Cihan Tastan

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Contact Info

Life Lives In The Details But The Details Are Around Universe

Cihan Tastan

Life lives in details!

  • Major Department: Molecular Biology and Genetics
  • Minor Department: Computer Engineering
  • Undergraduate @ Middle East Technical University since 2006

Research papers by cihan tastan

Cihan Tastan

Research Interest

Infact, the real "Interest"ing issue is the ability to look into small pretty eyes of a cancer child!

My Research will be on Scientist position at Cancer and Virology Relationship by integrating novel technices of Bioinformatics and Synthetic Biology approaches.

Now Project Studies

METUSYBORG >> E-CO SENSOR: Cells can sense and respond to the presence of various gas molecules such as oxygen, nitrogen and carbon monoxide using gas sensor proteins. CooA is a carbon monoxide (CO) sensing transcription factor. It is a member of the cAMP receptor protein (CRP)/fumavate nitrate reduction (FNR) family of transcriptional regulators. CooA switches on oxidation enzymes in Rhodospirillum rubrum (a purple, nonsulfur, phototrophic bacterium) which enables the bacterium to use CO as a carbon source. CO is an odorless and colorless gas which can be extremely lethal. Our aim is to develop a cell sensor which can detect a wide range of CO concentration in the environment. We are building CooA and CooA-responsive promoter biobricks which will be transformed into E.coli. Fluorescent proteins (GFP and RFP) will be utilized as dose-responsive signals of ambient CO.

METU_TURKEY_SOFTWARE >> B-IO GUIDE: As Synthetic Biology is on the rise, iGEM also grows up and part numbers in partsregistry increase with submission of more constructs each year. Our first milestone is to perform more useful standardization on parts-entry due to facing some difficulty while running our algorithms. We also used Software Requirements Specification, Software Design Description and Quality Plan approaches to define requirements for each part and building blocks, risks and design art elements of the designed software program. Next, we have used graph theoretic modeling to visualize relations between parts and to standardize representation of the parts as much as possible. It will help us while trying to find input-output relations between either biobrick parts or constructs. By this way, our program as a Biobrick Guide will provide alternative pathway choices to users for construction of the most reliable devices with respect to given inputs and expected outputs.

My Dilemmas

One day, I will handle all my dilemmas!

- [1] (Codon) Bias to Virus: During transfection of viruses to host cells, ı wonder that whether virus genome replication exposes to codon bias (codon preferences). If there is such a case for replication of viruses within the host cells, then can we modify this property to use it against the inflammation by viruses. That is, by developing perfectly the host cell against the virus, so the virus would not be able to replicate due to codon preferences. Of course, during such a modification within the host cell, we have to pay attantion Engineered codon biases not to affect normal expression of host proteins.

- [2] Brat Transcription: I wonder that can Transcription take place during Replication? Because of that timeless and interesting replication event, ı named this case as Brat...

- [3] Sonic Energy Synthesis: Maybe one day energy producing pathway can be reengineered so that we can produce energy from sound, especially from vibrating particles, as photosynthesis, oxidative phosphorylation and nitrogen fixation...

- [4] Plasmid PCR: I want to be able to perform plasmid multiplication through PCR reaction as in proliferation of linear DNA fragments. Replication ways of different species can be searched to find appropriate enzymes for Plasmid PCR. Therefore, overnight waiting is removed and extra material used for transformation can be disappeared so on...

My Pitfall

Indeed,I know that we do not know any thing about life rather than we know!

- Bias to Virus in bacteria: Normally, interferon allow communication between cells to trigger the protective defenses of the immune system that eradicate pathogens or tumors. They increase the ability of uninfected host cells to resist new infection by virus in multicellular organisms. From this phenomenon, ı have thought that can we simulate this like communication within a bacterial culture with an viral infection? That is, with viral infection to bacteria, it will trigger a programmed cell death, leading to further propagation of virus in bacterial culture. With the help of such a project, ı thought that some viral dieases propagating in bacterial culture can be prevented. After some research, ı and my friends -E.Kalyoncu and F.Guzey- have found that a mazEF-mediated death pathway can act as a defense mechanism that prevents the spread of bacterial phage infection, allowing bacterial populations to behave like multicellular organisms in a study performed in 2005 by Hanna Engelberg-Kulka et al. published in Journal of Cell Science. In other words, such an synthetic biology mixed viral infection project exists naturally in bacteria.



Memberships & Awards

In fact, World is a Game, a Toy and an Amusement


Memberships

2010

  • Member of METUSYBORG Team in iGEM 2010 @ MIT
  • Member of METU_TURKEY_SOFTWARE Team in iGEM 2010 @ MIT
  • Moderator of SYNBIOWORLD Web Site Since January 2010 : http://www.synbioworld.org/content.php


2009

METU_GENE 2009 "A Fast Healing Mechanism; Wound Dressing":

In case of bulk loss of tissue or non-healing wounds such as burns, trauma, diabetic, decubitus and venous stasis ulcers, a proper wound dressing is needed to cover the wound area, protect the damaged tissue, and if possible to activate the cell proliferation and stimulate the healing process. By this purpose, designing a wound dressing which is natural, non-toxic, and biodegradable and imitating the actual wound healing mechanism which is forming on open wounds in mammalian tissues is our main purpose.By this wound covering, we will fasten the healing process, and protect the wounded area from infectious agents. In this wound dressing, there will be 4 layers including polyurethane layers and our bacteria colonies. Our bacteria colonies will be capable of synthesizing human epidermal growth factor and keratinocyte growth factor. The communication between these bacteria colonies will be dependent on quorum sensing molecules.


Awards

- METU_TURKEY iGEM 2010 Team was Gold Medal Winner with "E-CO SENSOR" Project.Look: http://2010.igem.org/Team:METU_Turkey

- METU_TURKEY_SOFTWARE iGEM 2010 Team was Silver Medal Winner with "B-IO GUIDE" Project.Look: http://2010.igem.org/Team:METU_Turkey_Software

- METU_GENE iGEM 2009 Team was Silver Medal Winner with "Wound Dressing" Project.Look: http://2009.igem.org/Team:METU-Gene

- National Molecular Biology And Genetics Semposium at Ege University 2008 Scientific Film Competition Bronz Award : http://www.dnatube.com/video/1362/Conversion-of-blood-groups

Presentations :

Oral

[1]Tastan C. Is O. Guzey F. Kalyoncu E. Atayol S. SEREF C. E-CO SENSOR: Carbon monoxide sensing cell sensor with Enhanced Dynamic Range EDR. International Genetically Engineered Machine Competition 2010 at Massachusetts Institute Of Technology, Cambridge, Boston, MA, USA, 5-8 November 2010

[2]Tastan C. Agca A. Yilmaz B. Matar H. Wakhid A. Syauqhy M. B-IO GUIDE: Synthetic Biology Software Program. International Genetically Engineered Machine Competition 2010 at Massachusetts Institute Of Technology, Cambridge, Boston, MA, USA, 5-8 November 2010

[3]Tastan C. & Is O. Introduction to synthetic biology and theoretical information about Our IGEM team pojects and organization. Istanbul Technical University, Istanbul, Turkey, 17-20 August 2009

[4]Tastan C. Is O. Guzey F& Oz, T Wound Dressing: Designing a controlled release system composed biomaterials and releasing human growth factors in a way that fasten the normal healing process. International Genetically Engineered Machine Competition 2009 at Massachusetts Institute Of Technology, Cambridge, Boston, MA, USA, 28 October-2 November 2009

Poster

[1]E-CO SENSOR: Carbon monoxide sensing cell sensor with Enhanced Dynamic Range EDR . International Genetically Engineered Machine Competition 2010 at Massachusetts Institute Of Technology, Cambridge, Boston, MA, USA, 5-8 November 2010 http://2010.igem.org/files/poster/METU_Turkey.pdf

[2] B-IO GUIDE: Synthetic Biology Software Program International Genetically Engineered Machine Competition 2009 at Massachusetts Institute Of Technology, Cambridge, Boston, MA, USA, 5-8 November 2010 http://2010.igem.org/files/poster/METU_Turkey_Software.pdf

[3]Wound Dressing: Designing a controlled release system composed biomaterials and releasing human growth factors in a way that fasten the normal healing process. International Genetically Engineered Machine Competition 2009 at Massachusetts Institute Of Technology, Cambridge, Boston, MA, USA, 28 October-2 November 2009 http://2009.igem.org/files/poster/METU-Gene.pdf

Publications(Private Research)

  1. DüNyA artık DNA! 16 May 2010 [1] [1]
  1. Zaman Makinesinin Olasiligi ve Imkansizligi 17 Feb. 2009 [1] [2]
  1. Ya Mars'ta yaşamaya mecbur kalırsak? 16 Feb. 2009 [1] [3]
  1. Arıların Yok Olması ve Hayatın Sonu 28 June 2008 [1] [4]

Papers @ Magazine

  1. DüNyA artık DNA! @ Bilimsel Makaleler Haberler Temmuz 1[1] [1]
  1. iGEM: Genç Genetik Mühendisleri ve Sentetik Biyoloji Projeleri Yarışıyor! @ ODTÜLÜ Dergisi Haziran 2010 [1] [2]
  1. Ya Marsta yaşamaya mecbur kalırsak? Makaleler Ağustos 2009[1] [3]

Competitions & Meetings

- The 1st Bio:Fiction Science, Art & Filmfestival aims at attracting public awareness to synthetic biology and its ramifications for our daily life in the future http://www.bio-fiction.com

- COMPETITION DESCRIPTION: PREDICT HIV PROGRESSION aims to do this by having contestants find markers in the HIV sequence which predict a change in the severity of the infection (as measured by viral load and CD4 counts). http://kaggle.com/hivprogression


Suggested Podcasts

- Synthetic Biology Online: A podcast series designed to educate both the layman and professionals about synthetic biology by Eric Ma from University of British Columbia: http://www.ericmajinglong.com/synbiopodcast/

- This Week in Virology(TWIV): A weekly netcast about viruses - the kind that make you sick. Vincent Racaniello and Dickson Despommier, science Professors from Columbia University, deconstruct viruses, how they cause illness, and how you can prevent infections: http://www.twiv.tv/




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