

   TUBA AKÜNAL

   TEL: +90 232 412 6725

  E-mail:tuba.akunal@deu.edu.tr

 

SERGÜL BULUT

 TEL: +90 232 412 8666

E-mail:sergul.bulut@deu.edu.tr

 

HUMAN RESOURCES

    ÖZCAN ÇAKMAK

   TEL: +90 232 412  8660

   E-mail:ozcan.cakmak@deu.edu.tr

 

  EFE BİLGİ

  TEL: +90 232 412 8660

  E-mail:efe.bilgi@deu.edu.tr

 

FEYZİ ÖNDER

TEL: +90 232 412 8663

E-mail:  feyzi.onder@deu.edu.tr 

FINANCE OFFICE

     HAKTAN GÜNER

      TEL: +90 232 412 6763

      E-mail: haktan.guner@deu.edu.tr

     

ASSET MANAGEMENT

MERAL KASMAN  

     TEL: +90 232 412 8675

      E-mail: meral.kasman@deu.edu.tr

HAKAN SAVRAN  

     TEL: +90 232 412 8677

      E-mail: hakan.savran@deu.edu.tr

 

DOCUMENT OFFICE

 EFE BİLGİ

  TEL: +90 232 412 8660

  E-mail:efe.bilgi@deu.edu.tr


İZMİR INTERNATIONAL BIOMEDICINE AND GENOME INSTITUTE

Institute Director                         Prof. Sefa KIZILDAĞ

Institute Vice-Director                Prof. Zekiye SULTAN ALTUN

Institute Vice-Director                Assoc. Prof. Ahmet KARAKAŞLI

Institute Secretary                      Alkan DURMUŞ

 

Faculty Members
Prof. Hülya AYAR KAYALI
Prof. Hüsnü Alper BAĞRIYANIK
Prof. Mehmet ÖZTÜRK
Prof. Safiye Neşe ATABEY
Prof. Şerife Esra ERDAL BAĞRIYANIK
Prof. Şermin GENÇ
Assoc. Prof. H.Güneş ÖZHAN
Assoc. Prof. Can KÜÇÜK
Assoc. Prof.  Muhammed Kasım DİRİL
Assoc. Prof. Duygu SAĞ WİNGENDER
Assoc. Prof.  Şerif ŞENTÜRK
Assoc. Prof.  Sinan GÜVEN
Assist. Prof.  Hani ALOTAİBİ
Assist. Prof.  Gökhan KARAKÜLAH
Assist. Prof.  Zeynep KOÇER
Assist. Prof. Serhat TOZBURUN
Assist. Prof.  Ezgi KARACA EREK
Assist. Prof.  YAVUZ OKTAY

 

Foreing Faculty Members
Assoc. Prof. Ralph MEUVISSEN
Assist. Prof. Gerhard WINGENDER
Assist. Prof. Athanasia PAVLOPULOU
Visiting Professor
Prof. Brian I.CARR

 

Lecturer
Dr. Hasan Buğra ÇOBAN

 

Specialists
Spec. Evin İŞCAN 
Spec. Güldane Bilge KILIÇ

 

Foreign Specialists
Spec. Hongling YUAN 
Spec. Vanesa Segovia BUCHELI
Spec.Xiaozhou HU

 


Current AnnouncementsArchive
Duyuru Bulunamadı
Duyuru Bulunamadı

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ LİSANSÜSTÜ EĞİTİM PROGRAMLARI

Genom Bilimleri ve Moleküler Biyoteknoloji Anabilim Dalı

İngilizce Moleküler Biyoloji ve Genetik Yüksek Lisans Programı 

İngilizce Moleküler Biyoloji ve Genetik Doktora Programı 

İngilizce Moleküler Biyoloji ve Genetik Bütünleşik Doktora Programı


o 2016-2017 AKADEMİK TAKVİM
o LİSANSÜSTÜ PROGRAMLARA BAŞVURU ÖN KOŞULLARI
o ÖĞRENİM VİZESİ VE İKAMETGÂH TEZKERESİ ALABİLMEK ICİN YAPILACAK ISLEMLER
o 2017-2018 GÜZ YARIYILI ÖZEL ÖĞRENCİLİK BAŞVURULARI


 

 Meral YAKUT ÖZTÜRK  ( Enstitü Sekreter V. )


Birim Kalite Komisyonu

Prof. Dr. Zekiye Sultan ALTUN Komisyon Başkanı
Doç. Dr. Ahmet KARAKAŞLI Üye
Enstitü Sekreteri V. Meral YAKUT ÖZTÜRK Üye
Öğr. Gör. Mine İNANÇ DEMİR Üye

 

Prof. Dr. Sefa Kızıldağ Enstitü Müdürü
Prof. Dr. Zekiye Sultan Altun Enstitü Müdür Yardımcısı
Doç. Dr. Ahmet Karakaşlı Enstitü Müdür Yardımcısı
Prof. Dr. Hüsnü Alper Bağrıyanık Üye

 

Prof. Dr. Sefa Kızıldağ Enstitü Müdürü
Prof. Dr. Zekiye Sultan Altun Enstitü Müdür Yardımcısı
Doç. Dr. Ahmet Karakaşlı Enstitü Müdür Yardımcısı
Prof. Dr. Hasan Havıtçıoğlu Üye
Prof. Dr. Nur Olgun Üye
Prof. Dr. Ogün Sercan Üye

Prof. Dr. Zekiye Sultan ALTUN

Doç. Dr. Ahmet KARAKAŞLI


Prof. Dr. Sefa KIZILDAĞ


 

  1. Hizmet Damgalı Pasaport Talep Formu

  2. Özel Öğrenci Başvuru Formu

  3. Seçmeli Ders Belirleme Formu (YL)

  4. Seçmeli Ders Belirleme Formu (PHD)

  5. Öğrenci İlişik Kesme Formu

  6. Mezuniyet Belgesi Talep Dilekçesi 




 

ENSTİTÜ SEKRETERLİĞİ

   MERAL YAKUT ÖZTÜRK  ( Enstitü Sekreter V. )

    TEL: +90 232 412 8654 

    E-mail: meral.yakut@deu.edu.tr

 

ÖZEL KALEM 

  AYŞE GÜL ÖZCAN

  TEL: +90 232 412 8651

 

ÖĞRENCİ İŞLERİ

   DİLEK DÜZYOL ŞENGEZER (Şef)

   TEL: +90 232 412 67 25

   E-mail:dilek.sengezer@deu.edu.tr


  ÖĞR. GÖR. SERGÜL BULUT GÖKDERMEN

  TEL: +90 232 412 67 25

  E-mail: sergul.bulut@deu.edu.tr


  ÖZLEM ALKU

  TEL: +90 232 412 67 25

  E-mail: ozlem.alku@deu.edu.tr

 

HALKLA İLİŞKİLER  BİRİMİ

 ÖĞR. GÖR. SERGÜL BULUT GÖKDERMEN

  TEL: +90 232 412 67 25

  E-mail: sergul.bulut@deu.edu.tr

 

KALİTE VE AKREDİTASYON  BİRİMİ

ÖĞR. GÖR. MİNE İNANÇ DEMİR

 TEL: +90 232 412 8660

 E-mail: mine.demir@deu.edu.tr

TEL+90 232 412  8663

 

ULUSLARARASI İLİŞKİLER  VE İNSAN KAYNAKLARI BİRİMİ

  TUBA AKÜNAL

  TEL: +90 232 412  6717

  E-mail:tuba.akunal@deu.edu.tr 

 

İDARİ VE MALİ İŞLER BİRİMİ

 HAKTAN GÜNER  ( Taşınır Kayıt Yetkilisi )

 TEL: +90 232 412 6763

 E-mail: haktan.guner@deu.edu.tr

 

YAZI İŞLERİ VE EVRAK KAYIT BİRİMİ

   FEYZİ ÖNDER

    TEL: +90 232 412 6717

    E-mail:feyzi.onder@deu.edu.tr

       


 

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ MÜDÜRLÜĞÜ

Enstitü Müdürü                              Prof. Dr. Sefa KIZILDAĞ

Enstitü Müdür Yardımcısı           Prof. Dr. Zekiye SULTAN ALTUN

Enstitü Müdür Yardımcısı           Doç. Dr. Ahmet KARAKAŞLI

Enstitü Sekreter V.                        Meral Yakut Öztürk

 

Enstitümüz kadrosunda bulunan Öğretim Üyesi Görev Yeri
Doç.Dr.H.Güneş ÖZHAN  Biyotıp ve Sağlık Teknolojileri A.D.
Dr. Öğr.Üyesi Hani ALOTAİBİ  Biyotıp ve Sağlık Teknolojileri A.D.
Dr. Öğr.Üyesi Gökhan KARAKÜLAH  Genom Bilimleri ve Moleküler Biyoteknoloji A.D.
Dr. Öğr.Üyesi Zeynep KOÇER  Biyotıp ve Sağlık Teknolojileri A.D.
Dr. Öğr.Üyesi Şerif ŞENTÜRK  Genom Bilimleri ve Moleküler Biyoteknoloji A.D.
Dr. Öğr.Üyesi Serhat TOZBURUN Genom Bilimleri ve Moleküler Biyoteknoloji A.D.
Dr. Öğr.Üyesi Ezgi KARACA Biyotıp ve Sağlık Teknolojileri A.D.

 

Yabancı Uyruklu Öğretim Üyesi Görev Yeri
Doç.Dr.Ralph MEUVISSEN İzmir Uluslararası Biyotıp ve Genom Enstitüsü
Dr. Öğr.Üyesi Gerhard WINGENDER Biyotıp ve Sağlık Teknolojileri A.D.
Dr. Öğr.Üyesi Athanasia PAVLOPULOU Genom Bilimleri ve Moleküler Biyoteknoloji A.D.
 Yabancı Uyruklu Misafir Öğretim Üyesi Görev Yeri
Prof.Dr.Brian I.CARR İzmir Uluslararası Biyotıp ve Genom Enstitüsü

 

Öğretim Görevlileri Görev Yeri
Öğr. Gör. Dr. Hasan Buğra ÇOBAN Genom Bilimleri ve Moleküler Biyoteknoloji A.D.

 

Uzmanlar Görev Yeri
Öğr. Görevlisi Evin İŞCAN  Biyotıp ve Sağlık Teknolojileri A.D.
Öğr. Görevlisi Güldane Bilge KILIÇ  Genom Bilimleri ve Moleküler Biyoteknoloji A.D.

 

Yabancı Uyruklu Uzmanlar Görev Yeri
Öğr. Görevlisi Hongling YUAN  İzmir Uluslararası Biyotıp ve Genom Enstitüsü
Öğr. Görevlisi Vanesa Segovia BUCHELI Genom Bilimleri ve Moleküler Biyoteknoloji A.D.
Öğr. Görevlisi Xiaozhou HU Biyotıp ve Sağlık Teknolojileri A.D.

 

 

 

 

 


İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ AKADEMİK VE İDARİ PERSONEL SAYILARI 

  • 7 Öğretim Üyesi
  • 3  Sözleşmeli Yabancı Uyruklu Öğretim Üyesi
  • 1 Yabancı Uyruklu Misafir Öğretim Üyesi
  • 3 Yabancı Uyruklu Uzman
  • Öğretim Görevlisi
  • 13 İdari Personel

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ ÖĞRENCİ SAYILARI ( SON 3 YIL)

 

AKADEMİK YIL Yüksek Lisans Doktora Toplam
2016-2017 24 16 40
2017-2018 21 37 58
2018-2019 9 1 10

 


athanasia.pavlopoulou@deu.edu.tr

 

OVERVIEW

In the post-genomics era, there is undoubtedly a plethora of accumulated genomic, genetic and proteomic data. However, there is a growing gap between the biological molecules (DNA, RNA and proteins) with experimentally determined function/structure and the ones that have not been assigned to any functional/structural annotation. To handle this overwhelming amount of information, we apply bioinformatics and systems biology methods for processing, analyzing, and interpreting biological data in a meaningful way.

RESEARCH INTERESTS

My main research interests include:

  • Application of bioinformatics methods for the analysis and meta-analysis of cancer genetics and genomics data.
  • Phylogenetics & Comparative genomics.
  • Analysis of biological sequences
  • Biological networks.
  • Development of bioinformatics pipelines for the analysis of biological data.

Athanasia Research Figure

Lab Members

Pavlopoulou lab is currently seeking highly motivated graduate students interested in biostatistics. If interested, please contact athanasia.pavlopoulou@deu.edu.tr

PUBLICATIONS (selected)
Full list and citations can be found at Pubmed and Google Scholar: “Athanasia Pavlopoulou”
• Nikitaki Z, Holá M, Donà M, Pavlopoulou A, Michalopoulos I, Angelis KJ, Georgakilas AG, Macovei A, Balestrazzi A (2018) Integrating plant and animal biology for the search of novel DNA damage biomarkers. Mutation Research/Reviews in Mutation Research, 775: 21-38
• Pavlopoulou A* (2018) RecA: a universal drug target in pathogenic bacteria. Frontiers in Bioscience, 23: 36-42
• Geronikolou SA, Pavlopoulou A, Kanaka-Gantenbein C, Chrousos G (2018) Inter-species functional interactome of nuclear steroid receptors (R1). Frontiers in Bioscience, 10: 208-228
• Geronikolou SA, Pavlopoulou A, Cokkinos D, Chrousos G (2017) Interactome of Obesity: Obesidome. Advances in Experimental Medicine and Biology, 987: 233-241
• Pavlopoulou A*, Bagos PG, Koutsandrea V, Georgakilas AG (2017) Molecular determinants of radiosensitivity in normal and tumor tissue: A bioinformatic approach. Cancer Letters, 403: 37-47
• Nikitaki Z, Pavlopoulou A, Holá M, Donà M, Michalopoulos I, Balestrazzi A, Angelis KJ, Georgakilas AG (2017) Bridging Plant and Human Radiation Response and DNA Repair through an In Silico Approach. Cancers, 9: 6
• Dimitriou NM, Tsekenis G, Balanikas EC, Pavlopoulou A, Mitsiogianni M, Mantso T, Pashos G, Boudouvis AG, Lykakis IN, Tsigaridas G, Panayiotidis MI, Yannopapas V, Georgakilas AG (2017) Gold nanoparticles, radiations and the immune system: Current insights into the physical mechanisms and the biological interactions of this new alliance towards cancer therapy. Pharmacology & Therapeutics, 178: 1-17
• Galtsidis S, Logotheti S, Pavlopoulou A, Zampetidis CP, Papachristopoulou G, Scorilas A, Vojtesek B, Gorgoulis V, Zoumpourlis V (2017) Unravelling a p73-regulated network: The role of a novel p73-dependent target, MIR3158, in cancer cell migration and invasiveness. Cancer Letters, 388: 96-106
• Kontou PI#, Pavlopoulou A#, Dimou NL, Pavlopoulos GA, Bagos PG (2016) Data and programs in support of network analysis of genes and their association with diseases. Data in Brief, 8: 1036-1039
• Kontou PI#, Pavlopoulou A#, Dimou NL, Pavlopoulos GA, Bagos PG (2016) Network analysis of genes and their association with diseases. Gene, 590: 68-78
• Pavlopoulou A*, Oktay Y, Vougas K, Louka M, Vorgias CE, Georgakilas AG (2016) Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. Cancer Letters, 380: 485-493
• Pavlopoulou A, Savva GD, Louka M, Bagos PG, Vorgias CE, Michalopoulos I, Georgakilas AG (2016) Unraveling the mechanisms of extreme radioresistance in prokaryotes: Lessons from nature. Mutation Research/Reviews in Mutation Research, 767: 92-107
• Skourti E, Logotheti S, Kontos CK, Pavlopoulou A, Dimoragka PT, Trougakos IP, Gorgoulis V, Scorilas A, Michalopoulos I, Zoumpourlis V. (2016) Progression of mouse skin carcinogenesis is associated with the orchestrated deregulation of mir-200 family members, mir-205 and their common targets. Molecular Carcinogenesis, 55: 1229-1242
• Pavlopoulou A, Scorilas A (2014) A comprehensive phylogenetic and structural analysis of the carcinoembryonic antigen (CEA) gene family. Genome Biology and Evolution 6: 1314–1326
• Vlachakis D, Pavlopoulou A, Roubelakis MG, Feidakis C, Anagnou NP, Kossida S (2014) 3D molecular modeling and evolutionary study of the Trypanosoma brucei DNA Topoisomerase IB, as a new emerging pharmacological target. Genomics, 103: 107-113
• Georgakilas AG#, Pavlopoulou A#, Louka M, Nikitaki Z, Vorgias CE, Bagos PG, Michalopoulos I (2015) Emerging molecular networks common in ionizing radiation, immune and inflammatory responses by employing bioinformatics approaches. Cancer Letters, 368: 164-172
• Pavlopoulou A, Spandidos DA, Michalopoulos I (2015) Human cancer databases (review). Oncology Reports, 33: 3-18
• Pavlopoulou A, Vlachakis D, Balatsos NA, Kossida S (2013) A comprehensive phylogenetic analysis of deadenylases. Evolutionary Bioinformatics Online, 9: 491-497
• Logotheti S, Pavlopoulou A, Galtsidis S, Vojtesek B, Zoumpourlis V (2013) Functions, divergence and clinical value of TAp73 isoforms in cancer. Cancer and Metastasis Reviews, 32: 511-534
• Vlachakis D, Pavlopoulou A, Kazazi D, Kossida S (2013) Unraveling microalgal molecular interactions using evolutionary and structural bioinformatics. Gene, 528: 109-119
• Vlachakis D, Tsiliki G, Pavlopoulou A, Roubelakis MG, Tsaniras SC, Kossida S (2013) Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology. Evolutionary Bioinformatics Online, 9: 203-213
• Vlachakis D, Pavlopoulou A, Tsiliki G, Komiotis D, Stathopoulos C, Balatsos NA, Kossida S (2012) An integrated in silico approach to design specific inhibitors targeting human poly(a)-specific ribonuclease. PLoS One, 7: e51113
• Attwood TK, Coletta A, Muirhead G, Pavlopoulou A, Philippou PB, Popov I, Romá-Mateo C, Theodosiou A, Mitchell AL (2012) The PRINTS database: a fine-grained protein sequence annotation and analysis resource–its status in 2012. Database (Oxford), 2012: bas019
• Pavlopoulou A, Michalopoulos I. (2011) State-of-the-art bioinformatics protein structure prediction tools (Review). International Journal of Molecular Medicine, 28: 295-310
• Pavlopoulou A, Kossida S (2010) Cytosine methyltransferases as tumor markers. Current Genomics 11: 568-577
• Pavlopoulou A, Pampalakis G, Michalopoulos I, Sotiropoulou G (2010) Evolutionary history of tissue kallikreins. PLoS One, 5: e13781
• Pavlopoulou A, Kossida S (2009) Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases. Genomics, 93: 350-357
• Pavlopoulou A, Kossida S (2007) Plant cytosine-5 DNA methyltransferases: structure, function, and molecular evolution. Genomics, 90 :530-541*Corresponding author
#Equal contribution

Collaborations
www.compgen.org/home
dielectricsgroup.physics.ntua.gr/georgakilas


Brian Carr brianicarr@hotmail.com

 

OVERVIEW

Hepatocellular carcinoma (HCC) appears to consist of several poorly-defined phenotypes, with several distinct poor prognostic factors, such as high alpha-fetoprotein (AFP) and presence of portal vein thrombosis (PVT). Recently, systemic inflammation has been identified as a major independent poor prognosis factor, based on the Glasgow score that utilizes serum C-reactive protein (CRP) and albumin levels. This implicated the tumor microenvironment (inflammation) in prognosis and thus as an influence on the biology of the tumor itself.

RESEARCH INTERESTS

Our over-all aims are to: A, identify distinct clinical HCC profiles/phenotypes; to B, study the effects of inflammatory mediator influence on HCC growth and invasion in vitro; and C, to continue our previous studies on multikinase drug resistance in HCC cells and to learn how to enhance the effects of these agents on HCC growth inhibition.

RESEARCH HIGHLIGHTS

We have collaborated with a group of 15 Turkish institutions that treat HCC, to assemble a 1700 HCC patient database for phenotype analysis. We have published one paper (in Oncology) with 3 more in press, to show that Turkish HCC, which is predominantly HBV based- and thus similar to Chinese but not Western HCC in this respect- is broadly similar to western HCC, with regard to presence of PVT, importance of AFP and our identification of the characteristics of that 50% of patients that do not have elevated AFP levels. Interestingly, HCC in different regions of Turkey may have marked variations, such as the high incidence of HDV infection in HCC patients in the Diyabakir region.

We have worked on the significance of albumin and C-reactive protein (CRP) on HCC biology. We reasoned that to have such important clinical prognostic significance (high CRP and low albumin predict poor outcomes). These 2 proteins must have effects. Directly or indirectly on HCC biology. In 2017 we published 2 papers to show that low albumin levels were associated with more aggressive tumor parameters of larger tumors and more portal vein invasion, that could explain the poor prognosis 8by contrast, higher serum albumin levels were associated with smaller tumors). We followed this up, by showing that pure albumin in tissue culture could slow HCC cell line growth a limit invasiveness. This sets the scene for future experiments to test these ideas in animals. We have recently shown that high CRP levels are associated with larger and more aggressive tumors in Turkish HCC patients (in press) and we are beginning to study the actions of pure CRP on and in (CRP is synthesized by cells of liver origin) HCC cells in culture.

In collaboration with the labs of Profs Nese Atabey and Esra Erdal, we are working in the development of Regorafenib-resistant and double Regorafenib/Sorafenib resistant HCC cell lines, to examine both the peculiarities of their cell signaling compared to the parental cells and also to identify possible mechanisms of limiting their resistance to drug growth-inhibitory actions. Furthermore, since both Sorafenib and Regorafenib are FDA-approved for treating HCC patients, they are quite toxic (multiple side-effects) and thus we are examining ways to enhance the effects on HCC cells of both drugs when used at low concentrations.

PUBLICATIONS (from Pubmed)
Full list and citations: Google Scholar: Brian Carr
Carr BI, Guerra V, Steel JL, Lin SN. A comparison of patients with hepatitis B- or hepatitis C-based advanced stage hepatocellular carcinoma. Seminars in Oncology 2015; 42: 309-315.
• Pancoska P, Skala L, Nesetril J, Carr BI. Evaluation of total HCC lifespan, including both clinically evident and pre-clinical development, using combined Network Phenotyping Strategy and Fisher information analysis. Seminars in Oncology 2015; 42: 339-346
Carr BI Viruses and Cancer: Guest Editorial Seminars in Oncology 2015; 42: 189-90
• D’Alessandro R, Refolo MG, Lippolis C, Giannuzzi G, Carella N, Messa C, Cavallini A, Carr BI. Modulation of Regorafenib effects on HCC cell lines by epidermal growth factor. Cancer Chemotherapy and Pharmacology 2015; APRIL 24 EPUB
• Facciorusso A, Licinio R, Carr BI, Di Leo A, Barone M. MEK 1/2 inhibitors in the treatment of hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol. 2015 Apr 27:1-11
• D’Alessandro R, Messa C, Refolo MG, Carr BI. Modulation of sensitivity and resistance to multikinase inhibitors by microenvironmental platelet factors in HCC. Expert Opinion on Pharmacotherapy. 2015; 16: 2773-2780
• Lippolis C, Refolo MG, D’Alessandro R, Carella N, Messa C, Cavallini A, Carr BI. Resistance to multikinase inhibitor actions mediated by insulin like growth factor-1. J Exp Clin Cancer Res. 2015; 34 (1):90. PMID: 26329608
• Pančoška P, Skála L, Nešetřil J, Carr BI. Validation of the Concept of a Common Typical Time of Disease Duration for Hepatocellular Carcinoma Patients Using the Fisher Information Processing of Tumor Imaging Results Combined With Network Phenotyping Strategy Quantification of Individual Patient Clinical Profile Patterns. Semin Oncol. 2015;42:672-8. PMID: 26320070
Carr BI and Guerra V. Low alpha-fetoprotein levels are associated with improved survival in hepatocellular carcinoma patients with portal vein thrombosis. Dig. Dis. Sciences 2016; 61:937-947
Carr BI and Guerra V. HCC extrahepatic metastasis in relation to tumor size and ALKP levels. Oncology 2016; 90:136-142
Carr BI and Guerra V. A Hepatocellular Carcinoma Aggressiveness Index and its relationship to liver enzyme levels. Oncology 2016; 90:215-220
• Modulation of doxorubicin actions in hepatocellular carcinoma cells by Insulin-like Growth Factor-I. Biochemistry & Analytical Biochemistry 2016;5: 256. doi:10.4172/2161- 1009.1000256
• Yilmaz Y, Erdal Y, Atabey N, Carr BI. Platelets, microenvironment and hepatocellular carcinoma: a review. Biochemistry and Analytical Biochemistry 2016;5;2. doi:10.4172/2161-1009.1000281
• Mazzocca A, Ferraro G, Misciagna G, Carr BI. A systemic evolutionary approach to cancer: hepatocarcinogenesis as paradigm. Medical Hypotheses 2016; 93: 132-137
Carr BI, Guerra V, Giannini EO et al. An HCC Aggressiveness Index and blood GTP, bilirubin and platelet levels. J. Integrative Oncology 2016; 5:172. doi:10.4172/2329-6771.1000172
• Pinato DJ et al. The ALBI grade provides objective hepatic reserve phenotyping across each BCLC stage of hepatocellular carcinoma. J. Hepatology 2017; 66: 338-346
• Rozen R, Menachem Y, Carr BI, Shibolet O. Liver Transplantation for a Patient with Hepatocellular Carcinoma with Vascular Invasion and Exceeding Milan Criteria-Happy End Despite it all. J Gastrointest Cancer. 2016 Nov 11. [Epub ahead of print] • Carr BI, Guerra V, Giannini EG et al A Liver Index and its relationship to indices of HCC Aggressiveness. J. Integrative Oncology 2016; 5:3 DOI: 10.4172/2329-6771.1000178
• Marino IR, Carr BI. New Developments in Orthotopic Liver Transplant for Hepatocellular Carcinoma. Exp Clin Transplant. 2017 Mar;15 (Suppl 2):1-6
• Bağırsakçı E, Sahin E, Atabey N , Erdal E, Carr BI. Role of Albumin in growth inhibition in Hepatocellular Carcinoma. Oncology May 2017; 93: 136-142
Carr BI, Guerra V. Validation of a Liver Index and its Significance for HCC Aggressiveness. J. Gastrointestinal Cancer 2017; June 20; doi: 10.1007/s12029-017-9971-4. EPub
Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J. Biol Markers 2017; 32: e391-e396
• Akkiz H, Carr BI, Yalcun K, Guerra V et at. Characteristics of hepatocellular carcinoma aggressiveness factors in Turkish patients. Oncology 2017|; Dec 6. doi: 10.1159/000484564. [Epub ahead of print]. PMID: 29207378
Carr BI, Akkiz, H, Uskudar O, Yalcin K et al. HCC with low- and normal- alphafetoprotein levels. Clinical Practice 2018 (in press)
• D’Alessandro R, Refolo MG, Lippolis C, Carella N, Messa C, Cavallini A, Carr BI. Strong enhancement by an IGF1-R antagonist of migration inhibition due to Sorafenib, vitamin K1 or both in hepatocellular carcinoma cell lines. Cellular Oncology 2018 (in press)


Lace Front Wigs   ,
hair extensions   ,
E20-260   ,
200-310   ,
1z0-061   ,
300-115   ,
640-916  
200-105   ,
300-315   ,
210-060  
700-501  
200-125  
E20-260  
400-101   ,
300-101  
200-125  
300-075   ,
200-125   ,
200-310  
full lace wigs   ,
full lace wigs   ,
200-125   ,
human hair wigs   ,
human hair extensions   ,
U Part Wigs   ,
Lace Front Wigs   ,
Deep Part Lace Wigs   ,
360 lace frontal   ,
Glueless Full Lace Wigs   ,
full lace wigs   ,
Thick Style Wigs   ,
Lace Closure   ,
Celebrity Lace Wigs   ,
Lace Frontal   ,
Long Style Wigs   ,
Silk Closure   ,
200-125   ,
200-310   ,
70-532  
70-533   ,
300-075   ,
210-260   ,
1Z0-067   ,
300-115  
100-105  
E22-186  
210-065  
000-611  
C2090-919  
300-365   ,
210-060   ,
MB2-712   ,
70-980   ,
oracle-catalog  
C2010-517  
C2020-702  
1Z0-100  
E20-065  
E20-515  
HPE0-J74  
HP2-K35  
HP0-M101  
300-075  
300-115  
100-105  
300-101  
210-065  
70-532  
E10-110  
E20-381  
200-125  
210-260   ,
400-101  
70-533  
640-916  
70-347   ,
300-209  
70-534  
352-001  
820-424  
74-678  
000-611  
1Z0-061  
1Z0-062  
1Z0-051  

Growth Factor Signaling in Cancer

 

Research Atabey Lab nese.atabey@deu.edu.tr
Members




Ezgi Bağırsakçı, MSc Student
Mesude Angın, MSc Student
Dehan Çömez, MSc Student
Gülsün Bağcı, MSc Student

 

OVERVIEW

Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer and the third leading cause of cancer-related deaths worldwide. Hepatocyte growth factor (HGF)/c-Met signaling is particularly important in the development of HCC as it controls growth, survival, migration and differentiation of tumor cells. Others and we have shown that abnormalities in HGF/c-Met signaling are implicated in tumor development and progression in a variety of cancers. The increase in c-Met expressing stem/progenitor cells in the liver is required for hepatocarcinogenesis, and high c-Met expression is correlated with metastasis, poor prognosis, and drug resistance. An elevated HGF level is uncommon in tumorigenesis except for breast tumors. Therefore, ligand-independent c-Met activation in HCC is a critical phenomenon that should be investigated further.

RESEARCH INTERESTS

Our group is focused on signaling pathways that modulate the growth, motility, and invasion of hepatocellular carcinoma and using this molecular knowledge to improve the diagnosis and treatment of HCC. Our aim is to understand the molecular mechanisms behind the aggressive behavior and drug resistance in HCC and to translate this molecular knowledge to improve diagnosis and treatment.

Currently, our projects encompass:

1) The molecular mechanisms of HGF/c-Met mediated invasion and metastasis in HCC,
2) The effects of tumor microenvironment on the regulation of signaling networks and cellular behaviors of HCC,
3) The roles of non-coding RNAs in the regulation of c-Met signaling in HCC,
4) Fabrication and validation of a new lab-on-a-chip device for early diagnosis of metastasis.

In the next 5 years, we aim to:

• Identify the role of HGF/c-Met signaling in the regulation of glucose metabolism in HCC and further use this knowledge for developing strategies to prevent HCC.
• Understand the functional role of the HGF/c-Met axis in acquired sorafenib resistance in HCC cells and to improve targeted therapies of HCC patients.
• Fabricate and validate a Lab-on-a-chip (LOC) system that can predict the metastatic and invasive ability to circulate tumor cells (CTCs) in HCC and that can also determine the effects of drugs on tumor metastasis.
Neşe Atabey

Lab members:

Atabey lab is currently seeking highly motivated PhD students. If interested, please contact nese.atabey@deu.edu.tr

 

PUBLICATIONS (selected)
Full list and citations : Google Scholar : Nese Atabey
• İşcan E, Güneş A, Korhan P, Yılmaz Y, Erdal E, Atabey N. The regulatory of heparin on c-Met signaling in hepatocellular carcinoma cells. J Cell Commun Signal. 2016 Dec 14. [Epub ahead of print] • Saygideger-Kont Y, Minas TZ, Jones H, Hour S, Celik H, Temel I, et al. Ezrin Enhances EGFR Signaling and Modulates Erlotinib Sensitivity in Non-Small Cell Lung Cancer Cells. Neoplasia. 2016;18(2):111-20. doi: 10.1016/j.neo.2016.01.002. PubMed PMID: 26936397; PubMed Central PMCID: PMCPMC5005263.
• Firtina Karagonlar Z, Koc D, Sahin E, Avci ST, Yilmaz M, Atabey N, et al. Effect of adipocyte-secreted factors on EpCAM+/CD133+ hepatic stem cell population. Biochemical and biophysical research communications. 2016;474(3):482-90. doi: 10.1016/j.bbrc.2016.04.137. PubMed PMID: 27131739.
• Firtina Karagonlar Z, Koc D, Iscan E, Erdal E, Atabey N. Elevated HGF Expression as an Autocrine c-Met Activation Mechanism in Acquired Resistance to Sorafenib in HCC Cells. Cancer Sci. 2016 Jan 20. doi: 10.1111/cas.12891.
• Karagonlar ZF, Korhan P, Atabey N. Targeting c-Met in Cancer by MicroRNAs: Potential Therapeutic Applications in Hepatocellular Carcinoma. Drug Dev Res. 2015 Nov;76(7):357-67. doi: 10.1002/ddr.21274.
• Gunes A, Iscan E, Topel H, Avci ST, Gumustekin M, Erdal E, Atabey N. Heparin treatment increases thioredoxin interacting protein expression in hepatocellular carcinoma cells. Int J Biochem Cell Biol. 2015; 65:169-8.
• Korhan P, Erdal E, Kandemiş E, Cokaklı M, Nart D, Yılmaz F, Can A, Atabey N. Reciprocal activating crosstalk between c-Met and caveolin 1 promotes invasive phenotype in hepatocellular carcinoma. PLoS One. 2014; 9(8): e105278.
• Korhan P, Erdal E, Atabey N. miR-181a-5p is downregulated in hepatocellular carcinoma and suppresses motility, invasion and branching-morphogenesis by directly targeting c-Met. Biochem Biophys Res Commun. 2014; 450 (4):1304-12.
• Bozkaya G, Korhan P, Cokakli M, Erdal E, Sagol O, Karademir S, Korch C, Atabey N. Cooperative interaction of MUC1 with the HGF/c-Met pathway during hepatocarcinogenesis. Mol Cancer. 2012;11: 64.
• Ozen E, Gozukizil A, Erdal E, Uren A, Bottaro DP, Atabey N. Heparin inhibits Hepatocyte Growth Factor induced motility and invasion of hepatocellular carcinoma cells through early growth response protein 1. PLoS One. 2012;7:e42717.
• Kunter I, Erdal E, Nart D, Yilmaz F, Karademir S, Sagol O, Atabey N. Active form of AKT controls cell proliferation and response to apoptosis in hepatocellular carcinoma. Oncol Rep. 2014;31(2):573-80.
• Gumustekin M, Kargi A, Bulut G, Gozukizil A, Ulukus C, Oztop I, Atabey N. HGF/c-Met overexpressions, but not met mutation, correlates with progression of non-small cell lung cancer. Pathol Oncol Res. 2012 (2):209-18.
PATENTS
• Bottaro, D. P., Giubellino A., Atabey S. N., Soriano J. V., Breckenridge D. E.ve Burke T. R. (2011). Inhibition of cell motility, angiogenesis, and metastasis, Pub No: US7871981 B2.
• Atabey, S. N., Bottaro D. P., Breckenridge D. E., Gao Y., Soriano J. V.ve Yao Z. J. (2001). Inhibition of cell motility and angiogenesis by inhibitors of the Grb2 SH2-domain, Pub No: WO2001028577 A3.

 

ibg ResearchStaff Woman

Ayşim GÜNEŞ, PhD

a.gkizil@hotmail.com

Erkan Kahraman

Erkan KAHRAMAN, PhD

erkankahraman@gmail.com

ibg ResearchStaff Woman

Hande Topel

Yeliz Yılmaz

Yeliz YILMAZ

yelizyg@gmail.com


Etkinlik başvurularınız için aşağıdaki formu doldurduktan sonra lütfen etkinlik sorumlumuza e-posta ile iletiniz.

iBG Etkinlik Talep Formu


Cell Culture Room

  • Class II Biosafety Air Cabinet Thermo Scientific Holten Safe 2010 (3 Pcs)
  • Refrigerator +4 Ugur – USS 748 Lt. Vertical Vertical (1 Unit)
  • CO2 Incubator Thermo Scientific Hepa Class 100 (1 pc)
  • Water Bath General Purpose Core- NB9 (1 Unit)
  • Phase Contrast Inverted Microscope Olympus – CKX41 (1 Piece)
  • Table Top Centrifuge Hettich Universal 320 (1 pc)
  • Vortex Device Genie2 (1 Piece)
  • Fume Hood (1 pcs)
  • Vacuum Pump KNF lab (3 Pcs)
  • Autoclave table systec DE-45 (1 pcs)

B008 Sterilization chamber

  • Ice Maker Brema – IF90 (1 Piece)
  • Semi Analytic Balance Sartorius (1 Piece)
  • Analytical Balance Sartorius (1 unit)
  • Sterilization Oven (1 unit)
  • Autoclave – Small size (2 pcs)

Use of all devices in laboratory B005

  • Precision Balance Sartorius GE512-OCE 1 piece
  • Cell Concentration Determination Device Beckman Coulter 1 Unit
  • Ultra Pure Water Device Thermo TKA Smart2pure 12UV / UF 1 piece
  • Gel Imaging Device 1 Unit
  • Deep freezer -20 Siemens 1 unit
  • Deep freezer +4 Siemens 1 unit
  • Deep Freezers -20 Bosch – GSN51AW30 3 pieces
  • Refrigerator +4 Ugur USS 748 LT. Vertical Vertical 2 Pieces
  • High Voltage Power Supply Thermo OWL -EC300XL2 1 Unit
  • Low Voltage Power Supply Thermo OWL -EC3000XL2 1 Unit
  • Electronic Bunzen Integra 1440 1 Unit
  • Laboratory Type Microwave Oven Bosch HMT 72G420 1 Unit
  • Vacuum Pump KNF N840 FT 18 34 LT / DK 10 1 Unit
  • Mechanical Mixer Boeco-Multishaker PSU20 1 Unit
  • Mechanical Mixer Wisestir-MSH-20A 1 piece
  • PCR Rotary Table Top Microfluid Beckman Coulter – 22R Centrifuge 1 Piece
  • General Purpose Desktop Microfuge Beckman Coulter Allegra X-15 R Centrifuge 1 Unit
  • Quick Precision Mini Centrifuge IKA Mini G 1 Pcs
  • Deep Freezers -86 Thermo Forma 1 Unit
  • Western blot, mini vertical electrophoresis, 1 set
  • Nanodrop / spectrophotometer 1 unit
  • Heater block 1 piece
  • Pullers 1 Unit
  • Gradient PCR device 1 unit
  • Vortex (Genie 2) device 4 pieces
  • WMSC10 with magnetic stirrer / heater 1 unit
  • PCR- SimpliAmp / Thermal cycler Applied Biosystems 1 Unit
  • Stuart orbital Incubator SI500 1 Unit

 

ANA SAYFA YÖNERGE ÇALIŞMA İZNİ ÖN TALEP FORMU BAŞVURU FORMU ÜYELER İLETİŞİM

 

Prof.Dr. Ensari GÜNELİ Başkan
Prof.Dr. H. Alper BAĞRIYANIK Başkan Yardımcısı
Prof. Dr. Belgin ÜNAL Üye
Doç.Dr. Ralph Meuwissen Üye
Doç.Dr. H. Güneş ÖZHAN Üye
Yrd.Doç.Dr. Ayşe Banu DEMİR Üye
Uzm. Umur KELEŞ Üye
Hakkı Muammer KARAGÖZ Üye
Uzm. Kerem ESMEN Üye
Bilg. İşlt. Tuba AKÜNAL Sekreter

 

HOME DIRECTIVES PRE-REQUEST FORM APPLICATION FORM MEMBERS CONTACT

 

Prof. Ensari GÜNELİ Chair
Prof. H. Alper BAĞRIYANIK Vice-Chair
Prof. Belgin ÜNAL Member
Assoc.Prof. Ralph Meuwissen Member
Assoc.Prof. H. Güneş ÖZHAN Member
Assist.Prof. Ayşe Banu DEMİR Member
Spec. Umur KELEŞ Member
Hakkı Muammer KARAGÖZ Member
Spec. Kerem ESMEN Member
Comp.Op. Tuba AKÜNAL Secretary

810-403|
200-125 ccna book|
CISSP|
200-310 desgn pdf|
300-101|
300-115|
400-101 ccie|
300-320|
70-534 study guide|
117-303|
300-070 ciptv1|
300-320|
AWS SYSOPS|
300-075|
ADM-201|
EX200|
210-060|
70-534 pdf|
220-901 dumps|
cissp dumps|
300-101 vce|
300-115 vce|
400-101 vce|
300-320|
300-070 ciptv1 dumps|
200-125 dumps|
AWS SYSOPS|
300-075|
EX200|
SY0-401|
300-208|
CABA|
CSM-001|
70-347|
70-346|
CSSLP|
CWNA-106|
117-303|
70-483|
adm-201 certification |
200-125 ccna cost|
300-075|
210-260|
300-115 pdf|
300-101 route pdf|
210-065|
400-101 pdf|
210-060|
70-534 practice test|
200-125 vce|
300-075|
210-260|
300-115|
300-101 dumps|
210-065|
400-101 questions|
210-060|
aws sysops certification|
200-125 ccna exam cost|
300-075|
210-260|
300-115 vce|
300-101|
210-065|
400-101 dumps|
210-060|
810-403 study guide|
210-260 dumps|
300-320 dumps|
1k0-001 polycom|
1z0-808 dumps|
98-365 study guide|
300-206 senss book|
ex200 exam dump|
200-125 ccna pdf|
200-120 vce|
cism vs cissp|
70-346 practice test|
200-310 desgn|
ex200 dumps|
ex300 dumps|
cissp salary|
cissp-issap training|
100-105 icnd1|
sy0-401 dump


HOME DIRECTIVES PRE-REQUEST FORM APPLICATION FORM MEMBERS CONTACT

Click here to see İBG_AELEC 2017 Meeting Calendar.

[vfb id=21]

 

HOME DIRECTIVES PRE-REQUEST FORM APPLICATION FORM MEMBERS CONTACT

 

DEU logo DOKUZ EYLUL UNIVERSITY
IZMIR INTERNATIONAL BIOMEDICINE AND GENOME INSTITUTE
DIRECTIVES OF THE LOCAL ETHIC COMITTEE FOR ANIMAL EXPERIMENTS (IBG-AELEC)
iBG Logo
 

OBJEVTIVES
Article 1.

The aim of this protocol is to determine the acceptable minimal ethical standards, to deliver opinion, demarcate the borders for applications, to assess the applications from this point of view for keeping, raising, making observations on them, producing, using for experiments, isolating from nature and transporting of all animals that are used for experiments, experimental research, training, testing and health service applications at DEU, iBG or other institutions. By forming a Laboratory Animals Local Ethics Committee (HAYDEK) it aims to give judgment about ethics principles; and to inspect, approve and (where necessary) to terminate research proposals, including the essential procedures, and the presentation of planned studies.

EXTENT
Article 2.

(1) The protocol contains, all required permissions to be taken before the application to DEU, iBG and other institutions where animals are used for experimental purposes, establishment of Dokuz Eylul University Local Animal Ethics Committee for this reason, The procedures and principles of the work, the tasks of the establishment and the training, supervision and obligations.

(2) (1) This protocol does not contain:

  1. Non-experimental agricultural applications,
  2. Non-experimental clinical veterinary applications,
  3. Clinical experiments that are done for marketing competency to commercial veterinary health products,
  4. Applications that are done by registered or certified livestock enterprises,
  5. Applications whose primary purpose is identification of an animal.

BASIS
Article  3.

This protocol is established with regards to the;

DESCRIPTIONS
Article 4.

As it is in this directive;

  1. Ministry: TR Ministry of Forest and Water Affairs,
  2. CITES Agreement: Convention on International Trade in Endangered Species of Wild Fauna and Flora as published in the Official Gazette no. 22672 on 20/6/1996,
  3. Work Permit: DThe permit given by the Ministry of Food, Agriculture and Livestock to institutions that use, produce and supply laboratory animals,
  4. Experiment: Any type of procedure that is applied to laboratory animals for scientific reasons,
  5. Laboratory Animal: Free-living or producing larvae forms, live cephalopods and any type of vertebrates except for human being including mammals after the last one thirds of their embryonic development stage,
  6. Experiment Unit: Units where all types of procedures regarding animal experimentation is done, with the authorization from the Ministry of Food, Agriculture and Livestock,
  7. Ethics: The universal system of moral principles that regulate the borders of applications that can be done at the units where animals are used in scientific experiments that affect human and animal lives,
  8. General Manager: Head of Directorate General for Nature Conservation and National Parks,
  9. General Directorate: General Directorate for Nature Conservation and National Parks,
  10. CECAE: Central Ethical Committee for Animal Experiments,
  11. IBG-AELEC: Izmir International Biomedicine and Genome Institute Local Ethical Committee for Animal Experiments,
  12. Animal Welfare Unit: A unit that must be founded within institutions that are authorized to handle, produce, supply, and research on animals, composed of at least one responsible veterinary doctor, a veterinary health technician or a veterinary health technical. At the user institutions the unit must be formed of maximum three people one of which is a personnel from above group and one of them should be local ethical committee member,
  13. Humane Euthanasia Method: To terminate the life of an animal without causing too much stress, physical or sensorial pain peculiar to its species,
  14. In-vivo Experiment: Experiment that is done on living things,
  15. Good Laboratory Practice: The quality management system of both the planning, executing, recording, reporting and storing health and environment safety works in addition to the clinical research and the management methods,
  16. User: A person who is authorized to utilize animals in the procedures,
  17. Institution: Any type of portable or fixed building and their additions that have the work permission by the Ministry of Food, Agriculture and Livestock,
  18. Project: A work program that has a specific scientific purpose and contains one or more procedures,
  19. Procedure: Using animals for known or undefined experimental and educational reasons, giving pain to the animal as much as or more than an injection, torture, suffering or permanent damage pertaining to good veterinary applications and processes including procedures such as delivering a baby animal, breeding and sustaining of genetically modified animals,
  20. Secretary: The person or persons who makes the necessary coordination, correspondence and keeps records in the Ethical Committee,
  21. Senior Technician: A person who graduated from associate veterinary study programs after high school education,
  22. Technician: A person who graduated from one of following: Agricultural Technical School of the Ministry of Education Veterinary Department; Veterinary Health Technical School, Animal Health Officer School or Animal Health Officer Technical School which once were founded under Ministry of Food, Agriculture and Livestock,
  23. Animal Health Official: A person graduated from any vocational School,
  24. DEU: Dokuz Eylul University,
  25. Species: The biological group of organisms that have common characteristics and in which two individuals can produce fertile offspring,
  26. 3R Principle: The Principle that was formed by W.M.S. Russell and R.L. Burch in 1959:
    • Replacement (Replacement); methods which avoid or replace the use of animals in research,
    • Reduction (Reduction); use of methods that enable researchers to obtain comparable levels of information from fewer animals, or to obtain more information from the same number of animals,
    • Refinement (Refinement); use of methods that alleviate or minimize potential pain, suffering or distress, and enhance animal welfare for the animals used.
  27. Authorized Person: the person that is responsible for the laboratory animal unit within Dokuz Eylul University where the animal breeding, housing and procedures are performed.

FORMATION OF THE LOCAL ETHICS COMMITTEE FOR ANIMAL EXPERIMENTS (IBG-AELEC), QUALIFICATIONS AND ASSİGNMENT OF THE MEMBERS

Article 5.

(1) FORMATION OF THE LOCAL ETHICS COMMITTEE FOR ANIMAL EXPERIMENTS (IBG-AELEC), QUALIFICATIONS AND ASSİGNMENT OF THE MEMBERS

The IBG-AELEC is composed of:

  1. A full time veterinarian with Certificate in Laboratory Animal Science, who is responsible of breeding, producing and the daily care of laboratory animals with at least one year of experience on animal experiments,
  2. One representative from each unit in which laboratory animals are currently being utilized,
  3. A civil member, a Turkish Citizen, with no mutual interest with the institute and who has no connection to any experiments on laboratory animals, neither do his/her close relatives,
  4. A Turkish citizen member who is member of a non-governmental organization,
  5. At least one member of the committee has to have at least one year of experience in in vivo animal experiments, and holding a Ph.D. or specialty in medicine. Ethical experts in medicine or veterinary medicine are preferred in IBG-AELEC. The composition of IBG-AELEC can be decided by the institution due to their needs and administrative structure. IBG-AELEC may consult and invite experts from different fields whenever needed.

(2) ASSIGNMENT TO IBG-AELEC and TERM OF OFFICE

  1. The Ethical Committee is composed of mininum 5 maximum 18 members. The rector of DEU assigns the chair, vice-chair and the members of the ethical committee for 4 years. The member whose term of office expires may be appointed by the rector again.
  2. Membership of a member is terminated when he/she skips the meetings three times in a row without any excuse. The chair of the committee and the veterinary must be working full time.
  3. The secretary of ethical committee is assigned by the rector of DEU and he/she is responsible of accepting applications, regulating AELEC’s work and of archiving the resolutions.

IBG-AELEC WORKING METHOD
Article 6.

  1. IBG-AELEC meets twice a month with participation of at least two-thirds of the members with the agenda specified by the chair.
  2. The decisions in IBG-AELEC meetings are made according to the majority of votes. In case of equality of votes, it is decided due to the casting vote.
  3. All records regarding laboratory animals within IBG-AELEC are kept by the authorized veterinarian in the animal welfare unit who is responsible for laboratory animal breeding and care and IBG-AELEC controls this processes.. These records should contain the information regarding the number and species of the animals, where they were obtained, when they were transferred to the institution they are used by and all procedures performed on animals. These records are kept at least 5 years.
  4. In order to evaluate the applications, IBG-AELEC prepares an application form that should contain the following information:
    1. The title of the project.
    2. The name, surname, title, institution, division, telephone, e-mail, task in the project and the signature of the project coordinator and of the other researchers involved.
    3. The place and duration of the procedures.
    4. Training certificates of the participants who will perform the animal procedures.
    5. The date of the application.
    6. The project proposal.
    7. The abstract of the project written in a simplified, daily language.
    8. The source of the animals, the approximate animal number, the age and species of the animals.
    9. Description of the procedures that will be performed on the animals.
    10. Description of the pain, agony and permanent injury caused by the procedures.
    11. Description of how the 3R principles (Replacement, Reduction, Refinement,) are applied to the procedures.
    12. The anesthesia, analgesia and other pain relieving methods to be used in the procedures.
    13. Description of measures that will prevent lifelong agony or reduce the pain.
    14. Determination of the humane euthanasia methods at the end of the procedures.
    15. Description of the experimental or observational strategies and data analysis techniques to reduce the number of animals, the agony, pain and suffering caused by the procedures, and the eventual environmental effects.
    16. To state whether animals are going to be used for more than one project.
    17. The housing, breeding and care conditions of the animals.
    18. The competence of the participants in the project.
    19. The commitment letter.
  5. IBG-AELEC gives permission for a project for maximum 5 years. When a time extension is required, extra time may be granted as long as the reason is justified.
  6. All applications and decisions are recorded with date and registry number. Records are kept for at least 5 years.
  7. Applications are done by the project coordinator. For dissertations, the project coordinator is the academic advisor.
  8. IBG-AELEC assesses the applications as:
    • Approved,
    • Demands revision,
    • Conditional approval,
    • Not approved.

    The written decisions are pronounced to the applicants in maximum 40 work days. Evaluation is included in this period. If the project is too complex or multidisciplinary, and requires experts from different fields, IBG-AELEC may extend the time only for once for maximum 15 working days. The applicant is informed about this extension beforehand with the reason and amount of time needed. IBG-AELEC may demand preliminary experiments to be performed with a small number of animals in order to test the feasibility of the project. In this case, the final approval is given according to the principles applied for conditional approvals.

  9. While assessing the project of a member of the IBG-AELEC, the applicant can neither attend nor vote in the meeting.
  10. Projects assessed as “Demands Revision” are re-evaluated after being revised. Projects assessed with “Conditional approval” are observed by the animal welfare unit for a while specified by IBG-AELEC, and after being evaluated and reported back whether it meets the necessary conditions or not, go under evaluation again by IBG-AELEC as either “Approved” or “Not Approved”.The working principles and methods of the animal welfare units are regulated according to the regulation of the “Ministry of Food, Agriculture And Livestock”, 28141.
  11. IBG-AELEC inspects the granted projects for any changes that would adversely affect animal welfare.If the approved project does not comply with, IBG-AELECwill cancel the given ETHIC approval. When an approval is cancelled, the animal welfare unit rearranges the conditions of the animals to ensure that the animals used or intended to be used are not negatively affected.
  12. After the project is approved by IBG-AELEC, any changes in the project or any changes in the participants needs to be reported to IBG-AELEC in written form by the project manager after being approved by all the members of the project.
  13. The following interventions are not subject to the approval of the ethics committee:
    1. Clinical applications for diagnosis and treatment,
    2. Procedures performed on dead animals or their tissues, slaughterhouse materials and waste fetuses,
    3. Milking an animal,
    4. Collection of feces or bedding samples,
    5. Sampling by swab.
  14. The permission from the General Directorate about the use of wild animals from nature to identify a species replaces the permission of IBG-AELEC.
  15. In case the field research is conducted in more than one city, it’s sufficient to get approval from the ethical committee of one of these cities.
  16. All records of IBG-AELEC are kept open to the control of the Center for Animal Experiments (CECAE) and Ministry.
  17. IBG-AELEC may obtain the written opinions of experienced experts if necessary or invite them to the IBG-AELECmeeting for oral or written opinion.

DUTIES of IBG’s HADYEK
Article  7.

  1. To prepare protocols about the work plan and essentials of IBG-AELEC in accordance with the ethical principles and good laboratory practices determined by CECAE and the Directive on Animal Ethics Committee Work plan and Essentials.
  2. To approve or refuse the protocols for the procedures to be performed on the laboratory animals by determining the ethical acceptable limits of all the procedures to be carried out.
  3. To supervise the use of laboratory animals in the institution in accordance with the 3R principles and ethical rules and to make necessary arrangements for this purpose.
  4. To contribute to the development and verification of alternative methods which may provide the same or higher level information as those obtained using the laboratory animal, but which involve procedures in which no or less animals or less painful procedures are used, and to encourage research in this area.
  5. To ensure that the procedures on the animals are carried out in accordance with the approved protocol, and to decide on a termination if necessary.
  6. To ensure that the required training is received by the personnel working with laboratory animals and approve animal experiments only if a Certificate in Laboratory Animal Science is provided. To organize certificate programs for this purpose when necessary.
  7. To check the production, breeding, housing and transportation conditions of the laboratory animals and the laboratory conditions and equipment of the experiments are ethically appropriate.
  8. To submit statistical data sheets and annual activity report to the CECAE regarding the use of the laboratory animals.
  9. To ensure the disposal of wastes and medical wastes resulting from animal experiments within the framework of the Environment Law dated 9/8/1983 and numbered 2872 and relevant legislation.
  10. To ensure that laboratory animals are recorded and monitored within the framework of the provisions of the Law on the Protection of Animals (No. 5199) and related legislation.
  11. To notify CECAE 30 days before the certificate courses are held.
  12. To inform CECAE about the certificate programs they have organized and the information about the trainees who have successfully passed the training.
  13. To decide whether it is proper or not to own or send the animals back to farms after they undergo the procedures.

AUTHORISATION AND OPERATION PRINCIPLES of IBG-AELEC
Article 8.

IBG-AELEC works in line with the following principles;

  1. To prevent ill-treatment of laboratory animals that are required to be used in scientific research and education.
  2. To ensure that the animals are used within the scope of the purposes set out in article 5 of the Directive on Animal Ethics Committee Work plan and Essentials.
  3. To ensure that animals are not used in experiments with severe pain, stress, or equivalent suffering, but if they must be used, it should be based on sound scientific grounds.
  4. To publicise prevention of animals in painfull experiments at educational congresses, conferences and seminars.
  5. To ensure that scientifically reliable data is obtained by inflicting as little pain on animals as possible and by introducing them to the least stress.
  6. To prepare appropriate conditions for the laboratory animals during research and provide them with the best physiological, behavioral and environmental conditions.
  7. To provide the animal care under appropriate conditions by suitably trained personnel.
  8. To ensure that laboratory experiments to be carried out on live animals are conducted under the supervision of a veterinarian in charge.
  9. To ensure that researchers define humane endpoints of the conditions when the experiments need to be terminated.
  10. To disapprove the animal experiments if there are alternative methods of obtaining the information searched that have proven valid, and to prevent the repetition of previous detailed experiments.
  11. To ensure that the most appropriate animal species and method for the scientific experimentation is selected, with minimum number of animals to obtain meaningful experimental results.
  12. To ensure that an appropriate anesthesia procedure is applied to animals in experiments that give unnecessary pain and suffering and that appropriate pain reliever and anesthesia is used in research.
  13. To prevent the use of anesthesia if it gives more trauma to the animal than the experiment itself, and if it does not fit the purpose of the experiment.
  14. To comply with ethical principles and experimental purposes, the following measures can be taken by the veterinarian;
    1. To ensure giving painkillers to the animal subjected to great deal of suffering after anesthesia, and if it is not possible to cure, euthanize it with a humane method,
    2. To ensure the euthanasia procedures be done with satisfactory justifications during or at the end of the experiments,
    3. To ensure to put the animals down that are under severe and persistent pain or suffering that can not maintain a normal life and pose a risk to both their health and others’ with a humane method.
  15. To provide healthy living conditions for the test animals used in the experiments that will continue to live afterwards.
  16. To decide whether the experiments that expose animals to intense and long-lasting pain are done or not considering the ethical principles, the benefits to be gained from the research and the agony of animals.
  17. To reduce the number of animals used in experiments by letting them be used more than once in the experiments as long as the animal’s well-being does not deteriorate and it does not deviate the experiment from its scientific purposes.
  18. To ensure that the tissues and organs of the dead animals used in the experiments are utilized in other applications.
  19. Avoid practices that may result in potential severe pain, suffering, and agony which is nonrecoverable.
  20. To approve procedures to be carried out only under the supervision the animal welfare unit of IBG-AELEC.
  21. To follow the changes to be made in the approved projects, the content and the persons to participate in the work and ensure that the necessary permissions are obtained.

PRACTICES RELATED TO ANIMAL EXPERIMENTS AND RESEARCH LABORATORY ANIMALS
Article 9.

(1) Issues regarding the animals used in the researh applied to IBG-AELEC:

  1. The complete experimental procedure that will be performed must be approved by the IBG-AELEC.
  2. The following animals can be used for experiments in accordance with the regulations made by the DEU-HADYEK, unless a general or special exemption has been taken;
    1. Mouse (Mus musculus),
    2. Rat (Rattus norvegicus),
    3. Guinea pig (Cavia pocellus),
    4. Syrian (golden) hamster (Mesocricetus auratus),
    5. Chinese hamster (Cricetulus griseus),
    6. Mongolian gerbil (Meriones unguiculatus),
    7. Rabbit (Oryctolagus cuniculus),
    8. Dog (Canis familiaris),
    9. Cat (Felis catus),
    10. All species of non-human primates
    11. Frog [Xenopus (laevis, tropicalis), Rana (temporaria, pipiens)],
    12. Zebrafish (Danio rerio).

    All species and animals used in experiments and legal tests must be registered and provided from a breeder and/or a supplier.

  3. Stray animals such as cats and dogs living in the streets can not be used in experiments. However, However, these animals can be used in experiments when there is a need to study the health and well-being of these animals, there is a serious danger to the environment, human and animal health and there is enough scientific justification showing that studies can be only achieved by using stray-animals in the experiments.
  4. Non-human primates can only be used in experiments, in exceptional cases and with the explicit scientific justification showing that the purpose of the procedure cannot be achieved by using any animal other than a non-human primate.
  5. Big hominoidea cannot be used in any type of experiments.
  6. Within the framework of national legislation and international conventions, endangered and protected species and the species listed in the Appendix 1 of CITES Convention are permitted to be used in the following cases:
    1. If the procedure has one of the purposes specified in subclause (1) of clause (b) of the first paragraph of Article 5, and clauses (c) and (d).
    2. If there is a scientific justification showing that the purpose of the procedure can not be achieved with species other than the relevant species.
  7. A scientific experiment on wild animals taken from their natural environment can be approved only if the alternative species are not sufficient for the purpose of the experiment. After the approval of IBG-AELEC, a permission is taken from the General Directorate.

SEVERITY CLASSIFICATION OF THE EXPERIMENTS, ANESTHESIA AND IMPLEMENTATION OF ANESTHESIA, ACT OF KILLING AND OTHER RELATED HANDLINGS DURING
Article 10.

The procedures related to anesthesia and its implementation, killing and severity classification of experiments are carried out in accordance with the articles 21 and 22, and Annex-8 and Annex-9 of the Directive on Protection And Welfare Of Laboratory Animals Used For Experiments and Other Scientific Purposes published in the Official Gazette dated 13/12/2011 and numbered 28141 by Ministry of Food, Agriculture and Livestock.

RE-USE OF ANIMALS IN THE EXPERIMENTS
Article 11.

(1) Reuse of an animal previously used in one or more experiments is allowed in the following situations:

  1. If the actual severity of the previous experiments is “mild” or “moderate”.
  2. If the animal’s general health status has completely recovered.
  3. If the new experiment is classified as “mild”, “moderate” or ” non-recoverable”.
  4. If it has been deemed appropriate by a veterinarian who will be able to evaluate previously performed procedures on the animal.

(2) In exceptional cases, after the examination of the animal by a veterinarian and by excluding subparagraph (a), an animal may be allowed to be re-used in an experiment involving severe pain, suffering or equivalent discomfort provided that the animal will not be used more than once.

TERMINATION OF EXPERIMENTS
Article 12.

(1) Every experiment is terminated when no more observations on the experiment can be performed, or when genetically modified animal breed or species are no longer be traced and If pain, suffering, and permanent damage equal to or more than the one needle penetration on an ongoing basis is expected, the experiments are terminated.

(2) At the end of an experiment, a veterinarian decides if an animal should survive. If an animal continues to survive, appropriate care and accommodation services are provided for its health condition. If the animal continues to live with moderate or severe pain, suffering, distress, and permanent damage, its life is terminated.

PROJECT APPLICATIONS
Article 13.

Projects to be accepted to IBG-AELEC:

  1. All laboratory animal research projects that are carried out by DEU academic staff, especially iBG staff,
  2. Projects and studies that include learning a method / model and manual handling practice,
  3. Multicenter research projects that iBG participates as a partner center,
  4. Research projects that are carried out by researcers from other agencies and organizations that apply DEU Experimental Animal Laboratory for experimental studies.

The Applicantions to the Ethical Committee is done by filling out the Turkish or English version of the “Experimental Animal Ethics Committee Application Form” and submitting it to IBG-AELEC secretariat. The applications for thesis studies are made by the academic advisor as the coordinator of the project and in the other research projects, applications are done by project coordinators. The applications to be made from outside the university are done with the official letter of the project manager from his institution.

RESPONSIBILITIES OF THE APPLICANT
Article 14.

In the application to the Committee, personal declaration is essential and the applicants sign a commitment form.

  1. They accept the accuracy of the information they provide on their application forms.
  2. They undertake not to start the experiments without the approval of IBG-AELEC.
  3. They accept to carry out the procedures on the test animals in accordance with the issues specified in the application form and they agree to open their working order to the members of IBG-AELEC incase IBG-AELEC wants to observe their work. Any changes to the research project after the approval of İBG-HADYEK should be notified to İBG-HADYEK in a written form and an approval should be obtained again.
  4. Applications must be made at least 5 (five) business days prior to the announced meeting date in order for the applications to be considered for the first scheduled meeting.
  5. It is compulsory for people out of Dokuz Eylul University to attach the permission document obtained from the unit where the studies are carried out to their ethical committee application.
  6. Applications for the thesis studies must be made by the “Academic Advisor” as “Coordinator ” and applications for other projects must be made by an academic staff with a doctorate or equivalent degree as “Coordinator of the Project”. It is compulsory to attach permit documents from animal owners for the applications on field or clinical trials.

PROPERTIES AND PROJECT FORMAT IN PROJECT APPLICATION
Article 15.

(1) The research project should describe the purpose, design, methodology, statistical aspects and organization of the work to be done.

The projects are edited in accordance with scientific criteria so as not to exceed 4-6 pages. The name of the research, type (experimental, preliminary study, thesis study, etc.) the name of the researchers, their place of employment, the contact address should be on the first page.

(2) Project Format

Filling out the application form:

Title page: The project name, the institutions of participating researchers, tasks and signatures, the research, and the contact details, department and etc.of the project coordinator.

Project Title: must be clear, short, and scientific that describes the whole project without abbreviations or jargons.

Project Summary: It should include goals of the project, the objectives, the materials/methods, the predicted damages and benefits, the species and the trait of the animals to be used in accordance with the 3R principles.

Introduction: The project’s rationale with relevant literature should be given in detail. Literature should be placed in the text according to the order of use.

Objective: The objective of the project reflecting the basic hypothesis should be written clearly and briefly.

Method: The research design, the experimental groups and the justifications for the study design, the drug doses, the route of administration, the place where the drugs are obtained, the literature on drugs if available, the amount of biological samples to be taken, the sampling and storage method, details on evaluation and test methods to be performed with literary support if available, selecting appropriate statistical method, surgical procedure to be performed on animals, brief information on postoperative care, methods of evaluation of laboratory findings, detailed technical information should be given on the place where the animals are to be kept, the conditions of the animals being kept and the permission certificate from the laboratory where testing is carried out, the method of termination of the experiment, time, cages and the companies where the necessary materials and equipment are obtained should be given in details.

Innovations that the project will bring:   The innovations and contributions that the project will bring to the literature should be stated briefly.

References: Must be written in the order of use in the project and must be written according to the Index Medicus format at the end of the project.

Project coordinator should submit the application to IBG-AELEC by adding his or her letter (Annex 1).

The first application should include:

  • A letter of Application,
  • 3 copies of IBG-AELEC Ethics Committee Application Form (1 original and 2 copy),
  • 3 copies of Certificate in Laboratory Animal Science (of the researcher who is to do the animal manipulations),
  • 3 copies of IBG-AELEC declaration letter (1 original and 2 copy) (Annex 2),
  • One CD including the electronic application form of IBG-AELEC,
  • Three copies of basic literature the project is based on (supporting hypotheses, tools and methods of the project),
  • If company support is to be provided on the research budget, a conflict of interest document should be added (Annex 3).
  • During the APPLICATION to IBG-AELEC;
    1. Related forms / documents (see Annex 1, Annex 2 and Annex 3) can be found in the “Academics” / “Ethics Committees” section on the web page of Dokuz Eylul University
    2. Forms / documents will be submitted to IBG-AELEC Secretariat. These documents are:
    3. Letter of Application (Annex-1)
    4. Declaration Letter (1 Original, 2 copy)
    5. Three Project Application Forms (1 Original, 2 copy)
    6. Conflict of Interest Document (Annex-3)
    7. Three literature supporting the research
    8. CD in which the Project Application Form and the supporting documents are saved
    9. Certificate in Laboratory Animal Science (of the researcher who is to do the animal manipulationS- 3 copy)

EVALUATION OF PROJECTS AND DECISION MAKING
Article 16.

(1) Projects are evaluated according to following criteria:

  1. The scientific, educational or legal justifications,
  2. The reasons for animal use,
  3. Realization of the procedures in a maximum humane and environmentally sensitive way,
  4. The predicted scientific benefits and the value for education,
  5. Compatibility to the 3R principle,
  6. Severity classification of experiments,
  7. The benefits to be gained and the suffering of animals,
  8. The compliance of killing method, procedures, anesthesia, re-use, care and housing conditions with the regulations,
  9. The decision to make a retrospective evaluation and timing

(2) The people to do the project evaluation for IBG-AELEC should be chosen regarding their competence in experimental design, animal experimentation or animal care and nutrition.

(3) The project evaluation must be transparant. The project evaluation is carried out in an impartial manner for the protection of intellectual property rights and confidential information.

(4) A member of IBG-AELEC is appointed as a reporter for each appropriate application. The reporter evaluates the project and explains his/her assessment to the Committee members at the meeting. The Board discusses the project. If the committee deems necessary, it can invite the researcher in charge to the meeting and ask questions and points that need explanation.

(5) After the project evaluation, IBG-AELEC makes its decision as ‘approved’, ‘demands revision’, ‘conditional approval’ and ‘not approved’. If one of the Ethics Committee Members participates in the project, he/she should not vote on that project. The applications that receive ‘demands revision’ is re-evaluated by the Ethics Committee after the applicant revises the project. The projects that receive ‘conditional approval’ will be monitored for a specific time that is determined by the decision of the Ethics Committee. Then the fulfillment of the required conditions will be re-evaluated and the decision will be finalized whether the project is ‘approved or ‘not approved. IBG-AELEC may evaluate whether the persons who will be practicing in laboratory animals are competent or not and if a person is believed not to have enough experience IBG-AELEC may offer the applicant to work with an experienced researcher in the field for a specific time to gain experience.

(6) The Ethics Committee approvals are given for 5 years and are valid for this period. Additional time may be requested for the projects that cannot be completed within this period.

(7) In the research protocol, it is mandatory to notify the ethics committee and obtain its approval to make changes after the initial Ethics Committee approval. No changes in a protocol can be made without the approval of the ethics committee. The study will be stopped if the protocol changes that are not approved by the ethics committee are implemented.

(8) All researchers working in the units of Dokuz Eylul University who will do research in the fields related to the activities described in Article 1 of “Dokuz Eylul University-Animal Experiments Local Ethics Committee Directive” are required to obtain the approval of IBG-AELEC with a written application.

(9) All national and international scientific publications related to the activities described in the Article 1 of IBG-AELEC Directive, are required to include the statement “Approved by the Ethics Committee” or “Complies with the Ethics Committee Principles”.

(10) The responsibility of the ethical issues originating from declaring “Approved by the Ethics Committee” or “Complies with the Ethics Committee Principles”, which appears in all national and international scientific publications of research related to the activities described in the Article 1 of IBG-AELEC Directive, without applying the Ethics Committee, belongs to the authors(s) of the publication.

RETROSPECTIVE ASSESSMENT
Article 17.

(1) The following aspects can be evaluated retrospectively in the documents reported to IBG-AELEC:

  1. Whether the goals of the project have been achieved or not.
  2. The number of animal species used, the harm given and the severity classification.
  3. Elements that can contribute to the implementation of the 3R principle.

(2) All projects where non-human primates are used, including procedures with long-lasting and untreatable severe pain, suffering, and agony,, torture and misery, are assessed retrospectively.

(3) Projects other than the provisions of paragraph 2 can be exempted from retrospective assessment.

TRAINING OF THE PERSONNEL DEALING WITH LABORATORY ANIMALS
Article 18.

In accordance with the Article 7/c of this directive, IBG-AELEC determines whether the persons who will deal with laboratory animals are qualified or not and then issues “Certificate in Laboratory Animal Science” to the persons who are trained according to the regulations executed by the Ministry of Forestry and Water Management. of Laboratory animal users can not perform experiments, training or to test procedures on these animals or keep these animals in their work places. In case the person who plans to use laboratory animals in the work submitted for approval has no certificate, the work is not approved. The persons who apply to get a “Certificate in Laboratory Animal Science” are required to fulfill the following conditions:

  1. To have taken minimum 80-hour-training that includes theoretical and practical courses,
  2. To prove that they have participated in at least 80% of the mandatory training,
  3. To certify that they have succeeded (> 70/100) in the examination at the end of the training.

LAST TERMS
PRIVACY
Article 19.

The correspondences of the ethics committee are confidential. No information is provided to third parties except for the authorized institutions described by the related legislation and the Directive of TR Ministry of Forestry and Water Affairs on Local Animal Ethics Committee Work Plan and Essentials.

ENFORCEMENT
Article 20.

This Directive is presented to the Central Ethical Committee for Animal Experiments after being approved by the Decision of the Senate of Dokuz Eylül University and shall enter into force on the date of its approval by the Central Ethical Committee for Animal Experiments.

EXECUTION
Article 21.

The terms of this directory are executed by the Rector of DEU.

 


HOME DIRECTIVES PRE-REQUEST FORM APPLICATION FORM MEMBERS CONTACT

IBG-AELEC Secretariat

Tuba AKUNAL
tuba.akunal@deu.edu.tr
+90(232) 412 67 70
www.ibg.deu.edu.tr/en/ibg-aelec

Address

Izmir International Biomedicine and Genome Institute (iBG-izmir)
Dokuz Eylul Universitesi Saglik Yerleskesi
Balcova 35340 Izmir/TURKEY


 

HOME DIRECTIVES PRE-REQUEST FORM APPLICATION FORM MEMBERS CONTACT

The researchers who will apply for an Ethics Committee Approval, have to submit their forms to the Ethics Committee Secretariat after uploading their projects to the system.

Click here to see İBG_AELEC 2017 Meeting Calendar.

Please fill in the Application Form, “Conflict of Interest” and “IBG-AELEC contract” after reading the section below.

Application Requirements:
The application documents are as follows:
1- Approved Experimental Study Permit Pre-Request Form
2- The Application Form, the Contract at the end of the form will be signed by all researchers.
3- “Conflict of Interest” is to be signed by all researchers
4- Resume and Certificate in Laboratory Animal Science of one of the researchers
5- Minimum 3 maximum 7 literature related to the subject.

You can find the application documents below:

 

Application Form Contract Conflict of Interest Letter of Application

Please click here to upload the documents you have filled.


 

HOME DIRECTIVES PRE-REQUEST FORM APPLICATION FORM MEMBERS CONTACT

Researchers who will apply for Ethics Committee Approval are required to obtain “Experimental Study Permit” approval before completing the Ethics Committee Application form. Please download the “Experimental Study Permit Pre-Request Form” from the link below.

Experimental Study Permit Pre-Request Form

Click here to see İBG_AELEC 2017 Meeting Calendar.

You can upload the completed form to the system here.
[vfb id=’22’]

 

HOME DIRECTIVES PRE-REQUEST FORM APPLICATION FORM MEMBERS CONTACT

IBG-HADYEK has been established to conduct ethical review on research proposals for all experimental, testing and educational purposes involving animal experimentation in iBG-izmir and all processes related to production, maintenance, housing and transport of experimental animals.

iBG-AELEC Meeting Calendar

IBG-HADYEK application process is as follows:


Dokuz Eylul University Izmir International Biomedicine and Genome Institute is established on 09/03/2015 by the Council of Ministers after the approval of the University Senate.

The Institute has two departments: Genome Sciences and Molecular Biotechnology and Biomedicine and Health Technologies. Genome Sciences and Molecular Biotechnology has M.Sc., Ph.D. and Integrated Ph.D. programs in “Molecular Biology and Genetics”.

Our programs are interdisciplinary and international. The institute provides students with the opportunity to conduct basic and translational research.

All of the programs are taught in English.


Dokuz Eylül Üniversitesi İzmir Uluslararası Biyotıp ve Genom Enstitüsü üniversite Senatosu tarafından onaylanarak, 09/03/2015 tarihinde Bakanlar Kurulu Kararı ile kurulmuştur.

Enstitünün Genom Bilimleri ve Moleküler Biyoteknoloji ve Biyotıp ve Sağlık Teknolojileri isimli iki anabilim dalı mevcuttur. Genom Bilimleri ve Moleküler Biyoteknoloji A.D.’da “Moleküler Biyoloji ve Genetik” Yüksek Lisans, Doktora ve Bütünleşik Doktora programları bulunmaktadır.

Programlarımız disiplinler arası ve uluslararası özellik taşımaktadır. Enstitümüzde öğrencilere temel ve uygulamalı araştırmaların ön planda olduğu araştırmalar yapma olanağı sunulmaktadır.

Programların tamamında öğretim dili İngilizcedir.


 

ANA SAYFA YÖNERGE ÇALIŞMA İZNİ ÖN TALEP FORMU BAŞVURU FORMU ÜYELER İLETİŞİM

Etik Kurul Onayı almak için başvuracak araştırıcıların Etik Kurul Başvuru formunu doldurmadan önce “Deneysel Çalışma İzni” onayı almaları gerekmektedir. Lütfen aşağıdaki bağlantıdan “Deneysel Çalışma İzni Ön Talep Formu”nu indirerek dikkatlice doldurunuz.

Deneysel Çalışma İzni Ön Talep Formu

İBG-HADYEK 2017 Toplantı Takvimini görmek için tıklayın.
Doldurmuş olduğunuz ön talep formunu aşağıdan sisteme yükleyebilirsiniz.
[vfb id=’22’]

 

ANA SAYFA YÖNERGE ÇALIŞMA İZNİ ÖN TALEP FORMU BAŞVURU FORMU ÜYELER İLETİŞİM

İBG-HADYEK 2017 Toplantı Takvimini görmek için tıklayın.

[vfb id=21]

 

ANA SAYFA YÖNERGE ÇALIŞMA İZNİ ÖN TALEP FORMU BAŞVURU FORMU ÜYELER İLETİŞİM

Hadyek Sekreterya

Tuba AKÜNAL
tuba.akunal@deu.edu.tr
0(232) 412 67 70
www.ibg.deu.edu.tr/tr/ibg-hadyek

Adres

İzmir Uluslararası Biyotıp ve Genom Enstitüsü (iBG-izmir)
Dokuz Eylül Üniversitesi Sağlık Yerleşkesi
Balçova 35340 İzmir


 

ANA SAYFA YÖNERGE ÇALIŞMA İZNİ ÖN TALEP FORMU BAŞVURU FORMU ÜYELER İLETİŞİM

 

DEU logo DOKUZ EYLÜL ÜNİVERSİTESİ
İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ
HAYVAN DENEYLERİ YEREL ETİK KURULU
YÖNERGESİ
iBG Logo
 

AMAÇ
Madde 1.

Bu Yönergenin amacı, İzmir Uluslararası Biyotıp ve Genom Enstitüsü (İBG), Dokuz Eylül Üniversitesinde (DEÜ) ve müracaat durumunda diğer kurum ve kuruluşlarda bilimsel deneysel araştırma, test, sağlık hizmetleri uygulamaları, eğitim-öğretim amaçlı olarak kullanılacak tüm deney hayvanlarının barındırılmaları, üretilmeleri, doğadan izole edilmeleri, nakledilmeleri, deneylerde kullanılmaları ve üzerlerinde gözlem yapılması ile ilgili tüm süreçlerde etik bakımdan kabul edilebilir minimum standartları saptamak, etik ilkeler doğrultusunda görüş bildirmek, uygulamaların sınırlarını belirlemek ve araştırma önerilerini bu açıdan incelemek üzere oluşturulacak “Deney Hayvanları Yerel Etik Kurulu”nun (HADYEK) kuruluş ve çalışma esaslarına, yapılması planlanan işlemlerin sunulmasına, araştırma önerilerinin incelenmesine, uygulanmalarına izin verilmesine, uygulamaların izlenmesine ve gerektiğinde sonlandırılmasına ilişkin esasları belirlemektir.

KAPSAM
Madde 2.

(1) Yönerge İBG, DEÜ ve başvuru durumunda diğer kurum ve kuruluşlarda deney amacıyla kullanılacak hayvanların kullanımından önce alınması gereken izinleri, bu amaçla DEÜ İBG-HADYEK’in oluşturulmasını, çalışma usul ve esaslarını, kurulun görevleri ile eğitim, denetim ve yükümlülüklerini kapsar.

(2) Bu Yönerge:

  1. Deneysel olmayan tarımsal uygulamaları,
  2. Deneysel olmayan klinik veteriner hekimliği uygulamalarını,
  3. Veteriner sağlık ürünlerine pazarlama yetkisi verilebilmesi için gereken klinik deneyleri,
  4. Kayıtlı veya onaylı hayvancılık işletmelerinin yapmakla yükümlü olduğu uygulamaları,
  5. Birincil amacı bir hayvanın kimliklendirilmesi olan uygulamaları kapsamaz.

DAYANAK
Madde  3.

Bu Yönerge;

TANIMLAR
Madde 4.

Bu Yönerge’de geçen;

  1. Bakanlık: TC. Orman ve Su İşleri Bakanlığını,
  2. CITES Sözleşmesi: 20/6/1996 tarihli ve 22672 sayılı Resmî Gazete’de yayımlanan Nesli Tehlikede Olan Yabani Hayvan ve Bitki Türlerinin Uluslararası Ticaretine İlişkin Sözleşmeyi,
  3. Çalışma izni: Deney hayvanı kullanıcı, üretici ve tedarikçi kuruluşlara Gıda, Tarım ve Hayvancılık Bakanlığınca verilen belgeyi,
  4. Deney: Bilimsel amaçlarla hayvanlar üzerinde gerçekleştirilecek her türlü prosedür veya prosedürler bütününü,
  5. Deney hayvanı: Prosedürlerde kullanılan, serbest yaşayan veya çoğalan larva biçimleri, canlı kafadanbacaklılar ve normal fetal gelişimlerinin son üçte birlik döneminden itibaren memeliler dahil, insan olmayan herhangi bir omurgalı canlıyı,
  6. Deney ünitesi: Hayvanlar üzerinde her türlü prosedür veya prosedürlerin gerçekleştirildiği, Gıda, Tarım ve Hayvancılık Bakanlığı’ndan çalışma izni bulunan birimleri,
  7. Etik: Araştırmalarda kullanılacak hayvanlarla ilgili olarak insan ve hayvan yaşamını ilgilendiren bilimlerde yapılabilecek hareketlerin sınırları, hayvana yönelik yapılacak tutum ve davranışa yol gösterici evrensel kuralları,
  8. Genel Müdür: Doğa Koruma ve Milli Parklar Genel Müdürünü,
  9. Genel Müdürlük: Doğa Koruma ve Milli Parklar Genel Müdürlüğünü,
  10. HADMEK: Hayvan Deneyleri Merkezi Etik Kurulunu,
  11. İBG-HADYEK: İzmir Uluslararası Biyotıp ve Genom Enstitüsü Hayvan Deneyleri Yerel Etik Kurulunu,
  12. Hayvan refahı birimi: Üretici, tedarikçi, kullanıcı ve araştırmaya yetkili kuruluşlarda kurulması zorunlu olan, hayvanların refahı ve bakımından sorumlu, veteriner hekim, veteriner sağlık teknikeri veya veteriner sağlık teknisyeni unvanına sahip en az bir kişiden, kullanıcı kuruluşlarda ise bu unvanlardan birine sahip bir kişiye ilaveten biri yerel etik kurul üyesi olmak üzere en fazla üç kişiden oluşan birimi,
  13. İnsancıl öldürme metodu: Hayvanın kendi türüne has, en az fiziksel ve duyusal ağrı, eziyet ve sıkıntıya maruz kalacağı şekilde yaşamının sonlandırılmasını,
  14. İn vivo deney: Canlı ortamda yapılan deneyi,
  15. İyi laboratuvar uygulamaları: Klinik çalışmalar dışındaki sağlık ve çevre güvenliği çalışmalarının planlanması, yapılması, izlenmesi, kaydedilmesi, arşivlenmesi ve rapor edilmesi şartları ve yönetim usulleri ile ilgili kalite sistemini,
  16. Kullanıcı: Hayvanları prosedürlerde kullanmaya yetkili olan kişiyi,
  17. Kuruluş: Gıda, Tarım ve Hayvancılık Bakanlığınca çalışma izni bulunan, müştemilatı ile birlikte açık, kapalı, yarı açık, her türlü sabit ya da taşınabilir tesis, bina veya binalar grubunu,
  18. Proje: Tanımlanmış bilimsel bir amacı olan ve bir ya da daha fazla prosedürü kapsayan iş programını,
  19. Prosedür: Hayvanların; doğurtulması, kuluçkadan çıkarılması ya da genetiği değiştirilmiş hayvan soyunun devam ettirilmesi süreçleri dahil, iyi veteriner hekimlik uygulamalarına uygun olarak bir iğnenin batırılmasının yarattığına eşit veya daha fazla acı, eziyet, ızdırap veya kalıcı hasara sebep olabilecek şekilde, bilinen veya bilinmeyen sonuçları olan, deneysel, diğer bilimsel veya eğitici amaçlarla kullanılmasını,
  20. Sekreterya: Etik kurullarda gerekli koordinasyonu sağlayan, yazışmaları yapan ve kayıtları tutan kişi veya kişileri,
  21. Tekniker: Lise öğrenimi üzerine iki yıl süreli Veteriner Sağlık Önlisans programlarından mezun olan kişiyi,
  22. Teknisyen: Milli Eğitim Bakanlığına bağlı Tarım Meslek Lisesi Veteriner Sağlık Bölümü ile daha önce Gıda, Tarım ve Hayvancılık Bakanlığına bağlı olan Veteriner Sağlık Meslek Lisesi, Hayvan Sağlığı Memurları Okulu, Hayvan Sağlığı Memurları Meslek Lisesi okullarından herhangi birinden mezun kişiyi,
  23. DEÜ: Dokuz Eylül Üniversitesini
  24. Tür: Ortak özellikler taşıyan ve kendi aralarında döllenerek üreyebilen akraba canlıları içeren biyolojik grubu,
  25. 3R ilkesi: W.M.S Russell ve R.L. Burch tarafından 1959’da geliştirilen ve baş harflerinden dolayı 3R olarak anılan:
    • Replacement (Yerine Koyma); Mümkün olan her durumda, canlı hayvan yerine bilimsel açıdan geçerli başka alternatif bir yöntem ya da deneme stratejisinin uygulaması,
    • Reduction (Azaltma); proje hedeflerinden ödün vermeden kullanılacak hayvan sayısının olabildiğince azaltılması,
    • Refinement (Arındırma); hayvanlara acı, eziyet, ızdırap çektirecek ve kalıcı hasar yapacak prosedürlerin iyileştirilerek hayvan refahının artırılması ilkelerini ifade eder.
  26. Yetkili Kişi: Dokuz Eylül Üniversitesi IBG bünyesinde deney hayvanları yetiştiren ve barındıran birimlerle, Hayvan Kullanım Laboratuvarlarının sorumlusunu

İBG-HADYEK’in OLUŞUMU, ÜYELERİN NİTELİKLERİ ve ATANMASI
Madde 5.

(1) İBG-HADYEK OLUŞUMU ve ÜYELERİN NİTELİKLERİ

  1. Hayvan deneyleri konusunda en az bir yıl deneyimli, kurum içinde deney hayvanı yetiştirilmesi, üretilmesi ve bakımından sorumlu ve deney hayvanları kullanım sertifikasına sahip tam gün ünitede çalışan en az bir veteriner hekimden,
  2. Kurum içinde deney hayvanları ile çalışma yapan birimlerden birer temsilciden,
  3. Kendisi ve birinci derece yakınları, hayvanlar üzerinde deneysel çalışma yapmayan ve kuruluş ile çıkar ilişkisi olmayan Türkiye Cumhuriyeti vatandaşı sivil bir üyeden,
  4. Kurum ile çıkar ilişkisi olmayan sivil toplum kuruluşuna kayıtlı T.C. vatandaşı bir üyeden oluşur.
  5. İBG-HADYEK’te görev alacak en az bir üyenin in vivo hayvan deneylerinde en az bir yıl tecrübeli ve doktora veya tıpta uzmanlık derecesine sahip olması gereklidir. İBG-HADYEK’te tıp veya veteriner hekim etiği uzmanlarının da bulunması tercih edilir. Kurum ve kuruluşlar ihtiyaçlarına ve idari yapısına göre İBG-HADYEK kompozisyonunu belirleyebilirler. İBG-HADYEK gerektiğinde başka alanların uzmanlarından görüş alabilir, toplantılara davet edebilir.

(2) İBG-HADYEK’e ATANMA ve GÖREV SÜRELERİ

  1. Etik Kurul en az 5 en fazla 21 üyeden oluşur. Etik Kurul başkanı, vekili ve üyeleri 4 yıllığına rektör tarafından atanır. Görev süresi dolan üye tekrar rektör tarafından atanabilir.
  2. Bir takvim yılı içersinde izinsiz ve mazeretsiz 3 defa üst üste toplantıya katılmayan üyenin üyeliği düşer. Etik kurul başkanı ve veteriner hekim kurulda tam zamanlı çalışmak zorundadır.
  3. Etik kurul sekretaryası rektör tarafından atanır ve başvuruların alınması, kurulun düzenli çalışması ve kararların arşivlenmesinden sorumludur.

İBG-HADYEK’in ÇALIŞMA ŞEKLİ
Madde 6.

  1. İBG-HADYEK başkanın belirleyeceği gündemle ayda iki defa üyelerin en az üçte ikisinin katılımı ile toplanır.
  2. İBG-HADYEK toplantısında kararlar oy çokluğu ile alınır. Oy eşitliği halinde başkanın oyu yönünde karar verilir.
  3. İBG-HADYEK kuruluş bünyesinde kullanılan tüm deney hayvanlarına ilişkin kayıtlar, hayvan refahı biriminde görevli deney hayvanı yetiştirilmesi, üretimi ve bakımından sorumlu veteriner hekim tarafından tutulur veya tutturulur ve İBG-HADYEK bu işlemleri kontrol eder. Söz konusu kayıtlarda temin edilen hayvanların sayıları, türleri, temin edildikleri yerler, kullanıcı kuruluşa geldiği tarih ve yapılan tüm işlemler bulunur. Bu kayıtlar en az beş yıl süreyle muhafaza edilir.
  4. İBG-HADYEK, yapılacak başvuruları değerlendirmek için bir form hazırlar. Formda aşağıdaki bilgilerin bulunması zorunludur:
    1. Proje adı.
    2. Proje yürütücüsü adı, soyadı, ünvanı, kurumu, bölümü, telefonu, elektronik posta adresi, imzası
      Diğer araştırıcıların adı, soyadı, ünvanı, kurumu, bölümü, projedeki görevi, imzası.
    3. Prosedürün yapılacağı yer ve süresi.
    4. Canlı hayvanlar üzerinde prosedür uygulayacakların eğitim sertifikaları.
    5. Başvuru tarihi.
    6. Proje önerisi.
    7. Günlük dille yazılmış teknik olmayan proje özeti.
    8. Hayvan temin edileceği yer, tahmini hayvan sayısı, türü ve yaşı/ ağırlığı.
    9. Hayvanlar üzerinde gerçekleştirilecek işlemler.
    10. Prosedürlerin sebep olacağı acı, eziyet, ızdırap( rahatsızlık düzeyi) ve kalıcı hasar düzeyi.
    11. 3R (Replacement, Reduction, Refinement) ilkesinin prosedürlerde uygulanma şekli.
    12. Kullanılması planlanan anestezi, analjezi ve diğer ağrı kesici yöntemler.
    13. Hayvanların yaşamları boyunca acı ve ızdırap çekmemesi ya da çektikleri ızdırabın azaltılması için alınacak önlemler.
    14. Prosedürlerin sonlandırılmasında insancıl öldürme metodunun belirlenmesi.
    15. Hayvan sayısını ve prosedürlerin sebep olacağı acı, eziyet, ızdırap ya da olası çevresel etkileri asgariye indirmek için uygulanacak deneysel veya gözlemsel stratejiler ile veri analiz usulleri.
    16. Hayvanların birden fazla projede kullanılıp kullanılmayacağı.
    17. Hayvanların barındırma, yetiştirme ve bakım şartları.
    18. Projede yer alanların yetkinliği.
    19. Taahhütname.
  5. İBG-HADYEK tarafından projelere azami beş yıl süre ile izin verilir, süre uzatımı talebi olması halinde, talebin gerekçelendirilmesi şartıyla ek süre verilebilir.
  6. Bütün başvurular ve alınan kararlar, tarih ve sayı numarası verilerek kayıt altına alınır. Kayıtlar en az beş yıl süreyle muhafaza edilir.
  7. Başvurular, proje yürütücüsü tarafından yapılır. Tez çalışmaları için yürütücü, danışman öğretim üyesidir.
  8. İBG-HADYEK, yaptığı değerlendirme neticesinde:
    • Uygundur
    • Düzeltilmesi gerekir
    • Şartlı olarak uygun
    • Uygun değildir şeklinde karar verir.

    Kararlar başvuru sahibine başvurunun yapıldığı tarihten itibaren en geç kırk iş günü içinde yazılı olarak bildirilir. Bu süre proje değerlendirmesini de kapsar. Projenin karmaşıklığı veya birden çok bilim dalını ilgilendirdiği hallerde, Etik Kurul, sözü edilen süreyi bir defaya mahsus olmak üzere onbeş (15) iş gününü geçmeyecek şekilde uzatabilir. Uzatma sebebi ve süresi gerekçelendirilerek, süre sona ermeden proje yürütücüsü bilgilendirilir. Etik kurul, bir projenin yapılabilirliğini sınamak amacıyla az sayıda hayvan üzerinde ön deneylerin yapılmasını isteyebilir. Bu durumda kesin karar, “şartlı olarak uygun” kararı verilen projelerdeki usullere göre verilir.

  9. Etik kurul üyelerine ait başvurular görüşülürken ilgili kurul üyesi görüşmelere katılamaz ve oy kullanamaz.
  10. Bir proje hakkında “Düzeltilmesi gerekir” kararı verilen projeler, düzeltildikten sonra tekrar değerlendirilir. “Şartlı olarak uygun” kararı verilen projeler, etik kurul tarafından belirlenecek bir süre boyunca, hayvan refahı birimi tarafından izlenip, istenen şartların yerine getirilip getirilmediği değerlendirildikten sonra uygun ya da uygun değildir şeklinde karara bağlanır ve proje ile ilgili İBG-HADYEK’e rapor verilir. Hayvan refah biriminin çalışma usul ve esasları Gıda, Tarım Ve Hayvancılık Bakanlığının çıkarmış olduğu 28141 sayılı Deneysel ve Diğer Bilimsel Amaçlar İçin Kullanılan Hayvanların Refah ve Korunmasına Dair Yönetmeliğe  göre düzenlenir.
  11. İzin verilen projelerde hayvan refahını olumsuz etkileyecek herhangi bir değişiklik olup olmadığı İBG-HADYEK tarafından denetlenir. İBG-HADYEK, onaylanan projeye uyulmaması durumunda, verilen ETİK ONAY iptal edilir. Etik onayın iptal edilmesi durumunda; hayvan refahı birimi tarafından, projede kullanılan veya kullanılması öngörülen hayvanların refahının olumsuz yönde etkilenmemesi gerekli koşullar düzeltilerek sağlanır.
  12. İBG-HADYEK onayı alındıktan sonra projedeki ve çalışmaya katılacak kişilerdeki değişiklikler projedeki tüm araştırmacıların onayı alındıktan sonra proje yürütücüsü tarafından İBG-HADYEK’e yazılı olarak bildirilir ve onayı alınır.
  13. Aşağıdaki müdahaleler etik kurul’un iznine tabi değildir:
    1. Teşhis ve tedavi amaçlı klinik uygulamalar.
    2. Ölü hayvan veya dokusu, mezbaha materyalleri, atık fetuslar ile yapılan prosedürler.
    3. Süt sağma.
    4. Dışkı veya altlık örneği toplama.
    5. Sürüntü ile örnek alma.
  14. Tür tanımlama ile ilgili doğadan yaban hayvanı kullanılmasında Genel Müdürlükten alınan izin, İBG-HADYEK izni yerine geçer.
  15. Saha araştırmalarının birden fazla ilde yürütülmesi halinde sadece bir yerin HADYEK onayının alınması yeterlidir.
  16. Kayıtlar, Hayvan Deneyleri Merkezi Etik Kurulu (HADMEK) ve Bakanlığın denetimine açık tutulur.
  17. İBG-HADYEK, gerektiğinde konusunda deneyimli uzmanların yazılı görüşlerini alabilir veya İBG-HADYEK toplantısına davet ederek sözlü veya yazılı görüş isteyebilir.

İBG-HADYEK’in GÖREVLERİ
Madde  7.

  1. Hayvan Deneyleri Etik Kurullarının Çalışma Usul ve Esaslarına Dair Yönetmeliğin hükümlere göre HADMEK’in belirlediği etik ilkeler ve iyi laboratuvar uygulamaları çerçevesinde İBG-HADYEK çalışma usul ve esasları hakkında yönerge hazırlamak.
  2. Deney hayvanları üzerinde yapılacak tüm işlemlerin etik yönden kabul edilebilir sınırlarını belirleyerek yapılacak işlemlere ilişkin protokolleri onaylamak veya gerekçeli olarak red etmek.
  3. Kurum içinde deney hayvanı kullanılması sürecinin 3R ilkelerine ve etik kurallara uygun olarak sürdürülmesini denetlemek, bu amaçla gerekli düzenlemeleri yapmak.
  4. Deney hayvanı kullanılarak elde edilenlerle aynı veya daha yüksek düzeyde bilgi sağlayabilecek ancak hayvan kullanılmayan veya en az sayıda hayvan kullanılan ya da daha az acı verilen prosedürler içeren alternatif yöntemlerin geliştirilmesine ve doğrulanmasına katkıda bulunacak ve bu alanda araştırmayı teşvik edecek uygulamalar yapmak.
  5. Deney hayvanları üzerinde yapılacak işlemlerin onaylanmış protokole uygun olarak yapılmasını sağlamak, gerektiğinde sonlandırmasına karar vermek.
  6. Deney hayvanlarıyla çalışacak personelin gerekli eğitimi almasını sağlamak ve deney hayvanı kullanım sertifikası bulunması şartıyla hayvan deneyleri yapılmasına izin vermek. Bu amaçla gerektiğinde sertifika programları düzenlemek.
  7. Deney hayvanlarının üretim, yetiştirme, barındırma ve nakil şartları ile deneylerin yapıldığı laboratuvar şartları ve ekipmanının etik yönden uygun olup olmadığını denetlemek.
  8. Deney hayvanı kullanımı ile ilgili olarak istatistiki veri tabloları ile yıllık faaliyet raporunu hazırlayarak HADMEK’e sunmak.
  9. Deneysel çalışmalar sonunda ortaya çıkan atıklar ve tıbbi atıkların 9/8/1983 tarihli ve 2872 sayılı Çevre Kanunu ve ilgili mevzuat çerçevesince bertarafını sağlamak.
  10. 5199 sayılı Hayvanları Koruma Kanununun ve ilgili mevzuatın getirdiği hükümler çerçevesinde, deney hayvanlarının kayıt altına alınmalarını ve izlenebilmelerini sağlamak.
  11. Düzenlenecek eğitim sertifika programlarını otuz gün önce HADMEK’e bildirmek.
  12. Düzenledikleri sertifika eğitim programları ve eğitim sonunda başarılı olarak sertifika alan kursiyerler ile ilgili bilgileri HADMEK’e bildirmek.
  13. Deneyde kullanılan hayvanların, prosedür sonrası sahiplendirilmesi veya çiftçilik sistemine iadesinde sakınca görülüp görülmediği hakkında karar vermek.

İBG-HADYEK’in YETKİLERİ VE ÇALIŞMA İLKELERİ
Madde 8.

İBG-HADYEK aşağıda belirtilen ilkeler doğrultusunda çalışır;

  1. Bilimsel araştırmalarda ve eğitimde kullanılması zorunlu olan deney hayvanlarına kötü muameleleri engellemek.
  2. Deney hayvanlarını, Hayvan Deneyleri Etik Kurullarının Çalışma Usul ve Esaslarına Dair Yönetmeliğin 5 inci maddede belirtilen amaçları kapsamında kullanılmasını sağlamak.
  3. Ağır acı, stres ya da buna denk eziyet veren deneylerde bir hayvanın bir defadan fazla kullanılmamasını, zorunlu olarak kullanılması gerekiyorsa bunun sağlam bilimsel gerekçelere dayandırılmasını sağlamak.
  4. Eğitim amaçlı kongre, konferans ve seminerlerde ağrı ve acı veren deneylerin yapılmamasını sağlamak.
  5. Bilimsel açıdan güvenilir verinin, hayvanlara mümkün olduğu kadar az acı çektirerek ve onları en az strese sokarak elde edilmesini sağlamak.
  6. Araştırmalar süresince kullanılan deney hayvanlarına, türüne uygun şartlar hazırlamak ve en iyi fizyolojik, davranışsal ve çevresel şartların teminini sağlamak.
  7. Uygun şekilde eğitilmiş personel tarafından uygun şartlarda deney hayvanı bakımını sağlamak.
  8. Canlı hayvanlarda yapılacak deney amaçlı çalışmaların sorumlu veteriner hekim gözetiminde yapılmasını sağlamak.
  9. Araştırıcılar tarafından, deneylerin hangi durumlar yerine getirildiğinde sonlandırılacağına dair insani son noktaların belirlenmesini sağlamak.
  10. Araştırılan bilginin elde edilmesinde geçerliliği kanıtlanmış alternatif yöntemler varsa hayvan deneylerini etik olarak uygun görmemek ve daha önceden ayrıntılı olarak yapılmış deneylerin tekrar edilmesine engel olmak.
  11. Deney için en uygun hayvan türü ve yöntemin seçilmesini ve bilimsel olarak anlamlı sonuç verebilecek en az sayıda hayvan kullanılmasını sağlamak.
  12. Deney hayvanlarına gereksiz acı ve ağrı verecek deneylerde uygun bir anestezi usulünün uygulanmasını ve araştırmalarda uygun ağrı kesici ve anestezi kullanılmasını sağlamak.
  13. Anestezinin, hayvan için deneyin kendisinden daha fazla travmatik olması ve deneyin amacına uygun olmaması durumunda yapılmasını engellemek.
  14. Deneyin etik ilkelere göre ve amacına uygun olması için veteriner hekim kararı ile;
    1. Anesteziden çıktığında önemli oranda acıya maruz kalacak olan hayvanın ağrı kesici ile tedavi edilmesini, tedavi edilmesi mümkün değilse insancıl bir metotla öldürülmesini,
    2. Deney hayvanının araştırma sürecinde ya da sonunda hayatına son verilmesi işlemlerinin uygun gerekçelerle yapılmasını,
    3. Şiddetli ve sürekli ağrı çeken veya normal hayatını sürdüremeyecek duruma gelen deney hayvanları ile sağlığı ve çevresi için risk oluşturabilecek deney hayvanlarının insancıl bir metotla yaşamalarına son verilmesini sağlamak.
  15. Araştırmada kullanılan ve yaşamalarını sürdüren deney hayvanlarına, deney sonunda sağlıklı yaşam şartlarının teminini sağlamak.
  16. Hayvanları ağır ve uzun süreli acıya maruz bırakacak deneylerin yapılmasına, etik ilkeler ile araştırmadan elde edilecek fayda ve hayvanların çekeceği acı dikkate alınarak karar vermek.
  17. Bilimsel hedeften uzaklaşılmadığı ve hayvanın refahının bozulmadığı sürece hayvanlar üzerinde birden fazla uygulama yaparak, deneyde kullanılan hayvanların sayısını azaltmak.
  18. Deneyde kullanılarak ölen hayvanların doku ve organlarının paylaşılması kapsamında diğer başvurularda değerlendirilmesini sağlamak.
  19. Uzun süreli olması muhtemel şiddetli acı, eziyet ve ızdırapla sonuçlanan ve düzeltilmesi mümkün olmayan uygulamalardan kaçınmak.
  20. Yalnızca kendi bünyesindeki hayvan refahı biriminin denetiminde gerçekleştirilecek prosedürlere izin vermek.
  21. Onay verilen projelerde, içerikte ve çalışmaya katılacak kişilerde yapılacak değişiklikleri takip etmek ve gerekli izinlerin alınmasını sağlamak.

DENEY HAYVANLARI VE ARAŞTIRMALARA İLİŞKİN UYGULAMALAR
Madde 9.

(1) İBG-HADYEK’e başvuran çalışmalarında kullanılacak hayvanlara ilişkin hususlar:

  1. Deney hayvanları üzerinde yapılacak tüm prosedürlerin İBG-HADYEK tarafından onaylanmış olması zorunludur.
  2. İBG-HADYEK tarafından yapılan düzenlemelere uygun olarak alınmış bir genel veya özel istisna olmadıkça, deneylerde kullanılacak;
    1. Fare (Mus musculus),
    2. Sıçan (Rattus norvegicus),
    3. Kobay (Cavia pocellus),
    4. Suriye (altın) hamsteri (Mesocricetus auratus),
    5. Çin hamsteri (Cricetulus griseus),
    6. Moğolistan gerbili (Meriones unguiculatus),
    7. Tavşan (Oryctolagus cuniculus),
    8. Köpek (Canis familiaris),
    9. Kedi (Felis catus),
    10. İnsan dışı primatların bütün türleri
    11. Kurbağa [Xenopus (laevis, tropicalis), Rana (temporaria, pipiens)],
    12. Zebra balığı (Danio rerio),

    türlerinin ve deneyde kullanılacak tüm hayvanların kayıtlı yasal deney hayvanı üreticisi ve tedarikçilerinden alınmış olması şartı aranır.

  3. Kedi, köpek gibi evcil türlerin sokakta başıboş olanları, deneylerde kullanılmaz. Ancak, hayvanların sağlık ve refahı ile ilgili çalışmalara ihtiyaç duyulması, çevre, insan ve hayvan sağlığına karşı ciddi tehlike oluşturması ve çalışmanın amacının sadece başıboş hayvan kullanılarak gerçekleştirilebileceğine dair bilimsel gerekçeler sunulması hallerinde bu hayvanlar deneylerde kullanılabilir.
  4. İnsan dışı primatların deneylerde kullanılmasına, istisnai durumlarda ve prosedürün amacının insan dışı primatlar dışında bir tür kullanılarak gerçekleştirilemeyeceğine dair bilimsel bir gerekçe mevcutsa izin verilir.
  5. Büyük kuyruksuz maymunlar deneylerde kullanılamaz.
  6. Ulusal mevzuat ve uluslararası sözleşmeler çerçevesinde nesli tehlike altında olan ve korunan türler ile CITES Sözleşmesinin Ek-1 Listesindeki türlerin kullanılmasına aşağıda belirtilen durumlarda izin verilir:
    1. Prosedür, 5 inci maddenin birinci fıkrasının (b) bendinin (1) numaralı alt bendi ile (c) ve (d) bentlerinde belirtilen amaçlardan birine sahipse.
    2. Prosedürün amacının söz konusu türlerin dışındaki türler ile gerçekleştirilemeyeceğine dair bilimsel bir gerekçe mevcutsa.
  7. Doğadan alınmış yaban hayvanı üzerinde yapılacak deney bir bilimsel gerekçeyle; ancak diğer hayvanların deneyin amacı bakımından yeterli olmaması halinde onaylanır. Bu konuda yapılan çalışmalarda İBG-HADYEK onayından sonra Genel Müdürlükten izin alınır.

ANESTEZİ VE ANESTEZİ UYGULANMASI, ÖLDÜRME VE DENEYLERDE ŞİDDET SINIFLANDIRMASI İLE İLGİLİ İŞLEMLER
Madde 10.

Anestezi ve anestezi uygulanması, öldürme ve deneylerde şiddet sınıflandırması ile ilgili işlemler Gıda, Tarım ve Hayvancılık Bakanlığınca 13/12/2011 tarihli ve 28141 sayılı Resmî Gazete’de yayımlanan Deneysel ve Diğer Bilimsel Amaçlar İçin Kullanılan Hayvanların Refah ve Korunmasına Dair Yönetmeliğin 21 inci ve 22 nci maddeleri ile Ek-8 ve Ek-9’a göre yapılır.

HAYVANLARIN DENEYLERDE TEKRAR KULLANIMI
Madde 11.

(1) Daha önce bir ya da birkaç deneyde kullanılan bir hayvanın tekrar kullanılmasına aşağıdaki durumlarda izin verilir:

  1. Daha önceki deneylerin gerçek şiddeti “hafif” veya “orta” ise.
  2. Hayvanın genel sağlık durumu tamamen eski haline dönmüşse.
  3. Yeni deney “hafif”, “orta” veya “ düzelmez” olarak sınıflandırılmışsa.
  4. Hayvan üzerinde daha önce gerçekleştirilen prosedürleri değerlendirebilecek bir veteriner hekim tarafından uygun bulunmuşsa.

(2) İstisnai durumlarda, (a) bendini uygulama dışı bırakacak şekilde ve hayvanın veteriner hekim tarafından muayene edilmesinden sonra, hayvanın şiddetli acı, ızdırap veya eşdeğerini içeren bir deneyde birden fazla kullanılmaması şartıyla bir hayvanın tekrar kullanılmasına izin verilebilir.

DENEYİN SONLANDIRILMASI
Madde 12.

(1) Deneyle ilgili olarak daha fazla gözlemin yapılamayacağı hallerde ya da genetiği değiştirilmiş hayvan soyları ve nesilleri artık takip edilmiyorsa veya sürekli devam eden bir şekilde iğne batırılmasına eşdeğer ya da daha fazla acı, eziyet, ızdırap ve kalıcı hasar yaşaması bekleniyorsa deney sonlandırılır.

(2) Deneyin sonunda, bir hayvanın yaşamaya devam etmesine dair karar bir veteriner hekim tarafından alınır. Bir hayvanın yaşatılmaya devam etmesi durumunda, sağlık durumuna uygun bakım ve barınma hizmeti sağlanır. Hayvan orta veya şiddetli acı, eziyet, ızdırap ve kalıcı hasar ile yaşamaya devam ediyorsa yaşamına son verilir.

PROJELERİN BAŞVURULARI
Madde 13.

İBG-HADYEK’e kabul edilecek projeler:

  1. Öncelik İBG’de olmak üzere, DEÜ’de görevli akademik personelin yapacağı her türlü deney hayvanı araştırma projeleri,
  2. Bir yöntem/model öğrenilmesi ve el alıştırması için yapılacak testler ve çalışmalar,
  3. İBG’nin bir merkez olarak katıldığı çok merkezli araştırma projeleri,
  4. Başka kurum ve kuruluşların araştırmacıların İBG Deney Hayvanları Ünitesinde yapacakları çalışmalar.

Kurula başvurular,  Türkçe ya da İngilizce “Deney Hayvanları Etik Kurulu Başvuru Formu” doldurularak İBG-HADYEK sekreterliğine yapılır. Başvuruların, tez çalışmalarında yürütücü sıfatıyla danışman öğretim üyesi, diğer araştırma projelerinde ise proje yürütücüsü tarafından yapılır. Üniversite dışından yapılacak başvurular ise proje yürütücüsünün kendi kurumundan alacağı resmi üst yazı ile yapılır.

BAŞVURU SAHİPLERİNİN SORUMLULUKLARI
Madde 14.

Kurula başvurularda kişisel beyan esastır, başvuranlar taahhüt formu imzalar.

  1. Başvuru formlarında verdikleri bilgilerin doğruluğunu kabul ederler.
  2. İBG-HADYEK onayı olmadan deneylere başlamayacaklarını taahhüt ederler.
  3. Deney hayvanlarında yapılacak işlemleri başvuru formunda belirtilen hususlara uygun şekilde yapmayı ve İBG-HADYEK’in çalışmalarını izlemek istemesi durumunda çalışma düzenlerini İBG-HADYEK üyelerine açmayı kabul etmiş olurlar. İBG-HADYEK onayından sonra araştırma projesinde yapılan değişiklikler İBG-HADYEK’e yazılı olarak bildirilmeli ve onay alınmalıdır.
  4. Başvuruların planlanan ilk toplantıda gündeme alınabilmesi için, ilan edilmiş toplantı gününden en az 5 (beş) iş günü öncesinde başvurunun yapılmış olması gerekmektir.
  5. Dokuz Eylül Üniversitesi personeli olmayanların Dokuz Eylül Üniversitesi’nde yapacakları çalışmalar için çalışmanın yapılacağı birimden alınmış izin belgesini başvuru belgelerine eklemeleri zorunludur.
  6. Başvuruların, tez çalışmalarında “Yürütücü” sıfatıyla “Danışman Öğretim Üyesi” tarafından, diğer araştırma projelerinde ise doktora veya eşdeğer dereceye sahip öğretim görevlisi/üyesi statüsündeki “Araştırma Yürütücüsü” tarafından yapılması gereklidir. Saha ya da klinik çalışmalar için yapılacak başvurulara, hayvan sahiplerinden alınmış olan izin belgelerinin eklenmesi zorunludur.

PROJE BAŞVURUSUNDA ARANACAK ÖZELLİKLER ve PROJE FORMATI
Madde 15.

(1)Araştırma projesi, yapılacak çalışmanın amacını, tasarımını, yöntemini, istatistiksel yönleri ve örgütlenmesini tanımlamalıdır.

Projeler bilimsel kriterlere uygun olarak 4-6 sayfayı geçmeyecek şekilde hazırlanır. Araştırma adı, türü (deneysel, ön çalışma, tez çalışması vb) araştırmacıların adı, görev yerleri, iletişim adresi ilk sayfada olmalıdır.

(2)Proje formatı
Başvuru formunun doldurulması:

Başlık sayfası: Proje ismi / Katılan araştırmacıların kurumu, görevi ve imzaları/ Araştırmanın Türü ve yürütücünün iletişim bilgileri/Anabilim Dalı vb.

Proje Başlığı: Projenin tamamını tanımlayan kısaltma ve jargonlardan uzak, kısa, açık ve bilimsel olamalıdır.

Proje Özeti: Amaç, materyal-metot,  tahmin edilen hasar ve faydalar ile kullanılan hayvanların tür ve soy özellikleri, projenin hedefleri, 3R ilkesine uygun olarak yazılmalıdır.

Giriş: Projenin yapılma gerekçesi ve ilgili literatür bilgileri ayrıntılı bir şekilde verilmelidir.  Literatürler      kullanım sırasına göre metin içinde yerleştirilmelidir.

Amaç: Projenin temel hipotezini yansıtan amacı net ve kısaca yazılmalıdır

Yöntem: Araştırma dizaynı, deney grupları ve oluşturulma gerekçesi, ilaç dozları, ilaçların veriliş yolu, ilaçların nereden temin edildiği, varsa literatürü, alınacak biyolojik örneklerin miktarı, örnekleme ve saklama şekli, yapılacak değerlendirme ve test yöntemlerinin literatür desteği ile ayrıntılı bir şekilde verilmesi, uygun istatistik yöntemin seçilmesi,  hayvanlar üzerinde yapılacak cerrahi prosedür, post-operatif bakım, laboratuar  bulguların değerlendirme yöntemlerinin kısaca açıklanması, hayvan temin edilen yer, hayvanların barındırılma şartları  ve deney yapılacak laboratuardan izin belgesi, deney  sonlandırma yöntemi, zamanı, kafesleme, gerekli malzeme ve gereçlerin  elde edildiği firmalar gibi detaylı teknik bilgi verilmelidir.

Projenin getireceği yenilikler:  Projenin literatüre getireceği yenilikler ve katkılar kısaca belirtilmelidir.

Kaynaklar: Kullanım sırasına göre metne yerleştirilerek ve proje sonunda Index Medicus formatına göre yazılmalıdır.

Hazırlanan projeler; proje yürütücüsünün  dilekçesi  ile İBG-HADYEK’e  başvurulur.

İlk başvuruda bulunması gerekenler:

  • 1 Adet Başvuru Dilekçesi,
  • 3 Adet İBG-HADYEK Etik Kurul Başvuru Formu (1 ıslak imzalı, 2 nüsha fotokopi)
  • 3 Adet Deney hayvanı Kullanımı Sertifikası ( Hayvan manüplasyonunu görevli araştırmacının)
  • 3 Adet İBG-HADYEK taahhütnamesi(1 ıslak imzalı, 2 nüsha fotokopi)
  • 1 Adet İBG-HADYEK Başvuru formunun elektronik  ortamda kaydedilmiş örneği
  • 3 Adet Projeye dayanak olan (hipotez, gereç ve yöntemi destekleyen) temel literatürlerin fotokopisi
  • Araştırma bütçesinde firma desteği sağlanacak ise çıkar- ilişki belgesi eklenmelidir.
  • İBG-HADYEK’e  BAŞVURU aşamasında;
    1. İlgili formlar/belgeler (EK-1, EK-2, EK-3) Enstitü web sayfasında yayınlanan “Hayvan Deneyleri Etik Kurul” sekmesinden temin edilir.
    2. İlgili formlar/belgeler eksiksiz olarak doldurularak İBG-HADYEK Sekretaryasına teslim edilir. Bu belgeler:
    3. Başvuru dilekçesi Örneği(EK-1)
    4. Taahhütname Örneği(1 ıslak imzalı, 2 nüsha fotokopi) (EK- 2)
    5. Proje Başvuru Formu üç nüsha (1 ıslak imzalı, 2 nüsha fotokopi) olmalıdır.
    6. Çıkar İlişkisi Belgesi Örneği (EK-3) eksiksiz olarak doldurulur.
    7. Araştırmayı destekleyen 3 adet literatür
    8. Proje Başvuru Formu ve ilgili eklerin yüklendiği CD
    9.   Deney hayvanı Kullanımı Sertifikası ( Hayvan manüplasyonunu görevli araştırmacının-3 Adet)

PROJELERİN DEĞERLENDİRİLMESİ ve KARAR VERİLMESİ
Madde 16.

(1) Projeler aşağıda belirtilen kriterlere göre değerlendirilir.

  1. Bilimsel, eğitim veya yasal gerekçeleri,
  2. Hayvan kullanımı gerekçeleri,
  3. Prosedürlerin mümkün olan en insani ve çevreye duyarlı şekilde gerçekleştirilmesi
  4. Tahmin edilen bilimsel faydaları ve eğitim yönünden değeri,
  5. 3R ilkesine uyumu,
  6. Prosedür şiddetinin sınıflandırılması,
  7. Elde edilecek fayda ve hayvanların çekeceği acı,
  8. Öldürme yöntemi, işlemler, anestezi, tekrar kullanım, bakım-barınma koşullarının mevzuata uygunluğu
  9. Geriye dönük değerlendirme yapılmasına ve zamanlamasına karar verilmesi,

(2) İBG-HADYEK tarafından proje değerlendirmesini yapacak kişilerin; 3R ilkesi, deney tasarımı, hayvan deneyleri veya hayvan bakım ve beslenmesi konusunda yetkin olmasına göre seçilmesine dikkat edilir.

(3) Proje değerlendirmesi şeffaf olmalıdır. Fikri mülkiyet haklarının ve gizli bilgilerin korunması için, proje değerlendirmesi tarafsız bir şekilde gerçekleştirilir.

(4) Uygun başvurular için İBG-HADYEK üyelerinden biri raportör olarak atanır. Raportör projeyi inceler ve toplantıda kurul üyelerine değerlendirmesini açıklar. Kurulda proje tartışılır. Kurul gerekli görürse, çalışmayı yapmak isteyen araştırmacıyı toplantıya çağırarak soruları ve açıklama gereken noktaları sorabilir.

(5) İBG-HADYEK, yaptığı değerlendirme sonucunda proje hakkında yapılması uygun, düzeltilmesi gerekir, koşullu olarak uygun, ya da yapılması uygun değildir şeklinde karar verir. Etik Kurul üyelerinin isimleri olan projelerde ilgili kurul üyesi oy kullanamaz.   Düzeltilmesi gerekir kararı verilen başvurular, başvuru sahibi tarafından düzeldikten sonra, Etik Kurulda tekrar değerlendirilir. Koşullu olarak uygun kararı verilen projeler Etik Kurul tarafından belirlenecek belli bir süre boyunca izlenip, istenen koşulların yerine getirilip getirilmediği değerlendirildikten sonra uygun ya da uygun değildir şeklinde karara bağlanır. İBG-HADYEK, deney hayvanlarında uygulama yapacak kişilerin ehil olup olmadıklarını da değerlendirebilir ve yeterli görmemesi halinde eğitim almaları için alanlarında deneyimli bir araştırıcıyla/uzmanla bir süre çalışmalarını isteyebilir.

(6) Etik Kurul onayları 5 yıl için verilir. Bu süre içinde onaylar geçerlidir. Bu süre içinde bitirilemeyen  projeler için ek süre talep edilebilir.

(7) Araştırma protokolünde, Etik Kurul onayından sonra yapılmak istenen değişikliklerin Etik Kurula yazılı olarak bildirilmesi ve onayının alınması zorunludur. Etik kurulun onayı alınmaksızın hiçbir protokol değişikliği uygulanamaz. Çalışmada etik kurulca onaylanmamış protokol değişikliklerinin uygulanması durumunda çalışma durdurulur.

(8) Dokuz Eylül Üniversitesi birimlerinde, Dokuz Eylül Üniversitesi İBG-HADYEK Yönergesi Madde 1’de yer alan etkinliklerle ilgili uygulama yapacak olan tüm araştırmacılar yazılı olarak başvurarak İBG-HADYEK onayı almak zorundadırlar.

(9) İBG-HADYEK Yönergesi Madde-1’de yer alan etkinliklerle ilgili araştırmalara ilişkin ulusal ya da uluslararası nitelikli her türlü bilimsel yayında “Etik Kurul Onayı Alınmıştır” veya “Etik Kurul İlkelerine Uyulmuştur” ifadesine yer verilmek zorundadır.

(10) Etik Kurula başvurulmadan İBG-HADYEK Yönergesi Madde- 1’de yer alan etkinliklerle ilgili araştırmalara ilişkin ulusal ya da uluslararası nitelikli her türlü bilimsel yayında yer alacak olan “Etik Kurul Onayı Alınmıştır” veya “Etik Kurul İlkelerine Uyulmuştur” beyanından doğabilecek etik sorunların tüm sorumluluğu, yayının yazar / yazarlarına aittir.

GERİYE DÖNÜK DEĞERLENDİRME
Madde 17.

(1) İBG-HADYEK’e bildirilen dokümanlara göre geriye dönük aşağıdaki hususlar değerlendirilir:

  1. Projenin amaçlarına ulaşılıp ulaşılamadığı.
  2. Kullanılan hayvan türlerinin sayısı, hayvanlara verilen zarar ve prosedürlerin şiddeti.
  3. 3R prensibinin uygulanmasına katkıda bulunabilecek unsurlar.

(2) İnsan dışı primatların kullanıldığı tüm projeler ve uzun süreli ve iyileştirilemeyen şiddetli ağrı, eziyet ve ızdırap içeren prosedürler de dahil “şiddetli” olarak sınıflandırılan prosedürleri içeren projeler geriye dönük değerlendirmeye tabi tutulur.

(3) İkinci fıkra hükümleri dışındaki projeler geriye dönük değerlendirmeden muaf tutulabilir.

DENEY HAYVANI İLE UĞRAŞACAK PERSONELİN EĞİTİMİ
Madde 18.

İBG-HADYEK, bu Yönergenin 7/c maddesi gereği deney hayvanı ile çalışılacak kişilerin ehil olup olmadıklarını belirler, T.C. Orman ve Su İşleri Bakanlığınca düzenlenen mevzuata uygun olarak ‘Deney Hayvanı Kullanım Sertifikası’ verir. Deney hayvanı kullanıcıları, sertifika almadan bu hayvanlar üzerinde deney, eğitim, test amacıyla işlem yapamaz ve çalışma mekanlarında bu hayvanları barındıramazlar. Kurulun onayına sunulan çalışmalarda deney hayvanı kullanan kişinin kullanım sertifikası bulunmaması halinde kurulca çalışmaya onay verilmez. “Deney Hayvanı Kullanım Sertifikası” almak için kurula başvuranların aşağıdaki şartları taşımaları gereklidir.

  1. Teorik ve uygulamalı derslerin işlendiği en az 80 saat süreli eğitim almış olmak,
  2. Alınan eğitime devamın zorunlu olduğunu ve eğitimin en az %80’ine devam ettiklerini kanıtlamak,
  3. Eğitimin sonunda bir sınava girip başarılı olduklarını (70/100 puan) belgelemek.

SON HÜKÜMLER
GİZLİLİK
Madde 19.

Etik Kurul yazışmaları gizli olup, ilgili mevzuat ve Hayvan Deneyleri Etik Kurullarının Çalışma Usul ve Esaslarına Dair Yönetmelik’te belirtilen yetkili kurumlar dışında üçüncü şahıslara bilgi verilemez.

YÜRÜRLÜK
Madde 20.

Bu Yönerge, Dokuz Eylül Üniversitesi Senatosu Kararı ile kabul edildikten sonra Hayvan Deneyleri Merkezi Etik Kurulu’na sunulur ve bu Kurul tarafından onaylandığı tarihten itibaren yürürlüğe girer.

YÜRÜTME
Madde 21.

Bu Yönerge hükümleri DEÜ Rektörü tarafından yürütülür.

 


 

ANA SAYFA YÖNERGE ÇALIŞMA İZNİ ÖN TALEP FORMU BAŞVURU FORMU ÜYELER İLETİŞİM

Etik Kurul Onayı almak için başvuracak araştırıcıların projelerini, sisteme yükledikten sonra iBG-izmir Hayvan Deneyleri Etik Kurulu Sekreterliği’ne teslim etmeleri gerekmektedir.

İBG-HADYEK 2017 Toplantı Takvimini görmek için tıklayın.

Lütfen aşağıdaki başvuru koşulları bölümünü okuduktan sonra Başvuru Formunu ve Taahhütnameyi doldurunuz.

Başvuru Koşulları
Kurulumuza müracaat edenlerin hazırlayacakları Başvuru Belgeleri şunlardır:
1- Onaylanmış Deneysel Çalışma İzni Ön Talep Formu
2- Başvuru Formu, Form sonundaki taahhütname tüm araştırıcılar tarafından imzalanacak.
3- Çıkar İlişkisi Belgesi (tüm araştırıcılar tarafından imzalanacak)
4- Araştırıcılardan birinin özgeçmişi ve Deney Hayvanı Kullanım Sertifikası
5- Konuyla ilgili en az 3 en fazla 7 tane literatür.

Başvuru dökümanlarına aşağıdan ulaşabilirsiniz.

Başvuru Formu Taahhütname Çıkar ilişkisi belgesi Başvuru Dilekçesi

Doldurmuş olduğunuz dökümanları sisteme yüklemek için lütfen tıklayınız.


 

ANA SAYFA YÖNERGE ÇALIŞMA İZNİ ÖN TALEP FORMU BAŞVURU FORMU ÜYELER İLETİŞİM

iBG-HADYEK, iBG-izmir’de gerçekleştirilecek hayvan deneyi içerikli tüm deneysel, test ve eğitim amaçlı araştırmalar ve deney hayvanlarının üretim, bakım, barındırma ve nakledilme ile ilgili tüm süreçlerin etik olarak gözden geçirilmesi ve araştırma önerilerini incelemek üzere kurulmuştur.

iBG-HADYEK Toplantı Takvimi

iBG-HADYEK başvuru süreci aşağıdaki gibidir.


 

Dr. Ciğdem Özen
Molecular Biologist
cigdem.ozen@deu.edu.tr

 

  • List of critical equipments for USP
    • 3L, 5L, 10L glass bioreactors and 50L wave bioreactor
    • Biosafety cabinet class II
    • Cell culture CO2 incubators
    • Shaker CO2 incubator
    • Osmometer
    • Metabolic analyser
    • Cell counter
  • List of critical equipments for DSP
    • TFF system
    • AKTA system
    • Viral filtration system

 

  • Upstream Process Development (USP)
    • Mammalian cell culture process development for production of monoclonal antibodies and recombinant protein
    • Clone Selection based on the productivity and quality
    • Single cell selection
    • Cell line adaptation (Serum free or suspension)
    • Master cell bank (MCB) & working cell bank (WCB) generation
    • Media development (chemically defined)
    • Development of nutrients & feed strategy to increase culture growth and productivity (animal component free)
    • Scale up studies
    • Development of key aspects of monitoring & control technology
    • Scale down model for process characterization
    • Design of experiments (DOE) for optimization
    • Process Analytical Technology (PAT) Development
    • Production at pilot scale for preclinical and early clinical stage studies
    • Transfer technology and support
  • Downstream Process Development (DSP)
    • Development of recombinant therapeutic proteins and monoclonal antibody purification process
    • Prefiltration process development (right pre filtration selection to reduce the bioburden)
    • Chromatographic separation
    • Ultrafiltration and diafiltration development
    • Virus clearance studies
    • Scale down model for process characterization
  • cGMP Manufacturing service
    • iBG-Izmir will provide service to biotech industries for the production of recombinant proteins in bulk for their clinical trials and commercial use. Initially we will be able to provide up to 200L production capacity and in later phase up to 1000L. GMP facility is under construction will be ready to provide service in 2017

 

Core Manager

iBG-Izmir biopharmaceuticals unit has the caliber to provide service to the biotech industries for complete upstream and downstream process development including cell line development. We have perfect team of scientist with industrial and academic back ground with the capability to deliver and execute to meet the defined product quality.

We provide the following services below for biotech industries. If you are looking for the recombinant protein or biosimilar product development and/or for small scale manufacturing for preclinical studies please contact us we will be happy to help you.


Bilimsel Yayınlar

Brian I. Carr, Hikmet Akkiz, Oguz Uskudar, et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464.

Serhat Tozburun, Cedric Blatter, Meena Siddiqui, Eelco F. J. Meijer, and Benjamin J. Vakoc. Phase-stable Doppler OCT at 19 MHz using a stretched-pulse mode-locked laser. Biomedical Optics Express 2018; 9(3): 952-961. doi: 10.1364/BOE.9.000952.

Meena Siddiqui, Ahhyun S. Nam, Serhat Tozburun*, Norman Lippok, Cedric Blatter & Benjamin J. Vakoc. High-speed optical coherence tomography by circular interferometric ranging. Nature Photonics 2018 Jan 26; 12: 111–116. doi: 10.1038/s41566-017-0088-x.

Brian I. Carr, Hikmet Akkiz, Oguz Üsküdar et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464. doi: 10.4172/clinical-practice.1000393.

Sag D, Özkan M, Kronenberg M, Wingender G. Improved Detection of Cytokines Produced by Invariant NKT Cells. Sci Rep 2017 Nov 30; 7(1):16607. doi: 10.1038/s41598-017-16832-1.

U. Blache, J. Guerrero, S. Güven, A.S. Klar, A. Scherberich. Microvascular Networks and Models, In vitro Formation, in: W. Holnthoner, A. Banfi, J. Kirkpatrick, H. Redl (Eds.),. Vascularization for Tissue Engineering and Regenerative Medicine. Springer International Publishing Cham, 2017, pp. 1-40.

Cigdem Ozen, Meltem Ceylan Unlusoy, Nazanin Aliary, Mehmet Ozturk, Oya Bozdag Dundar. Thiazolidinedione or Rhodanine: A Study on Synthesis and Anticancer Activity Comparison of Novel Thiazole Derivatives. J Pharm Pharm Sci 2017 Nov; 20 (1): 415-427. doi:10.18433/J38P9R.

Gökhan Karakülah. RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes. Genomics 2017 Nov; 17. doi:10.1016/j.ygeno.2017.11.002.

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Oct 31;32(4):e391-e396. doi:10.5301/ijbm.5000300.

Refolo MG, D’Alessandro R, Lippolis C, Carella N, Cavallini A, Messa C, Carr BI. IGF-1R tyrosine kinase inhibitors and Vitamin K1 enhance the antitumor effects of Regorafenib in HCC cell lines. Oncotarget 2017 Sep 30; 8(61):103465-103476. doi:10.18632/oncotarget.21403.

Onur Tokel, Ahmet Turnalı, Ghaith Makey, et al. In-chip microstructures and photonic devices fabricated by nonlinear laser lithography deep inside silicon. Nature Photonics 2017 Sep; 11: 639–645. doi:10.1038/s41566-017-0004-4.

Ozen C, Ceylan-Unlusoy M, Ozturk M, Bozdag-Dundar O. A novel chromonyl thiohydantoin with anti-proliferative action on primary hepatocellular carcinoma cells. Med Chem Res 2017 Sep; 1-8. doi:10.1007/s00044-017-2037-0.

Yuqing Zhu, Vahid Serpooshan, Sean Wu, Utkan Demirci, Pu Chen, Sinan Güven. Tissue Engineering of 3D Organotypic Microtissues by Acoustic Assembly. In: Methods in Molecular Biology. Humana Press 2017 Sep; 1-12. doi: 10.1007/7651_2017_68.

Lina Zelinger, Gökhan Karakülah*, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew J. Brooks, Anand Swaroop. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Investigative Ophthalmology & Visual Science 2017 Sep; 58: 4422-4435. doi: 10.1167/iovs.17-21805.

Ozturk M, Batur T, Ekin U, Erdogan A, İscan E, Keles U, Oz O, Ozen C. Molecular Pathogenesis of Liver Cancer. J Gastrointest Cancer. 2017 Jul 17 (Review). doi: 10.1007/s12029-017-9957-2. [Epub ahead of print].

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Aug 28. doi: 10.5301/ijbm.5000300.

Ors A, Papin C, Favier B, Roulland Y, Dalkara D, Ozturk M, Hamiche A, Dimitrov S, Padmanabhan K. Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts. Biochem Cell Biol 2017 Aug; 95(4):491-499. doi: 10.1139/bcb-2016-0190.

Yılmaz Y, Güneş A, Topel H, Atabey N. Signaling Pathways as Potential Therapeutic Targets in Hepatocarcinogenesis. J Gastrointest Cancer 2017 Aug 18. doi: 10.1007/s12029-017-9958-1.

Carr BI, Guerra V. Validation of a Liver Index and Its Significance for HCC Aggressiveness. J Gastrointest Cancer 2017 Jun 20. doi: 10.1007/s12029-017-9971-4.

Ezgi Karaca*, João P.G.L.M. Rodrigues, Andrea Graziadei, Alexandre M.J.J. Bonvin, Teresa Carlomagno. M3: an integrative framework for structure determination of molecular machines. Nature Methods 2017. doi: 10.1038 / nmeth.4392.

Alural B, Ayyildiz ZO, Tufekci KU, Genc S, Genc K. Erythropoietin Promotes Glioblastoma via miR-451 Suppression. Vitam Horm. 2017;105:249-271. doi: 10.1016/bs.vh.2017.03.002. Epub 2017 Apr 19. PubMed PMID: 28629521.

Gökhan Karakülah. Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. Journal of Integrative Bioinformatics. 2017 (in press), doi: 10.1515/jib-2017-0009.

Sezgin E, Azbazdar Y, Ng XW, Teh C, Simons K, Weidinger G, Wohland T, Eggeling C, Ozhan G. Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments. FEBS J. 2017 Aug; 284(15): 2513-2526. doi: 10.1111/febs.14139.

Akyerli C., Yuksel S., Can O., Erson-Omay Z., Oktay Y.*, Cosgun E., Ulgen E., Erdemgil Y., San A., von Deimling A., Gunel M., Yakicier C., Pamir M.N., Ozduman K. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas. Journal of Neurosurgery. 2017 Jun; 16:1-13. doi: 10.3171/2016.11.

Schneider F, Waithe D, Clausen MP, Galiani S, Koller T, Ozhan G, Eggeling C, Sezgin E. Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS. Mol Biol Cell. 2017 Jun 1;28(11): 1507-1518. doi: 10.1091/mbc.E16-07-0536.

Oktay Y., Boylu C.A., Özduman K. Gliom Gelişiminde Genetik Yatkınlığın Rolü. Türk Nöroşirürji Dergisi. 2017 May; 27(2): 122-130.

Gökhan Karakülah, Aslı Suner. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics. 2017 (in press), doi:10.1016/j.ygeno.2017.05.008.

Bağırsakçı E., Şahin E., Atabey N., Erdal E. & Carr B.I. Role of Albumin in growth inhibition in Hepatocellular Carcinoma. Oncology. 2017 May 10. doi:10.1159/000471807.

Gümürdü A., Yildiz R., Eren E., Karakülah G., Ünver T., Genç Ş. & Park Y. MicroRNA exocytosis by large dense-core vesicle fusion. Scientific Reports. 2017 Mar 30; 7:45661. doi:10.1038/srep45661.

Marino IR, Carr B.I. New Developments in Orthotopic Liver Transplant for Hepatocellular Carcinoma. Exp Clin Transplant. 2017 Mar;15(Suppl 2):1-6.

Alural B, Genc S, Haggarty S. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biology Psychiatry. 2017 Feb; 6;73:87-103 doi: 10.1016/j.pnpbp.2016.03.010. Epub 2016 Apr 9. PubMed PMID: 27072377; PubMed Central PMCID: PMC5292013.

Pinato D., Sharma R., Allara E., Yen C., Arizumi T., Kubota K., Bettinger D., Jang J.W., Smirne C., Kim Y.W., Kudo M., Howell J., Ramaswami R., Burlone M.E., Guerra V., Thimme R., Ishizuka M., Stebbing J., Pirisi M. & Carr B.I. The ALBI grade provides objective hepatic reserve estimation across each BCLC stage of hepatocellular carcinoma. J. Hepatology, 2017 Feb; 66(2): 338-346. doi:http://dx.doi.org/10.1016/j.jhep.2016.09.008.

van Waalwijk van Doorn LJ, Gispert JD, Kuiperij HB, et al. Improved Cerebrospinal Fluid-Based Discrimination between Alzheimer’s Disease Patients and Controls after Correction for Ventricular Volumes. J Alzheimers Dis. 2017 Jan 24; 56(2):543-555. doi: 10.3233/JAD-160668

Park CG, Park Y & Suh BC. The HOOK region of voltage-gated Ca2+ channel β subunits senses and transmits PIP2 signals to the gate. J Gen Physiol. 2017 Jan 13. doi:10.1085/jgp.201611677.

Arslan N, Guzel O, Kose E, Yılmaz U, Kuyum P, Aksoy B, Çalık T. Is ketogenic diet treatment hepatotoxic for children with intractable epilepsy? Seizure. 2016 Dec; 43: 32-38. doi:10.1016/j.seizure.2016.10.024.

Ebru Diler, Turgay Unver & Gökhan Karakülah. Differential Expression of Hyperhydricity Responsive Peach miRNAs. Journal of Integrative Bioinformatics. 2016 Dec; 13(5): 308. doi:10.2390/biecoll-jib-2016-308.

İşcan E, Güneş A, Korhan P, Yılmaz Y, Erdal E, Atabey N. The regulatory role of heparin on c-Met signaling in hepatocellular carcinoma cells. J Cell Commun Signal. 2016 Dec 14; 1-12. doi:10.1007/s12079-016-0368-0.

Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Unver. PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs). PLoS ONE. 2016 Dec 9; 11(12): e0167698. doi:10.1371/journal.pone.0167698.

Calibasi Kocal G, Güven S, Foygel K, Goldman A, Chen P, Sengupta S, Paulmurugan R, Baskin Y, Demirci U. Dynamic Microenvironment Induces Phenotypic Plasticity of Esophageal Cancer Cells Under Flow. Sci Rep. 2016 Dec 2; 6:38221. doi: 10.1038/srep38221.

Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah*, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker, Ashley Walton, Rafael Villasmil, Jennifer Joanna Barb, Peter Jonathan Munson, Koray Dogan Kaya, Vijender Chaitankar, Tiziana Cogliati, Anand Swaroop. NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. Cell Reports. 2016 Nov 22; 17(9): 2460-2473. doi:http://dx.doi.org/10.1016/j.celrep.2016.10.074.

Arslan N, Kose E, Guzel O. The Effect of Ketogenic Diet on Serum Selenium Levels in Patients with Intractable Epilepsy. Biol Trace Elem Res. 2016 Nov 21. doi:10.1007/s12011-016-0897-7.

Erbayraktar Z, Alural B, Erbayraktar RS, Erkan EP. Cell division cycle 7-kinase inhibitor PHA-767491 hydrochloride suppresses glioblastoma growth and invasiveness. Cancer Cell Int. 2016 Nov 18;16:88. eCollection 2016. doi:10.1186/s12935-016-0364-8.

Muhammad Ayaz Mustufa, Cigdem Ozen, Imran Ali Hashmi, Afshan Aslam, Jameel Ahmed Baig, Gokhan Yildiz, Shoaib Muhammad, Imam Bakhsh Solangi, Naim ul Hasan Naqvi, Mehmet Ozturk and Firdous Imran Ali. Synthesis and bio-molecular study of (+)-N-Acetyl-α-amino acid dehydroabietylamine derivative for the selective therapy of hepatocellular carcinoma. BMC Cancer. 2016, Nov 14; 16: 883. doi:10.1186/s12885-016-2942-5.

Büyüköz M, Erdal E, Alsoy Altinkaya S. Nanofibrous gelatin scaffolds integrated with NGF-loaded alginate microspheres for brain tissue engineering. J Tissue Eng Regen Med. 2016 Nov 12. doi: 10.1002/term.2353.

Jeannot V, Busser B, Vanwonterghem L, Michallet S, Ferroudj S, Cokol M, Coll JL, Ozturk M, Hurbin A. Synergistic activity of vorinostat combined with gefitinib but not with sorafenib in mutant KRAS human non-small cell lung cancers and hepatocarcinoma. OncoTargets and Terapy. 2016, Nov 9; 9: 6843—6855. doi:10.2147/OTT.S117743.

Carr B.I., Guerra V., Giannini E.G. et al. A Liver Index and its Relationship to Indices of HCC Aggressiveness. J Integr Oncol. 2016 Oct;5(4). pii: 178. doi: 10.4172/2329-6771.1000178.

Erkan D, Kayali HA. Replacement of Soybean Meal with Animal Origin Protein Meals Improved Ramoplanin A2 Production by Actinoplanes sp. ATCC 33076. Appl Biochem Biotechnol. 2016 Sep;180(2):306-21. doi:10.1007/s12010-016-2100-1.

Hani Alotaibi, Nese Atabey, Kasım Diril, Esra Erdal, Mehmet Ozturk. Molecular Mechanisms of Hepatocellular Carcinoma, Chapter Hepatocellular Carcinoma Part of the series Current Clinical Oncology. Springer. 2016, Aug 27; 43-63. doi:10.1007/978-3-319-34214-6_3.

Alagoz Y., Gurkok T.,  Zhang B. & Unver T. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology. Sci Rep. 2016 Aug 3; 6:30910. doi: 10.1038/srep30910.

Bakır Y., Eldem V., Zararsız G. & Unver T. Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves. Plant Genome. 2016 Jul; 9(2). doi:10.3835/plantgenome2015.09.0080.

Marsano A, Medeiros da Cunha CM, Ghanaati S, Gueven S, Centola M, Tsaryk R, Barbeck M, Stuedle C, Barbero A, Helmrich U, Schaeren S, Kirkpatrick JC, Banfi A, Martin I. Spontaneous In Vivo Chondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells by Blocking Vascular Endothelial Growth Factor Signaling. Stem Cells Transl Med. 2016 Jul 26. doi: 10.5966/sctm.2015-0321.

Pavlopoulou A., Oktay Y., Vougas K., Louka M., Vorgias C.E., Georgakilas A.G. Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. Cancer Letters, 2016, Jul 19; 380(2):485-493. doi: 10.1016/j.canlet.2016.07.018.

Carr B.I., Guerra V., Giannini E.O. et al. An HCC Aggressiveness Index and Blood GTP, Blirubin and Platelet Levels. J. Integrative Oncology. 2016 Jun 20; 5:172. doi: 10.4172/2329-6771.1000172.

Oktay Y., Ülgen E., Can Ö., Akyerli C.B., Yüksel Ş., Erdemgil Y., Durası I.M., Henegariu O.I., Nanni E.P., Selevsek N., Grossmann J., Erson-Omay E.Z., Bai H., Gupta M., Lee W., Turcan Ş., Özpınar A., Huse J.T., Sav M.A., Flanagan A., Günel M., Sezerman O.U., Yakıcıer M.C., Pamir M.N. & Özduman K. IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation. Sci Rep. 2016 Jun 10; 6: 27569. doi: 10.1038/srep27569.

Yilmaz Y, Atabey N, Erdal E & Brian I. Carr. Platelets, Microenvironment and Hepatocellular Carcinoma. Biochemistry & Analytical Biochemistry, 2016 June 29; 5:281 (Review). doi:10.4172/2161-1009.1000281.

Antonio Mazzoccaa, Giovanni Ferrarob, Giovanni Misciagnac, Brian I. Carr. A systemic evolutionary approach to cancer: Hepatocarcinogenesis as a paradigm. Medical Hypotheses, 2016, Aug; 93: 132-137. doi:10.1016/j.mehy.2016.05.027.

Karakülah G, Karakuş M, Suner A, Demir S, Arserim SK, Töz S, Özbel Y. sandflyDST: a dynamic web-based decision support tool for the morphological identification of sandflies present in Anatolia and mainland Europe, and user study. Medical and Veterinary Entomology, 2016 June 24. doi:10.1111/mve.12182.

Can Küçük, Xiaozhou Hu, Qiang Gong, Bei Jiang, Adam Cornish, Philippe Gaulard, Timothy McKeithan, Wing C. Chan. Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma. The American Journal of Pathology, 2016 June; 186(6): 1435-1441. doi:10.1016/j.ajpath.2016.02.011.

Zeynep Firtina Karagonlar, Doğukan Koç, Eren Şahin, Sanem Tercan Avci, Mustafa Yilmaz, Neşe Atabey, Esra Erdal. Effect of adipocyte-secreted factors on EpCAM+/CD133+ hepatic stem cell population. Biochemical and Biophysical Research Communications, 2016 June 3; 474(3): 482-490. doi:10.1016/j.bbrc.2016.04.137.

Yakup Bakır, Vahap Eldem, Gökmen Zararsız, Turgay Unver. Global Transcriptome Analysis Reveals Significant Differences in Gene Expression Patterns Between The Non-Hyperhydric and Hyperhydric Leaves of Prunus persica. The Plant Genome, 2016, May; 9(2): 1-9.

Salimi R, Yener N, Safari R. Use and Evaluation of Newly Synthesized Fluorescence Probes to Detect Generated OH• Radicals in Fibroblast Cells. J Fluoresc. 2016 May; 26(3):919-24. doi: 10.1007/s10895-016-1780-9.

Firtina Karagonlar Z, Koc D, Iscan E, Erdal E, Atabey N. Elevated hepatocyte growth factor expression as an autocrine c‐Met activation mechanism in acquired resistance to sorafenib in hepatocellular carcinoma cells. Cancer Sci. 2016 Apr; 107(4):407-416 doi: 10.1111/cas.12891.

Carr BI & Guerra V. A Hepatocellular Carcinoma Aggressiveness Index and Its Relationship to Liver Enzyme Levels. Oncology 2016 Mar 15; 90(4). doi: 10.1159/000444394.

Gao LM, Zhao S, Liu WP, Zhang WY, Li GD, Küçük C, Hu XZ, Chan WC, Tang Y, Ding WS, Yan JQ, Yao WQ, Wang JC. Clinicopathologic Characterization of Aggressive Natural Killer Cell Leukemia Involving Different Tissue Sites. Am J Surg Pathol, 2016 Mar 11. doi: 10.1097/PAS.0000000000000634.

Carr BI & Guerra V. Low Alpha-Fetoprotein Levels Are Associated with Improved Survival in Hepatocellular Carcinoma Patients with Portal Vein Thrombosis. Digestive Diseases and Sciences, 2016 Feb 26; 61(3):937-947. doi: 10.1007/s10620-015-3922-3.

Ferroudj S, Yildiz G, Bouras M, Iscan E, Ekin U, Ozturk M. Role of fanconi anemia/BRCA pathway genes in hepatocellular carcinoma chemoresistance. Hepatol Res. 2016 Feb 16. doi: 10.1111/hepr.12675.

Carr BI & Guerra V. Hepatocellular Carcinoma Extrahepatic Metastasis in Relation to Tumor size and Alkaline Phosphatase Levels. Oncology 2016 Feb 12; 90(3):1-7. doi: 10.1159/000443480.

Durmaz I, Guven EB, Ersahin T, Ozturk M, Calis I, Cetin-Atalay R. Liver cancer cells are sensitive to Lanatoside C induced cell death independent of their PTEN status. Phytomedicine. 2016 Jan 15; 23(1):42-51. doi: 10.1016/j.phymed.2015.11.012.

Wingender G. From the deep sea to everywhere? Environmental antigens for iNKT cells. Arch Immunol Ther Exp, 2015 Dec 24 (Review). doi: 10.1007/s00005-015-0381-7.

Güzel O, Yılmaz U, Uysal U, Arslan N. The effect of olive oil-based ketogenic diet on serum lipid levels in epileptic children. Neurol Sci. 2015 Dec 23; 1-6. doi: 10.1007/s10072-015-2436-2.

Namkoong B, Guven S, Ramesan S, Liaudanskaya V, Abzhanov A, Demirci U. Recapitulating cranial osteogenesis with neural crest cells in 3-D microenvironments. Acta Biomaterialia, 2015 Dec 07. doi: 10.1016/j.actbio.2015.12.004.

Hanna RN, Cekic C, Sag D, Tacke R, Thomas GD, Nowyhed H, Herrley E, Rasquinha N, McArdle S, Wu R, Peluso E, Metzger D, Ichinose H, Shaked I, Chodaczek G, Biswas SK, Hedrick CC. Patrolling Monocytes Control Tumor Metastasis to the Lung. Science. 2015, Nov 20; 350(6263): 985-90.

Wingender G & Kronenberg M. Characterization of human T cell subsets via surface markers. Cytometry A, 2015, Oct 27; 87A; 1067-1069.

D’Alessandro R, Messa C, Refolo MG, Carr BI. Modulation of sensitivity and resistance to multikinase inhibitors by microenvironmental platelet factors in HCC. Expert Opinion on Pharmacotherapy. 2015 Oct 19; 16(18):1-8. doi: 10.1517/14656566.2015.1101065.

Wingender G, Sag D, Kronenberg M. NKT10 cells: a novel iNKT cell subset. Oncotarget. 2015 Sept 29; 6(29): 26552-26553 (Review). doi: 10.18632/oncotarget.5270.

Wingender G, Birkholz A, Sag D, Farber E, Chitale S, Howell AR, Kronenberg M. Selective conditions are required for the induction of iNKT cell hypo-responsiveness by antigenic stimulation. The Journal of Immunology. 2015 Sept 9; 195: 3838-3848. doi: 10.4049/jimmunol.1500203.

Lippolis C, Refolo MG, D’Alessandro R, Carella N, Messa C, Cavallini A, Carr BI. Resistance to multikinase inhibitor actions mediated by insulin like growth factor-1. Journal of Experimental & Clinical Cancer Research. 2015 Sept 2; 34(1):90. doi: 10.1186/s13046-015-0210-1.

Pančoška P, Skála L, Nešetřil J, Carr BI. Validation of the Concept of a Common Typical Time of Disease Duration for Hepatocellular Carcinoma Patients Using the Fisher Information Processing of Tumor Imaging Results Combined With Network Phenotyping Strategy Quantification of Individual Patient Clinical Profile Patterns. Seminars in Oncology. 2015 Aug; 42(4):672-678. doi: 10.1053/j.seminoncol.2015.05.004.

Gunes A, Iscan E, Topel H, Avci ST, Gumustekin M, Erdal E, Atabey N. Heparin treatment increases thioredoxin interacting protein expression in hepatocellular carcinoma cells. The International Journal of Biochemistry & Cell Biology. 2015 Aug; 65:169-181. doi: 10.1016/j.biocel.2015.05.025.

Hu X, Chan WC, Kücük C. Generation of a genetically engineered aggressive nk-cell leukemia cell line with stable IL2 expression. Acta Medica International. 2015 Jul; 2(2):78-84. doi: 10.5530/ami.2015.3.6.

Ozhan G and Weidinger G. Wnt/β-catenin signaling in heart regeneration. Cell Regen (Lond). 2015 Jul 8; 4(1):3. doi: 10.1186/s13619-015-0017-8

Alotaibi H, Basilicata MF, Shehwana H, Kosowan T, Schreck I, Braeutigam C, Konu O, Brabletz T, Stemmler MP. Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms. 2015 June; 1849(6):731-742. doi: 10.1016/j.bbagrm.2015.01.005.

Alural B, Ozerdem A, Allmer J, Genc K, Genc S. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Front Cell Neurosci. 2015 May 28; 9:209. doi: 10.3389/fncel.2015.00209.

Dilek Cevik, Gokhan Yıldız & Mehmet Ozturk. Common telomerase reverse transcriptase promoter mutations in hepatocellular carcinomas from different geographical locations. World J Gastroenterol. 2015 Jan 7; 21(1): 311–317. doi: 10.3748/wjg.v21.i1.311.

Alural B, Duran GA, Tufekci KU, Allmer J, Onkal Z, Tunali D, Genc K, Genc S. EPO Mediates Neurotrophic, Neuroprotective, Anti-Oxidant, and Anti-Apoptotic Effects via Downregulation of miR-451 and miR-885-5p in SH-SY5Y Neuron-Like Cells. Frontiers in Immunology. 2014 Sep 30; 5:475. doi: 10.3389/fimmu.2014.00475.

* Current address IBG.


TBMM’de 16/02/2015 yılında kabul edilen 9 Mart 2015 tarih ve 29290 sayılı T.C. Resmi Gazete’ de yayımlanan 2015/7321 karar sayısıyla, Dokuz Eylül Üniversitesi Rektörlüğü bünyesinde yer alan Hemodiyaliz-Transplantasyon Enstitüsünün adının, İzmir Uluslararası Biyotıp ve Genom Enstitüsü olarak değiştirilmesi kararlaştırılarak, enstitümüz eğitim-öğretim faaliyetlerine başlamıştır. Enstitümüze ilk öğrenci alımı 2016-2017 eğitim öğretim yılında yapılmıştır.

Enstitümüz bünyesinde Genom Bilimleri ve Biyoteknoloji Anabilimdalı kurulmuş olup eğitim faaliyetlerine başlamıştır. Yüksek lisans ve Doktora öğrencileri bu anabilim dalında eğitim görmektedir. Anabilimdalı bünyesinde görevli enstitüsü kadrosunda bulunan 1 doçent, 3 doktor öğretim üyesi bulunmaktadır. Bu öğretim üyelerimiz akademik faaliyetlerimizi üniversitemizin diğer akademik birimlerinden görevlendirme yapılarak eğitim öğretim faaliyetlerimizi yürütmektedir. Enstitümüz kuruluşunda açılan Biyotıp ve Sağlık Teknolojileri anabilimdalımız eğitim faaliyetlerine henüz başlamamıştır.

16/02/2015 yılında kurulan İzmir Uluslararası Biyotıp ve Genom Enstitüsünde Genom Bilimleri ve Moleküler Biyoteknoloji Anabilim Dalına bağlı Moleküler Biyoloji ve Genetik Yüksek Lisans ve Doktora Programları ile öğretime başlamıştır.

07/04/2015 tarihli 439 toplantı sayı numaralı senato kararı ve 28/04/2015 tarihli YÖK Kurul kararı ile “Genom Bilimleri ve Moleküler Biyoteknoloji Anabilim Dalı” ile “Biyotıp ve Sağlık Teknolojileri Anabilim Dalı” kurulmuştur. Enstititümüz ilk kuruluş aşamasında İzmir Biyotıp ve Genom Merkezi bünyesinde Şubat 2018 tarihine kadar faaliyet göstermiş bu tarihten sonra merkez ve enstitü faaliyetlerini ayrı olarak devam etmektedir.

Enstitümüz kuruluş aşamasındaki üniversite rektörümüz sayın Prof. Dr. Mehmet Füzün, kurucu müdürümüz sayın Prof.Dr. Mehmet Öztürk, Bilim Sanayi ve Teknoloji Bakanı Fikri Işık, İzmir Valisi Mustafa Toprak, Nobel ödülü sahibi Sir Tim Hunt’ın yanı sıra  çok sayıda yerli ve yabancı bilim insanının katılımıyla açılmıştır.

Enstititümüz ilk kuruluş aşamasında İzmir Biyotıp ve Genom Merkeziyle birlikte aynı bina içerisinde faaliyetlerine başlamıştır ve şuan faaliyetlerini aynı binada devam ettirmektedir.


 


Professor Brian Carr was born in Glasgow, Scotland in 1944 and grew up in London.

He graduated medical school at the University of London in 1967 and worked for several years in medicine and then in medical oncology. He realized that medical oncology was confusing and mainly witchcraft and decided to learn how to do research and was apprenticed at the Imperial Cancer Research Labs, London with Renato Dulbecco. After his molecular biology PhD (5′-mRNA capped ends) he moved after his advisor’s Nobel Prize with him to the USA.

He then repeated a solid tumor clinical Fellowship and simultaneous Post-Doc in chemical hepatocarcinogenesis at the McArdle Labs, Madison, WI. His first staff job was for 10 yr at the City of Hope, LA, first as Assistant and then as Associate Professor of Medicine, continuing to work on rodent hepatocarcinogenesis, with special interest in natural growth inhibitors (TGF beta).

He was then invited to set up the first liver cancer (HCC) group within the Liver Transplant Institute in Pittsburgh and was appointed as full Professor with tenure and worked there for 20 yr, both running the clinical HCC service and his lab working on HCC growth regulation.

His clinical interests have been for a long time in developing new HCC therapies, focussing initially on hepatic chemoembolization and subsequently on Yttrium-90 bead hepatic internal radioembolization and more recently on vitamin K as HCC therapy. Currently, he is analyzing HCC databases involving several thousand patients, to identify HCC phenotypes with differing clinical parameter patterns and prognoses. The main findings are that context is key, and that any given parameter (such as serum bilirubin or tumor mass) can only be understood in its total clinical context.

Scientifically, he spent several yr working on K vitamins, since their aberrant use is a key biochemical characteristic of HCC and helps identify one of the most important HCC tumor markers, DCP or des-gamma-carboxy prothrombin. DCP positive and AFP positive tumor cells have quite different regulation, just as AFP positive and AFP negative HCCs have differing phenotypes and prognosis. Vitamin K1 mediates inhibitory phosphorylation of Raf via PKC. Sorafenib is an FDA-approved HCC multikinase inhibitor working through direct Raf inhibition. Thus, vitamin K enhances Sorafenib-mediated Raf inhibition and thus enhances the HCC cell growth inhibition.

The clinical observations of HCC context, have led to the recent observations that blood platelet levels identify phenotypically different HCC patient subsets. This has been developed further by recently examining the actions of platelet lysates as promoters of HCC growth and invasion. This has been shown to be due in large part to platelet content of epidermal growth factor (EGF) and insulin-like growth factor 1 (IGF-1). These factors also modulate HCC growth sensitivity and resistance to multikinase inhibitors. Therefore, the net effect of these therapies depends in part on the tumor (HCC) microenvironment. Thus, clinical observations led to experimental mechanistic observations, that in turn have led to clinical application: translational work.
He has published 296 papers-mainly on HCC and 4 books, 3 of which are on HCC and one on Psychological Aspects of Cancer and has written the chapter on Liver Tumors for the last 3 editions of: Harrison’s Principles of Internal Medicine (19th edition, April 2015).

Contact Information: brianicarr@hotmail.com


The institute started its educational activities after the name of the Hemodialysis-Transplantation Institute founded in accordance with the decision published in the Official Gazette with the number of 2015/7321 on 09/03/2015 is changed into İzmir International Biomedicine and Genome Institute. The first student admission was made in the 2016-2017 academic year.

Genome Sciences and Biotechnology Department was established within the body of our institute and started its educational activities. Graduate and Ph.D. students are educated in this department. There are one associate professor and 3 assistant professors in the department. Biomedicine and Health Technologies department has not yet started training activities yet.

Founded on 16/02/2015, Izmir International Biomedicine and Genome Institute has begun Molecular Biology and Genetics Master and Doctoral Programs in the Department of Genome Sciences and Molecular Biotechnology.

Our institute has been active within İzmir Biomedicine and Genome Center until February 2018 during the first phase of its establishment.

The institute is opened with the participation of many domestic and foreign scientists such as Prof.Mehmet Füzün, the founding rector, our founding director, Prof.Dr. Mehmet Öztürk, Science Industry and Technology Minister Fikri Işık, Izmir Governor Mustafa Toprak as well as Nobel Laureate Sir Tim Hunt.


under_construction


iBG Affiliated Publications

Brian I. Carr, Hikmet Akkiz, Oguz Uskudar, et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464.

Serhat Tozburun, Cedric Blatter, Meena Siddiqui, Eelco F. J. Meijer, and Benjamin J. Vakoc. Phase-stable Doppler OCT at 19 MHz using a stretched-pulse mode-locked laser. Biomedical Optics Express 2018; 9(3): 952-961. doi: 10.1364/BOE.9.000952.

Meena Siddiqui, Ahhyun S. Nam, Serhat Tozburun*, Norman Lippok, Cedric Blatter & Benjamin J. Vakoc. High-speed optical coherence tomography by circular interferometric ranging. Nature Photonics 2018 Jan 26; 12: 111–116. doi: 10.1038/s41566-017-0088-x.

Brian I. Carr, Hikmet Akkiz, Oguz Üsküdar et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464. doi: 10.4172/clinical-practice.1000393.

Sag D, Özkan M, Kronenberg M, Wingender G. Improved Detection of Cytokines Produced by Invariant NKT Cells. Sci Rep 2017 Nov 30; 7(1):16607. doi: 10.1038/s41598-017-16832-1.

U. Blache, J. Guerrero, S. Güven, A.S. Klar, A. Scherberich. Microvascular Networks and Models, In vitro Formation, in: W. Holnthoner, A. Banfi, J. Kirkpatrick, H. Redl (Eds.),. Vascularization for Tissue Engineering and Regenerative Medicine. Springer International Publishing Cham, 2017, pp. 1-40.

Cigdem Ozen, Meltem Ceylan Unlusoy, Nazanin Aliary, Mehmet Ozturk, Oya Bozdag Dundar. Thiazolidinedione or Rhodanine: A Study on Synthesis and Anticancer Activity Comparison of Novel Thiazole Derivatives. J Pharm Pharm Sci 2017 Nov; 20 (1): 415-427. doi:10.18433/J38P9R.

Gökhan Karakülah. RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes. Genomics 2017 Nov; 17. doi:10.1016/j.ygeno.2017.11.002.

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Oct 31;32(4):e391-e396. doi:10.5301/ijbm.5000300.

Refolo MG, D’Alessandro R, Lippolis C, Carella N, Cavallini A, Messa C, Carr BI. IGF-1R tyrosine kinase inhibitors and Vitamin K1 enhance the antitumor effects of Regorafenib in HCC cell lines. Oncotarget 2017 Sep 30; 8(61):103465-103476. doi:10.18632/oncotarget.21403.

Onur Tokel, Ahmet Turnalı, Ghaith Makey, et al. In-chip microstructures and photonic devices fabricated by nonlinear laser lithography deep inside silicon. Nature Photonics 2017 Sep; 11: 639–645. doi:10.1038/s41566-017-0004-4.

Ozen C, Ceylan-Unlusoy M, Ozturk M, Bozdag-Dundar O. A novel chromonyl thiohydantoin with anti-proliferative action on primary hepatocellular carcinoma cells. Med Chem Res 2017 Sep; 1-8. doi:10.1007/s00044-017-2037-0.

Yuqing Zhu, Vahid Serpooshan, Sean Wu, Utkan Demirci, Pu Chen, Sinan Güven. Tissue Engineering of 3D Organotypic Microtissues by Acoustic Assembly. In: Methods in Molecular Biology. Humana Press 2017 Sep; 1-12. doi: 10.1007/7651_2017_68.

Lina Zelinger, Gökhan Karakülah*, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew J. Brooks, Anand Swaroop. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Investigative Ophthalmology & Visual Science 2017 Sep; 58: 4422-4435. doi: 10.1167/iovs.17-21805.

Ozturk M, Batur T, Ekin U, Erdogan A, İscan E, Keles U, Oz O, Ozen C. Molecular Pathogenesis of Liver Cancer. J Gastrointest Cancer. 2017 Jul 17 (Review). doi: 10.1007/s12029-017-9957-2. [Epub ahead of print].

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Aug 28. doi: 10.5301/ijbm.5000300.

Ors A, Papin C, Favier B, Roulland Y, Dalkara D, Ozturk M, Hamiche A, Dimitrov S, Padmanabhan K. Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts. Biochem Cell Biol 2017 Aug; 95(4):491-499. doi: 10.1139/bcb-2016-0190.

Yılmaz Y, Güneş A, Topel H, Atabey N. Signaling Pathways as Potential Therapeutic Targets in Hepatocarcinogenesis. J Gastrointest Cancer 2017 Aug 18. doi: 10.1007/s12029-017-9958-1.

Carr BI, Guerra V. Validation of a Liver Index and Its Significance for HCC Aggressiveness. J Gastrointest Cancer 2017 Jun 20. doi: 10.1007/s12029-017-9971-4.

Ezgi Karaca*, João P.G.L.M. Rodrigues, Andrea Graziadei, Alexandre M.J.J. Bonvin, Teresa Carlomagno. M3: an integrative framework for structure determination of molecular machines. Nature Methods 2017. doi: 10.1038 / nmeth.4392.

Alural B, Ayyildiz ZO, Tufekci KU, Genc S, Genc K. Erythropoietin Promotes Glioblastoma via miR-451 Suppression. Vitam Horm. 2017;105:249-271. doi: 10.1016/bs.vh.2017.03.002. Epub 2017 Apr 19. PubMed PMID: 28629521.

Gökhan Karakülah. Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. Journal of Integrative Bioinformatics. 2017 (in press), doi: 10.1515/jib-2017-0009.

Sezgin E, Azbazdar Y, Ng XW, Teh C, Simons K, Weidinger G, Wohland T, Eggeling C, Ozhan G. Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments. FEBS J. 2017 Aug; 284(15): 2513-2526. doi: 10.1111/febs.14139.

Akyerli C., Yuksel S., Can O., Erson-Omay Z., Oktay Y.*, Cosgun E., Ulgen E., Erdemgil Y., San A., von Deimling A., Gunel M., Yakicier C., Pamir M.N., Ozduman K. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas. Journal of Neurosurgery. 2017 Jun; 16:1-13. doi: 10.3171/2016.11.

Schneider F, Waithe D, Clausen MP, Galiani S, Koller T, Ozhan G, Eggeling C, Sezgin E. Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS. Mol Biol Cell. 2017 Jun 1;28(11): 1507-1518. doi: 10.1091/mbc.E16-07-0536.

Oktay Y., Boylu C.A., Özduman K. Gliom Gelişiminde Genetik Yatkınlığın Rolü. Türk Nöroşirürji Dergisi. 2017 May; 27(2): 122-130.

Gökhan Karakülah, Aslı Suner. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics. 2017 (in press), doi:10.1016/j.ygeno.2017.05.008.

Bağırsakçı E., Şahin E., Atabey N., Erdal E. & Carr B.I. Role of Albumin in growth inhibition in Hepatocellular Carcinoma. Oncology. 2017 May 10. doi:10.1159/000471807.

Gümürdü A., Yildiz R., Eren E., Karakülah G., Ünver T., Genç Ş. & Park Y. MicroRNA exocytosis by large dense-core vesicle fusion. Scientific Reports. 2017 Mar 30; 7:45661. doi:10.1038/srep45661.

Marino IR, Carr B.I. New Developments in Orthotopic Liver Transplant for Hepatocellular Carcinoma. Exp Clin Transplant. 2017 Mar;15(Suppl 2):1-6.

Alural B, Genc S, Haggarty S. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biology Psychiatry. 2017 Feb; 6;73:87-103 doi: 10.1016/j.pnpbp.2016.03.010. Epub 2016 Apr 9. PubMed PMID: 27072377; PubMed Central PMCID: PMC5292013.

Pinato D., Sharma R., Allara E., Yen C., Arizumi T., Kubota K., Bettinger D., Jang J.W., Smirne C., Kim Y.W., Kudo M., Howell J., Ramaswami R., Burlone M.E., Guerra V., Thimme R., Ishizuka M., Stebbing J., Pirisi M. & Carr B.I. The ALBI grade provides objective hepatic reserve estimation across each BCLC stage of hepatocellular carcinoma. J. Hepatology, 2017 Feb; 66(2): 338-346. doi:http://dx.doi.org/10.1016/j.jhep.2016.09.008.

van Waalwijk van Doorn LJ, Gispert JD, Kuiperij HB, et al. Improved Cerebrospinal Fluid-Based Discrimination between Alzheimer’s Disease Patients and Controls after Correction for Ventricular Volumes. J Alzheimers Dis. 2017 Jan 24; 56(2):543-555. doi: 10.3233/JAD-160668

Park CG, Park Y & Suh BC. The HOOK region of voltage-gated Ca2+ channel β subunits senses and transmits PIP2 signals to the gate. J Gen Physiol. 2017 Jan 13. doi:10.1085/jgp.201611677.

Arslan N, Guzel O, Kose E, Yılmaz U, Kuyum P, Aksoy B, Çalık T. Is ketogenic diet treatment hepatotoxic for children with intractable epilepsy? Seizure. 2016 Dec; 43: 32-38. doi:10.1016/j.seizure.2016.10.024.

Ebru Diler, Turgay Unver & Gökhan Karakülah. Differential Expression of Hyperhydricity Responsive Peach miRNAs. Journal of Integrative Bioinformatics. 2016 Dec; 13(5): 308. doi:10.2390/biecoll-jib-2016-308.

İşcan E, Güneş A, Korhan P, Yılmaz Y, Erdal E, Atabey N. The regulatory role of heparin on c-Met signaling in hepatocellular carcinoma cells. J Cell Commun Signal. 2016 Dec 14; 1-12. doi:10.1007/s12079-016-0368-0.

Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Unver. PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs). PLoS ONE. 2016 Dec 9; 11(12): e0167698. doi:10.1371/journal.pone.0167698.

Calibasi Kocal G, Güven S, Foygel K, Goldman A, Chen P, Sengupta S, Paulmurugan R, Baskin Y, Demirci U. Dynamic Microenvironment Induces Phenotypic Plasticity of Esophageal Cancer Cells Under Flow. Sci Rep. 2016 Dec 2; 6:38221. doi: 10.1038/srep38221.

Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah*, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker, Ashley Walton, Rafael Villasmil, Jennifer Joanna Barb, Peter Jonathan Munson, Koray Dogan Kaya, Vijender Chaitankar, Tiziana Cogliati, Anand Swaroop. NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. Cell Reports. 2016 Nov 22; 17(9): 2460-2473. doi:http://dx.doi.org/10.1016/j.celrep.2016.10.074.

Arslan N, Kose E, Guzel O. The Effect of Ketogenic Diet on Serum Selenium Levels in Patients with Intractable Epilepsy. Biol Trace Elem Res. 2016 Nov 21. doi:10.1007/s12011-016-0897-7.

Erbayraktar Z, Alural B, Erbayraktar RS, Erkan EP. Cell division cycle 7-kinase inhibitor PHA-767491 hydrochloride suppresses glioblastoma growth and invasiveness. Cancer Cell Int. 2016 Nov 18;16:88. eCollection 2016. doi:10.1186/s12935-016-0364-8.

Muhammad Ayaz Mustufa, Cigdem Ozen, Imran Ali Hashmi, Afshan Aslam, Jameel Ahmed Baig, Gokhan Yildiz, Shoaib Muhammad, Imam Bakhsh Solangi, Naim ul Hasan Naqvi, Mehmet Ozturk and Firdous Imran Ali. Synthesis and bio-molecular study of (+)-N-Acetyl-α-amino acid dehydroabietylamine derivative for the selective therapy of hepatocellular carcinoma. BMC Cancer. 2016, Nov 14; 16: 883. doi:10.1186/s12885-016-2942-5.

Büyüköz M, Erdal E, Alsoy Altinkaya S. Nanofibrous gelatin scaffolds integrated with NGF-loaded alginate microspheres for brain tissue engineering. J Tissue Eng Regen Med. 2016 Nov 12. doi: 10.1002/term.2353.

Jeannot V, Busser B, Vanwonterghem L, Michallet S, Ferroudj S, Cokol M, Coll JL, Ozturk M, Hurbin A. Synergistic activity of vorinostat combined with gefitinib but not with sorafenib in mutant KRAS human non-small cell lung cancers and hepatocarcinoma. OncoTargets and Terapy. 2016, Nov 9; 9: 6843—6855. doi:10.2147/OTT.S117743.

Carr B.I., Guerra V., Giannini E.G. et al. A Liver Index and its Relationship to Indices of HCC Aggressiveness. J Integr Oncol. 2016 Oct;5(4). pii: 178. doi: 10.4172/2329-6771.1000178.

Erkan D, Kayali HA. Replacement of Soybean Meal with Animal Origin Protein Meals Improved Ramoplanin A2 Production by Actinoplanes sp. ATCC 33076. Appl Biochem Biotechnol. 2016 Sep;180(2):306-21. doi:10.1007/s12010-016-2100-1.

Hani Alotaibi, Nese Atabey, Kasım Diril, Esra Erdal, Mehmet Ozturk. Molecular Mechanisms of Hepatocellular Carcinoma, Chapter Hepatocellular Carcinoma Part of the series Current Clinical Oncology. Springer. 2016, Aug 27; 43-63. doi:10.1007/978-3-319-34214-6_3.

Alagoz Y., Gurkok T.,  Zhang B. & Unver T. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology. Sci Rep. 2016 Aug 3; 6:30910. doi: 10.1038/srep30910.

Bakır Y., Eldem V., Zararsız G. & Unver T. Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves. Plant Genome. 2016 Jul; 9(2). doi:10.3835/plantgenome2015.09.0080.

Marsano A, Medeiros da Cunha CM, Ghanaati S, Gueven S, Centola M, Tsaryk R, Barbeck M, Stuedle C, Barbero A, Helmrich U, Schaeren S, Kirkpatrick JC, Banfi A, Martin I. Spontaneous In Vivo Chondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells by Blocking Vascular Endothelial Growth Factor Signaling. Stem Cells Transl Med. 2016 Jul 26. doi: 10.5966/sctm.2015-0321.

Pavlopoulou A., Oktay Y., Vougas K., Louka M., Vorgias C.E., Georgakilas A.G. Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. Cancer Letters, 2016, Jul 19; 380(2):485-493. doi: 10.1016/j.canlet.2016.07.018.

Carr B.I., Guerra V., Giannini E.O. et al. An HCC Aggressiveness Index and Blood GTP, Blirubin and Platelet Levels. J. Integrative Oncology. 2016 Jun 20; 5:172. doi: 10.4172/2329-6771.1000172.

Oktay Y., Ülgen E., Can Ö., Akyerli C.B., Yüksel Ş., Erdemgil Y., Durası I.M., Henegariu O.I., Nanni E.P., Selevsek N., Grossmann J., Erson-Omay E.Z., Bai H., Gupta M., Lee W., Turcan Ş., Özpınar A., Huse J.T., Sav M.A., Flanagan A., Günel M., Sezerman O.U., Yakıcıer M.C., Pamir M.N. & Özduman K. IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation. Sci Rep. 2016 Jun 10; 6: 27569. doi: 10.1038/srep27569.

Yilmaz Y, Atabey N, Erdal E & Brian I. Carr. Platelets, Microenvironment and Hepatocellular Carcinoma. Biochemistry & Analytical Biochemistry, 2016 June 29; 5:281 (Review). doi:10.4172/2161-1009.1000281.

Antonio Mazzoccaa, Giovanni Ferrarob, Giovanni Misciagnac, Brian I. Carr. A systemic evolutionary approach to cancer: Hepatocarcinogenesis as a paradigm. Medical Hypotheses, 2016, Aug; 93: 132-137. doi:10.1016/j.mehy.2016.05.027.

Karakülah G, Karakuş M, Suner A, Demir S, Arserim SK, Töz S, Özbel Y. sandflyDST: a dynamic web-based decision support tool for the morphological identification of sandflies present in Anatolia and mainland Europe, and user study. Medical and Veterinary Entomology, 2016 June 24. doi:10.1111/mve.12182.

Can Küçük, Xiaozhou Hu, Qiang Gong, Bei Jiang, Adam Cornish, Philippe Gaulard, Timothy McKeithan, Wing C. Chan. Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma. The American Journal of Pathology, 2016 June; 186(6): 1435-1441. doi:10.1016/j.ajpath.2016.02.011.

Zeynep Firtina Karagonlar, Doğukan Koç, Eren Şahin, Sanem Tercan Avci, Mustafa Yilmaz, Neşe Atabey, Esra Erdal. Effect of adipocyte-secreted factors on EpCAM+/CD133+ hepatic stem cell population. Biochemical and Biophysical Research Communications, 2016 June 3; 474(3): 482-490. doi:10.1016/j.bbrc.2016.04.137.

Yakup Bakır, Vahap Eldem, Gökmen Zararsız, Turgay Unver. Global Transcriptome Analysis Reveals Significant Differences in Gene Expression Patterns Between The Non-Hyperhydric and Hyperhydric Leaves of Prunus persica. The Plant Genome, 2016, May; 9(2): 1-9.

Salimi R, Yener N, Safari R. Use and Evaluation of Newly Synthesized Fluorescence Probes to Detect Generated OH• Radicals in Fibroblast Cells. J Fluoresc. 2016 May; 26(3):919-24. doi: 10.1007/s10895-016-1780-9.

Firtina Karagonlar Z, Koc D, Iscan E, Erdal E, Atabey N. Elevated hepatocyte growth factor expression as an autocrine c‐Met activation mechanism in acquired resistance to sorafenib in hepatocellular carcinoma cells. Cancer Sci. 2016 Apr; 107(4):407-416 doi: 10.1111/cas.12891.

Carr BI & Guerra V. A Hepatocellular Carcinoma Aggressiveness Index and Its Relationship to Liver Enzyme Levels. Oncology 2016 Mar 15; 90(4). doi: 10.1159/000444394.

Gao LM, Zhao S, Liu WP, Zhang WY, Li GD, Küçük C, Hu XZ, Chan WC, Tang Y, Ding WS, Yan JQ, Yao WQ, Wang JC. Clinicopathologic Characterization of Aggressive Natural Killer Cell Leukemia Involving Different Tissue Sites. Am J Surg Pathol, 2016 Mar 11. doi: 10.1097/PAS.0000000000000634.

Carr BI & Guerra V. Low Alpha-Fetoprotein Levels Are Associated with Improved Survival in Hepatocellular Carcinoma Patients with Portal Vein Thrombosis. Digestive Diseases and Sciences, 2016 Feb 26; 61(3):937-947. doi: 10.1007/s10620-015-3922-3.

Ferroudj S, Yildiz G, Bouras M, Iscan E, Ekin U, Ozturk M. Role of fanconi anemia/BRCA pathway genes in hepatocellular carcinoma chemoresistance. Hepatol Res. 2016 Feb 16. doi: 10.1111/hepr.12675.

Carr BI & Guerra V. Hepatocellular Carcinoma Extrahepatic Metastasis in Relation to Tumor size and Alkaline Phosphatase Levels. Oncology 2016 Feb 12; 90(3):1-7. doi: 10.1159/000443480.

Durmaz I, Guven EB, Ersahin T, Ozturk M, Calis I, Cetin-Atalay R. Liver cancer cells are sensitive to Lanatoside C induced cell death independent of their PTEN status. Phytomedicine. 2016 Jan 15; 23(1):42-51. doi: 10.1016/j.phymed.2015.11.012.

Wingender G. From the deep sea to everywhere? Environmental antigens for iNKT cells. Arch Immunol Ther Exp, 2015 Dec 24 (Review). doi: 10.1007/s00005-015-0381-7.

Güzel O, Yılmaz U, Uysal U, Arslan N. The effect of olive oil-based ketogenic diet on serum lipid levels in epileptic children. Neurol Sci. 2015 Dec 23; 1-6. doi: 10.1007/s10072-015-2436-2.

Namkoong B, Guven S, Ramesan S, Liaudanskaya V, Abzhanov A, Demirci U. Recapitulating cranial osteogenesis with neural crest cells in 3-D microenvironments. Acta Biomaterialia, 2015 Dec 07. doi: 10.1016/j.actbio.2015.12.004.

Hanna RN, Cekic C, Sag D, Tacke R, Thomas GD, Nowyhed H, Herrley E, Rasquinha N, McArdle S, Wu R, Peluso E, Metzger D, Ichinose H, Shaked I, Chodaczek G, Biswas SK, Hedrick CC. Patrolling Monocytes Control Tumor Metastasis to the Lung. Science. 2015, Nov 20; 350(6263): 985-90.

Wingender G & Kronenberg M. Characterization of human T cell subsets via surface markers. Cytometry A, 2015, Oct 27; 87A; 1067-1069.

D’Alessandro R, Messa C, Refolo MG, Carr BI. Modulation of sensitivity and resistance to multikinase inhibitors by microenvironmental platelet factors in HCC. Expert Opinion on Pharmacotherapy. 2015 Oct 19; 16(18):1-8. doi: 10.1517/14656566.2015.1101065.

Wingender G, Sag D, Kronenberg M. NKT10 cells: a novel iNKT cell subset. Oncotarget. 2015 Sept 29; 6(29): 26552-26553 (Review). doi: 10.18632/oncotarget.5270.

Wingender G, Birkholz A, Sag D, Farber E, Chitale S, Howell AR, Kronenberg M. Selective conditions are required for the induction of iNKT cell hypo-responsiveness by antigenic stimulation. The Journal of Immunology. 2015 Sept 9; 195: 3838-3848. doi: 10.4049/jimmunol.1500203.

Lippolis C, Refolo MG, D’Alessandro R, Carella N, Messa C, Cavallini A, Carr BI. Resistance to multikinase inhibitor actions mediated by insulin like growth factor-1. Journal of Experimental & Clinical Cancer Research. 2015 Sept 2; 34(1):90. doi: 10.1186/s13046-015-0210-1.

Pančoška P, Skála L, Nešetřil J, Carr BI. Validation of the Concept of a Common Typical Time of Disease Duration for Hepatocellular Carcinoma Patients Using the Fisher Information Processing of Tumor Imaging Results Combined With Network Phenotyping Strategy Quantification of Individual Patient Clinical Profile Patterns. Seminars in Oncology. 2015 Aug; 42(4):672-678. doi: 10.1053/j.seminoncol.2015.05.004.

Gunes A, Iscan E, Topel H, Avci ST, Gumustekin M, Erdal E, Atabey N. Heparin treatment increases thioredoxin interacting protein expression in hepatocellular carcinoma cells. The International Journal of Biochemistry & Cell Biology. 2015 Aug; 65:169-181. doi: 10.1016/j.biocel.2015.05.025.

Hu X, Chan WC, Kücük C. Generation of a genetically engineered aggressive nk-cell leukemia cell line with stable IL2 expression. Acta Medica International. 2015 Jul; 2(2):78-84. doi: 10.5530/ami.2015.3.6.

Ozhan G and Weidinger G. Wnt/β-catenin signaling in heart regeneration. Cell Regen (Lond). 2015 Jul 8; 4(1):3. doi: 10.1186/s13619-015-0017-8

Alotaibi H, Basilicata MF, Shehwana H, Kosowan T, Schreck I, Braeutigam C, Konu O, Brabletz T, Stemmler MP. Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms. 2015 June; 1849(6):731-742. doi: 10.1016/j.bbagrm.2015.01.005.

Alural B, Ozerdem A, Allmer J, Genc K, Genc S. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Front Cell Neurosci. 2015 May 28; 9:209. doi: 10.3389/fncel.2015.00209.

Dilek Cevik, Gokhan Yıldız & Mehmet Ozturk. Common telomerase reverse transcriptase promoter mutations in hepatocellular carcinomas from different geographical locations. World J Gastroenterol. 2015 Jan 7; 21(1): 311–317. doi: 10.3748/wjg.v21.i1.311.

Alural B, Duran GA, Tufekci KU, Allmer J, Onkal Z, Tunali D, Genc K, Genc S. EPO Mediates Neurotrophic, Neuroprotective, Anti-Oxidant, and Anti-Apoptotic Effects via Downregulation of miR-451 and miR-885-5p in SH-SY5Y Neuron-Like Cells. Frontiers in Immunology. 2014 Sep 30; 5:475. doi: 10.3389/fimmu.2014.00475.

* Current address IBG.


 

Core Manager
Çiğdem Özen, PhD, Specialist

The Hybridoma and Monoclonal Antibody Production Core Facility will provide service for researchers and biotechnology companies. The aim is to establish an efficient and affordable production of antibodies and other biological materials. Our service covers the whole process from antigen immunization in mice, rat or rabbit to production of purified monoclonal antibodies. We use hybridoma technology that includes generation of hybrid cell lines or hybridomas by fusing an antibodyproducing B cell with an immortal myeloma cell. The facility produces both monoclonal and polyclonal antibodies and provides antibody purification service using different benchtop chromatography techniques. Following purification of the antibody, the IgG type can also be characterized on request. Furthermore, the facility offers consultation service on all aspects of monoclonal antibody production.


 

Coordinator
Ralph Meuwissen, PhD
Members
Kasım Diril, PhD Duygu Sağ, PhD
Ensari Güneli, DVM, PhD Gerhard Wingender, PhD
Güneş Özhan, PhD

SCOPE
Advanced animal models of human diseases continue to expand their use for both descriptive basic research as well as applied preclinical research. In this program, we focus on preclinical research with a clear emphasis on functional drug screening and validation. Our ultimate goal will be the translation of these preclinical results on disease intervention into clinical trials. For this, we will use existing animal models and where appropriate; we will design novel, better-suited models. In vitro drug screen assays typically rely on simple interactions of chemicals with a drug target, such as receptor binding or enzyme activity inhibition. However, in vitro results often poorly correlate with in vivo results because of the complicated physiological environment is absent in the in vitro testing system. Although cell-based assays can provide some information, cultured cells still do not provide physiological conditions and complex interactions among different cell types and tissues. Therefore, results in animal studies are essential to validate high – throughput screening (HTS) hits and exclude compounds with unfavorable absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, which are responsible for more than half of compound attrition in costly clinical trials. Currently, in vivo assays are not usually performed until or after the lead optimization stage. This is partly due to the low speed and high cost of conventional animal models (typically rodents) and the relatively high number of preliminary hits from HTS. With alternative small-animal models, however, it is now possible to perform in vivo testing earlier in the development process. Thus, researchers have developed systems using both vertebrates (e.g. zebrafish) and invertebrates (e.g. the fruit fly Drosophila melanogaster) for drug screening. The small size, high fecundity, and experimental tractability of these animals enable costeffective and rapid screening of numerous compounds. The experimental animal facility at iBG-izmir maintains and utilizes the whole breath of animal model systems, namely: Drosophila, zebrafish and rodents (mice/rats)

FOCUS AREAS AND MILESTONES
The emphasis of each model system will be:
• Drosophila: Drosophila is being used frequently in high impact studies to model, for example, cancer and diabetes, because of the simple ability to perform genome-wide modifier and drug compound screens. Simple phenotypes associated with human mutations in conserved disease orthologs can be examined. We will establish novel animal models of diseases in the Drosophila system, to uncover genetic disease mechanism involving loss and gain of known pathway function. Furthermore, we will screen for pathway modifications by genetic and pharmacological modifiers. To best complement our work on wound healing, high priority will be placed on exploring the interactions between epithelial healing mechanisms and metabolic disorders, such as diabetes.

• Zebrafish: Wnt/β-catenin signaling pathway components are considered as preferred targets for drug development as malfunctioning of the pathway is associated with human diseases including cancer. Unfortunately, targeted treatment of the underlying cause of these diseases is currently not possible, since very few compounds are known to specifically inhibit β-catenin signaling. In the coming years, we aim to perform a drug screen for Wnt-related cancers using zebrafish, which has become an attractive model for high-throughput drug screening. Zebrafish embryos offer a unique system where pharmacological molecules can directly be added to the embryo water and become readily absorbed. They allow for direct observation of phenotypic hallmarks of cancer, such as enhanced cell proliferation and angiogenesis, reduced apoptosis, abnormal activation of oncogenes, repression of tumor suppressor genes and changes in cell migratory behavior. Compounds can be identified via embryonic screens and further validated in adults for their molecular mechanisms to pinpoint them as a target for a specific cancer type. For this purpose, we aim to exploit zebrafish as a drug discovery model and a biopharmaceutical service by collaborating with pharmaceutical companies to identify novel drug candidates. Another strength of the zebrafish system is that it represents an exclusive example of a highly regenerative vertebrate model, due to its distinct regenerative capacity in various organs and tissues including the heart, pancreas, liver, muscle, skin, blood and pigment cells, fins and the CNS. Here, we aim to establish part of the zebrafish facility as a unit that can serve to collaborate for the regeneration-related research projects of internal and external laboratories that would like to benefit from this unique regeneration model.

• Rodents (rats/mice): At iBG-izmir we will make use of well-established mouse models of cancer and metastasis (mainly liver and lung cancer), diabetes, obesity, experimental allergic encephalomyelitis (EAE), viral and bacterial infections, using wild-type and humanized mice. Some congenic rat strains for diabetes and obesity research will also be used. However, genetically modified mice strains will be the most suitable models for e.g. cancer and some other diseases. Our fully integrated transgenic core facility will not only enable us to adapt existing models but also to design new ones. Such advanced genetically modified mice will make use of state-of-the-art technologies, including Cre/lox, Flp/frt conditional alleles or Tet/on-off inducible transgenes. In this way we, will have accurate somatic mouse models for diseases that are ideally suited to test drug candidates for targeted therapy against defined molecular pathway(s). As described above, mice models are not practical for HTS of drugs, but rather will be used for preclinical therapy testing. For example, mice strains that express luciferase and fluorescent protein reporter alleles will enable us to follow disease interventions in real time by non-invasive in vivo imaging at our core facility. We will establish and maintain the essential number of genetically modified mice strains for the various diseases of interest. The core will also become a member of the European consortium for Mouse Phenotyping and Archiving Research Infrastructure (INFRAFRONTIER) to become the central facility for Turkey. Thereby, we will be access and participate in the large non-profit genetically modified mice repository, the European Mouse Mutant Archive (EMMA). These cooperations will greatly enhance the interaction with our European partners and our access to funding.

• Lastly, we will set up Patient Derived Xenotransplant (PDX) models for lung cancer. These PDX models recapitulate the heterogeneity of human cancer, to a much higher extend than conventional mouse models do. Recent experiments with severe immune compromised NOD-SCID-Gamma (NSG) recipient mice have shown very promising results in maintaining human primary tumor tissue characteristics after transplantation. PDX models are thus a very important supplement to our preclinical drug testing capacity. Here too we initiated participation efforts to become member of the EUROPDX consortium for mutual use and exchange of PDX cancer models between European partner institutes.

• Development and testing of drug HTS in both Drosphila and zebrafish systems. Here our focus will be on small molecule drug testing. Our minimal goals are the development of one or more candidates during the first 3 years, and the validation of at least one molecule after preclinical testing to allow its use for follow-up clinical trials. The funding will be obtained from TUBITAK and industrial partners.

• Development and optimization of genetically modified mice models for lung and liver cancer, as well as of PDX models for lung cancer. These models will be used to test preclinical and targeted be specific monoclonal antibodies, small molecules, or biosimilars. Our minimal goals during the first 3 years are the establishment and functional characterization of the mouse models, together with conclusive validation results for the candidate drug. Our mouse model should then be ready as a tool for preclinical testing to make candidate drugs ready for clinical trials. Funding will be obtained from TUBİTAK, European consortia (Infrafrontier), EU research funds and industrial partners.


 

Coordinator
Sinan Güven, PhD
Members
Neşe Atabey, PhD Ralph Meuwissen, PhD
Can Küçük, PhD Yavuz Oktay, PhD

SCOPE
Medical diagnostics is the key element for providing the right therapeutic approach to curing diseases. Finding, describing and correlating the chemical and physical symptoms of diseases demands devices equipped with highly precise and accurate sensors. Modern clinical approaches utilize different methods for diagnostics such as using specific biomarkers, hi-tech imaging systems, genomic analysis methods, high-throughput screening and point of care technologies. Bio-microdevices are miniaturized technologically engineered platforms that provide high and precise control over environmental variables and mimic the native physiological conditions of living organisms. Biosensor-supplied microdevices are excellent tools for diagnostics, as they minimize the sample volumes, analysis time and cost of tests. In the Program for Diagnostics and Medical Microdevices at iBG-izmir, we formed a multidisciplinary research team of bioengineers, molecular biologists, physicists, chemists and clinicians to develop micro- and nano-devices for diagnostics. With close clinical collaborations, we will implement the most current analytical techniques (such as next generation sequencing) and design biosensors for detection of diagnostic markers from patient samples (such as body fluids, circulating tumor cells or solid tissues). Cancer, infectious agents, metabolic, autoimmune and neurological diseases are in the scope of the program. For these we aim to generate reliable, rapid and cost effective micro- and nano-diagnostic devices. The minimal success criterion of the program is to bring an innovative, micro-/nanodiagnostic device on the medical market. iBG-izmir and this Innovation Program will advance the medical R&D activities in the region and will be a key component providing competitive products to the healthcare market. Furthermore, Dokuz Eylul University also hosts the BioIzmir initiative and DEPARK (Dokuz Eylul Technology Development Zone), which both focus on the industrial translation of medical innovations. The cooperation with these organizations will further increase the impact of this Innovation Program.

The program is going to obtain substantial funds from TÜBITAK, EU research funds, NIH partnerships, private and industrial funding.

FOCUS AREAS AND MILESTONES
• Develop and validate at least one reliable, rapid, low cost, easy to operate and cost-efficient diagnostic device.

• Apply for a patent of the developed device and its technology.

• Validation and commercialization of the device.


 

Coordinator
Yavuz Oktay, PhD
Members
Nur Arslan, MD Semra Hız Kurul, MD
 Can Küçük, PhD

SCOPE
The incidence of many rare diseases is much higher in Turkey due to the high rate of relative (consanguineous) marriages. The clinical presentation of such rare diseases is highly heterogeneous, and therefore the proper diagnosis and treatment of these diseases is currently challenging. Additionally, the genetic background of most of these diseases is poorly defined. However, the identification of the underlying genetic aberrations will likely lead to the development of better diagnostic, prognostic and therapeutic strategies. Recently, the discovery of nextgeneration sequencing (NGS)-based methodologies rendered it possible to identify disease-associated mutations with a genome-wide scope. The work within this program will apply whole-exome sequencing (WES) to identify specific mutations associated with rare diseases, with the aim to generate unique diagnostic panels. Moreover, we will identify driver mutations with the potential to function as novel therapeutic targets. Specifically, we plan to focus on rare diseases of the nervous system, such as epilepsy syndromes and neurodegenerative diseases.

FOCUS AREAS AND MILESTONES
5 year goals:
• Establish at least one multi-disciplinary consortium that involves pathologists, clinicians, genome and bioinformatics scientists.

• To collect and store all relevant rare disease-specific clinical and histopathological data in a central database for at least three rare disease types.

• To generate a NGS-based disease panel for at least two rare disease groups. Funding options: TUBITAK (1001, 1003, 1007 grant programs), Izmir Agency of Development (IZKA), and EU funding programs (Horizon 2020 etc).

Success criteria (3rd and 5th years):
• Exome and/or targeted sequencing and bioinformatic analysis of at least 300 patients within three years and of at least 500 patients within five years.

• Identification and validation of all mutations necessary for proper diagnosis in at least one rare disease within three years and of at least two rare disease within five years.

• Development of at least 2 NGS panels for 2 different rare diseases (5th year).


 

Coordinator
Şermin Genç, MD, PhD
Members
Kasım Diril, PhD Gerhard Wingender, PhD
Sinan Güven, PhD Yavuz Oktay, PhD

SCOPE
Neurological disorders include Alzheimer disease and other dementias, stroke, multiple sclerosis, Parkinson’s disease, brain tumors, traumatic disorders of the nervous system such as brain trauma, epilepsy and migraine. Hundreds of millions of people worldwide are affected by neurological disorders. For example, stroke is the third most common cause of death worldwide. Alzheimer’s disease is the most common type of dementia, affecting 35 million individuals in the world, with an expected threefold increase by 2050. Furthermore, multiple sclerosis, an inflammatory demyelinating disease of the brain and the spinal cord, affects two million people globally, with rates varying widely in different regions and populations. However, many aspects of etiology, genetics and pathogenesis of neurological disorders are still not clearly defined. In addition, for many of these diseases, no good predictive or diagnostic test is available. Finally, and most importantly, for many neurological disorders the current treatments are largely symptomatic and no final cure can be achieved. For these reasons, neurological disorders have become a major health problem for many countries, whose burden is expected to rise with the aging of the population. Turkey’s Science and Technology High Council declared ‘Neuroscience’ as one of the priority areas of health and technology. The Neurological Disorders Program at iBG-izmir aims to identify novel genes/mutations responsible for familial and non-familial neurological disorders, to discover new biomarkers and to develop novel therapeutic tools and approaches for the treatment of these disorders. To this end, we will study a wide range of patient samples, as well as established and newly generated in vitro and in vivo animal models of neurological disorders. The funding will be obtained from TUBITAK, Ministry of Health, industrial partners and EU research funds.

FOCUS AREAS AND MILESTONES
The focus areas and 5 years goals with milestones of the Program are as follows:

• Development of in vitro and in vivo models: 3D cultures of induced pluripotent stem cells to study differentiation
to neural stem cells, current type neural or glial cells. In addition to in vitro models, we aim to develop new transgenic animal models of neurological disorders. Our minimal goals are the development of one novel in vitro or in vivo model during the first 3 years, and another one within 5 years.

• Discovery of novel predictive genes/mutations: Many neurological disorders have a genetic etiology. We will investigate familial and non-familial forms of neurological disorders to find disease causing novel genes/mutations by whole exome sequencing. Our minimal goals are biobanking of at least 30 families during the first 3 years, and whole exome sequencing within 5 years.

• Biomarker discovery and development of diagnostic tools: Circulating serum micro RNAs (miRNAs), and other possible biomarkers will be investigated to find novel biomarkers for neurological novel mutations will be developed. Additionally, these biomarkers and novel driver mutations in neurological cancers could be possible targets for treatment. Our minimal goals are to identify one novel biomarker or target molecule during the first 3 years, and finish preclinical validation within 5 years.


 

Coordinator
Gerhard Wingender, PhD
Members
Duygu Sağ, PhD

SCOPE
Immunotherapy is the treatment of diseases via the alteration of the immune system. This can be achieved by inducing, enhancing or suppressing immune responses, depending on the context. Current approaches in immunotherapy are heavily biased to the adaptive immune system by targeting or utilizing conventional T and B cells. However, the innate immune system, and innate like T cells are known to be crucially involved in most, if not all, inflammatory responses. This is particular relevant for chronic inflammatory diseases. Nonetheless, only few immunotherapies based on the innate and innate-like immune system are currently under development. Recognizing the great potential for novel and innovative therapeutic approaches, this program focuses on these aspects, with a particular emphasis on macrophages and innate like T cells.

FOCUS AREAS AND MILESTONES
• Macrophage polarization as therapeutic target: Pro-inflammatory macrophages, which promote inflammation, are called M1 macrophages. In contrast, anti-inflammatory macrophages, which decrease inflammation and support tissue repair, are called M2 macrophages. How environmental factors influence this M1/M2 – balance is poorly defined. Recent intriguing findings by one program member demonstrated that the activity of a cholesterol transporter strongly influences this M1/M2 – balance. This altered macrophage balance had profound impact on tumor immunity. By linking cholesterol transporters to tumor immunity, this finding provides an unprecedented link between the metabolism and chronic inflammatory diseases, including cancer. The intermediate 3 years goal of this project is to find and characterize small molecules and/or monoclonal antibodies to modulate the activity of cholesterol transporters. The long-term 5 years goal is to utilize these reagents as therapeutic approach to alter macrophage polarization for cancer immunotherapy and potentially for metabolic/inflammatory diseases.

• iNKT cell based cell therapy: Innate T cells are a unique subset of T cells that combine features of innate NK cells and of adaptive memory T cells. The most prominent member of innate T cells are invariant Natural Killer (iNKT) cells. Following antigenic stimulation, iNKT cells rapidlyproduce copious amounts of various cytokines and thereby can have a pronounced effect on the immune system. They are known to impact an impressive variety of different immune reactions, ranging from chronic and acute inflammatory processes, including responses to pathogens and tumors, to autoimmune responses. As all humans share basically identical iNKT cells, their therapeutic potential is great. Recently, program members characterized a novel iNKT cell subset with potent IL-10-dependent regulatory function, which were termed NKT10 cells. These, NKT10 cells could impair anti-tumor immune responses and protect mice against experimental autoimmune encephalomyelitis (EAE), a
mouse model of multiple sclerosis. The intermediate 3 years goal of this project is to better characterize the regulatory mechanisms of NKT10 cells and to optimize their expansion in vitro and in vivo. The long-term 5 years goal is to utilize NKT10 cells as cell therapy for EAE and for obesity related metabolic diseases.

For both projects funding by one major national or international grant should be obtained within 3 years. We expect for both projects to acquire proof-of-concept preclinical in vivo data in wild type and humanized animals within a 5 years period.


 

Coordinator
Esra Erdal, PhD
Members
Nur Arslan, MD, PhD Sinan Güven, PhD
Neşe Atabey, PhD Güneş Özhan, PhD

SCOPE
Regenerative medicine is one of the most promising and rapidly advancing areas of modern medicine, as it focuses on innovative approaches to repair and replace cells, tissues and organs. Cell therapies implement patient oriented approaches, and provide novel venues for personalized medicine. At iBG-izmir, we will establish an internationally accredited cGMP facility for the production of therapeutic grade cells and tissues for humans. Our program brings together basic research scientists and clinicians focused on utilizing cells and stem cells in the reconstruction of tissues and organs, as well as engineering cells for therapeutic approaches. Cell therapies and regenerative medicine have already been applied in clinics as experimental and alternative methods. With this program we aim to develop and translate cell-based approaches as validated standard treatment method for clinicians. In this regard, we focus on basic and translational medical sciences utilizing cell therapies, design clinical trials and set new therapeutic standards. Achieving the goals of the program is strongly coupled with innovative thinking and creating value in therapeutic medicine.

FOCUS AREAS AND MILESTONES
• Developing cell based pre-clinical in vitro and in vivo disease models underlining the mechanisms of regeneration.
• Generating autologous and allogeneic adult mesenchymal stem cells from bone marrow, adipose tissue and dental pulp; or from specialized cells, like limbal stem cells, chondrocytes and hepatocytes. Implementing their use for cancer, trauma, plastic and reconstructive surgery, ophthalmology and dental applications.
• Developing and translating cell based therapy methods from Bench-to-Bedside in accordance with national and international guidelines.
• Design and start a clinical trial for cell-based therapy. Funding of the program will be obtained from TUBITAK, Ministry of Health, EU research funds and the Dokuz Eylul University Hospital.


 

Coordinator
Mehmet Öztürk, PhD
Vice Coordinator
Şerif Şentürk, PhD
Members
Hani Alotaibi, PhD Kasım Diril, PhD
Neşe Atabey, PhD Ensari Güneli, DVM, PhD
Hülya Ayar Kayalı, PhD Ralph Meuwissen, PhD
 

SCOPE
Targeted therapeutics are drugs or other substances such as antibodies acting on specific molecules (“molecular targets”) that are involved in the pathogenesis or complications of a disease. Targeted therapeutics are also called “precision medicines”. Most of targeted therapeutics approved by FDA or EMEA are used against cancer, but their field of application is rapidly spreading to other diseases such as autoimmune and rare diseases. The process of targeted therapeutics development usually starts by the discovery of a critical molecular target, followed by the choice of appropriate targeting molecules, in vitro and in vivo validation studies, production under cGMP conditions and clinical trials.

Many of the currently available targeted therapeutics are “biopharmaceuticals” with expired patents. Consequently, there is a growing interest in Turkey and other countries in the manufacturing of their generic forms called “biosimilars” as they are more affordable. Considering global trends and local needs, iBG-izmir decided to invest its scientific and technological means to cover a broad area of application starting from production of biosimilars and leading towards the development of innovative biopharmaceuticals. Investigation of innovative targeted drugs such as small chemical inhibitors will also be covered by the program. Accordingly, iBG-izmir is building a GMP facility accompanied by quality control, animal toxicology and pharmacology units, dedicated to biosimilar production, as well as state-of-the-art “drug discovery” facilities.

FOCUS AREAS AND MILESTONES
• Development and manufacturing of biosimilars: humanized monoclonal antibodies (Mabs) and antibodylike molecules are the initial focus area. Our minimal goals are the development of one of more biosimilar master cell banks during the first 3 years, and the production of at least one biosimilar molecule ready for initial clinical trials. The funding will be obtained from TUBITAK and industrial partners.

• Development of “biobetter” and innovative Mabs: A “biobetter Mab” is a novel antibody acting on a known target by a different mechanism for example via a different epitope. Several projects on anti-cancer Mab development against validated and novel target molecules will be launched. Our minimal goals are the development of one of more humanized Mab master cell banks during the first 3 years, and preclinical validation within 5 years. The funding will be obtained from TUBITAK, EU research funds and industrial partners.

• Development and validation generic small molecule inhibitors for combined therapy against refractory or relapsed cancer. Patient-derived (chemo)therapy naïve primary tumors together with their refractory or relapsed tumors can be used to screen anti-cancer small molecules efficacy against validated and novel targets from activated molecular pathways. Our minimal goals are the collection and availability of distinct sets of generic small molecules that will be tested in (primary) tumor cultures. This will be followed within 5 years by preclinical validation in our patient-derived-xenotransplant (PDX) models and our advanced, genetically modified animal models.

Funding will be obtained through TUBITAK, EU framework collaborations and industrial partners.


 

İzmir Uluslararası Biyotıp ve Genom Enstitüsü (iBG-izmir)
Dokuz Eylül Üniversitesi Sağlık Yerleşkesi
Balçova 35340 İzmir
Telefon: 0(232) 412 86 51
Faks: 0(232) 412 63 53
E-posta: ibg@deu.edu.tr
Izmir International Biomedicine and Genome Institute (iBG-izmir)
Dokuz Eylül University Saglik Yerleskesi
Balcova 35340 Izmir/TURKEY
Phone: 0(232) 412 86 51 
Fax: 0(232) 412 63 53 
E-mail: ibg@deu.edu.tr

Enstitü Sekreterliği

Enstitü Sekreter V. Meral Yakut Öztürk +90 232 412 8654 meral.yakut@deu.edu.tr
Özel Kalem Ayşe Gül Özcan +90 232 412 8651  aysegul.ozcan@deu.edu.tr

 

 

İdari Birimler

Öğrenci İşleri  Dilek Düzyol Şengezer (Şef) +90 232 412 67 25 dilek.sengezer@deu.edu.tr
Öğrenci İşleri  Özlem Alku +90 232 412 67 25 ozlem.alku@deu.edu.tr
Öğrenci İşleri  Öğr.Gör.Sergül Bulut Gökdermen +90 232 412 67 25 sergul.bulut@deu.edu.tr
Kurumsal İletişim ve Kalite Birimi Öğr. Gör. Mine İnanç Demir +90 232 412 8660 mine.demir@deu.edu.tr
Uluslararası İlişkiler Birimi  Tuba Akünal +90 232 412  6717 tuba.akunal@deu.edu.tr
İnsan Kaynakları Birimi +90 232 412  8663
Yazı İşleri ve Evrak Kayıt Birimi Feyzi Önder +90 232 412 6717 feyzi.onder@deu.edu.tr
İdari ve Mali İşler Birimi Haktan Güner +90 232 412 6763 haktan.guner@deu.edu.tr

 


 

Izmir International Biomedicine and Genome Institute (iBG-izmir)
Dokuz Eylul Universitesi Saglik Yerleskesi
Balcova 35340 Izmir/TURKEY
Phone: +90(232) 412 67 04
Fax: +90(232) 277 63 53
E-mail: ibg@deu.edu.tr
İzmir Uluslararası Biyotıp ve Genom Enstitüsü (iBG-izmir)
Dokuz Eylül Üniversitesi Sağlık Yerleşkesi
Balçova 35340 İzmir
Telefon: +90(232) 412 67 04
Faks: +90(232) 277 63 53
E-posta: ibg-izmir@deu.edu.tr

 


Güncel DuyurularDuyuru Arşivi

2018-2019 ÖĞRETİM YILI GÜZ YARIYILI DOKTORA HAFTALIK DERS PROGRAMI

  2018-2019 ÖĞRETİM YILI GÜZ YARIYILI DOKTORA HAFTALIK DERS PROGRAMI

Devamı

2018-2019 ÖĞRETİM YILI GÜZ YARIYILI YÜKSEK LİSANS HAFTALIK DERS PROGRAMI

 2018-2019 ÖĞRETİM YILI GÜZ YARIYILI  YÜKSEK LİSANS HAFTALIK DERS PROGRAMI 

Devamı

100/2000 YÖK DOKTORA BURSU DEĞERLENDİRME SONUÇLARI

100/2000 YÖK Doktora Bursu Değerlendirme sonuçları için tıklayınız.

Devamı

100/2000 YÖK DOKTORA BURSU SINAV BİLGİLERİ

2018/2019 Güz Yarıyılı 100/2000 YÖK Doktora Bursu sınav bilgileri için tıklayınız.

Devamı

100/2000 YÖK DOKTORA BURSU İLAN METNİ (2018-2019 GÜZ)

100/2000 YÖK DOKTORA BURSU İLAN METNİ (2018-2019 GÜZ)

Devamı

Kesin Kayıt İçin Gerekli Belgeler

KESİN KAYIT İÇİN GEREKLİ BELGELER 1) Yabancı Dil Belgesi 2) Diploma veya geçici mezuniyet belgesi onaylı örneği 3) Not Döküm...

Devamı

2018-2019 GÜZ DÖNEMİ KAZANANLAR LİSTESİ

2018 2019 GÜZ DÖNEMİ KAZANANLAR LİSTESİ

Devamı

2018-2019 Dönemi Yüksek Lisans ve Doktora Sınav Tarihi ve Yerleri

  2018-2019 Dönemi Doktora Sınav Tarihi ve Yerleri 2018-2019 Dönemi Yüksek Lisans Sınav Tarihi ve Yerleri Moleküler Biyoloji ve Genetik...

Devamı

Enstitümüz Yüksek Lisans ve Doktora Programları Ön kayıt İşlemleri 02-06 Temmuz 2018 Tarihleri Arasında Yapılacaktır.

Enstitümüz Yüksek Lisans ve Doktora Programları Ön kayıt İşlemleri 02-06 Temmuz 2018 Tarihleri Arasında Yapılacaktır. Lütfen Tıklayınız.

Devamı

Ön Kayıt Başvurularının Erişim Sayfası Üzerinden Yapılması

ÖN KAYIT BAŞVURULARININ ERİŞİM SAYFASI ÜZERİNDEN YAPILMASI Ön kayıt başvurusu DEBİS (Dokuz Eylül Üniversitesi Bilgi Sistemi) üzerinden Enstitü’nün ilan ettiği...

Devamı