LABORATORY RECORD

Name of the Laboratory:

Biochemistry Research Laboratory

Unit/Unit(s) Reported to:

Faculty of Engineering

Chemical Engineering and Applied Chemistry Department

Center

Sponsor Information:

DPT, COST, ATUBAP, AUBAP, Atilim University Resources

LABORATORY CONTACT INFORMATION

Address:

A-2 Building, Floor -3

WEB Address:

biochem.atilim.edu.tr

Telephone Number:

+90 (312) 586 85 28

Lab Director/Supervisor:

Assoc.Dr. S.Belgin İşgör

E-mail: belgin.isgor@atilim.edu.tr

Telephone +90 (312) 586 83 86

Lab Personnel:

 

Name Surname

Position

E-mail

Naznoosh Shomali

PhD Student

naznoosh_shomali @yahoo.com

Gulsah Merve Aslan

Master Student

technolog86@gmail.com

Mohammed Alwerfally

Master Student

werfally_84@yahoo.com

Suheda Koc

Master Student-volunteer

 

Sercan Cadirci

Master Student-volunteer

 

Khalid Sharro

Master Student-volunteer

 

MISSION OF THE LABORATORY

Mission of the Lab:

Education

Undergraduate √    Master’s  √    Doctorate √

Research

Undergraduate √    Master’s  √    Doctorate √

Service

 

 

ABOUT THE LABORATORY

Founding date:

2005

Laboratory Area

 100 m2

Specialty Area(s) of the Lab:

The aim of the research activities held by the biochemistry research group is to establish a link between basic sciences and engineering applications by employing tools to enhance current activities in the field. In general, with several collaborations through intramural and extramural research groups and institutions, biochemistry research group is working on different aspects of molecular target identification, drug-like molecule characterization, target enzyme profiling, compound profiling on a selected protein or enzyme target, assay miniaturization, evaluation of natural products of traditional and complementary medicine practices, and toxicology, biotechnology and medicinal biochemistry aspects of nano-technological products.

Current research activities also include bio-compatible nanoparticle synthesis and their characterization as drug carriers for controlled drug delivery tool development, and the characterization of different class of compounds for their capacity to use as therapeutic and diagnostic agents.

Competencies of the Lab:

 

Name

Function

Multimode microplate reader and software

UV-Visible Absorbance (Abs) and Fluorescence Intensity  (FI) measurements to perform Assay miniaturization,  protein, enzyme, and nucleic acid characterization,  analysis of signaling pathways, including antioxidant defense, xenobiotic and nanomaterial toxicity, signaling pathways mediated by kinase, phosphatase and transferase enzymes functional in development and prognosis of proliferative diseases including cancer and rheumatoid arthritis.

Cell culture laboratory

Maintenance of immortal cells, including human and animal model cells, to perform drug, nanoparticle and environmental toxicity analysis, analyze the effectiveness of drug and drug-like molecules and defining their novel bio-targets, performing cell based assays to investigate signaling pathways by cell viability, membrane permeability, apoptosis, target enzme (nuclear, membrane bound and cytosolic) activity and DNA integrity.

Wet Biochemistry Lab

The wet biochemistry section of the laboratory serve for the general purposes and requirements of the biochemistry research laboratory where protein and enzyme isolation, purification and characterization is performed to provide sources for the ongoing projects. This also includes the assay optimization and miniaturization for micro scale tasks, Optimization of analytical tools for biochemistry and biotechnology applications to develop tools for cost effective projects.

Electrophoresis and electroblotting section 

The effectiveness of drug and drug-like molecules, natural products (mushroom and plant extracts and components) are generally evaluated by the alterations in their target enzyme, nuclear, membrane bound and cytosolic protein expression levels. The changes in integrity of RNA and DNA molecules are another group of accepted targets for most toxicants and therapeutics. The Electrophoresis and electroblotting section of  biochemistry research laboratory mainly focus on the optimization of target specific protocols to analyze the changes in the levels or integrity of target proteins or biomolecules. Here, the general tool used is the Vertical and Horizontal Electrophoresis and Protein Blotters, accompanied by visualizing systems (imager) with suitable software.

Completed Projects till today/On-going Projects (for research labs):

 

Project Name

Relevant Institution/ Organization

Budget

Beginning Ending date  

Image Processing Based Automatic cell analysis system TOMA employed dye exclusion based  cell counting, viability testing and morphology analysis

DPT

40000 TL

2006-2010

The amount and viability of cells play an important role in the field of microbiology and cell biology. The basic cell counting process is through microscopic analysis using hemocytometer, performed by a technician. In this process, the most economical and widely used technique is dye-exclusion method to determine cell number and viability. In this study, a novel image based approach for cell counting (NIBA-C) is proposed with a capability of distinction between alive cells from death during the process. For evaluating the success of proposed method, the results obtained by the method are compared with microscopic cell viability count by virtue of classical dye-exclusion method. Artificial Neural Network is used to distinguish cell images from non-cells and death cell images from alive cells.

Publication: Ozkan, A., Isgor S.B., Tora, H., Uyar, P., Iscan, M., "An Alternative Method for Cell Counting", IEEE Conference Publications (IEEE Xplore), 11:1048-1051 pp., 2011 , DOI: 10.1109/ SIU.2011

Project Name

Relevant Institution/ Organization

Budget

Beginning Ending Date

Alginate nanocarrier systems for controlled drug release: Evaluation of  their in vitro effects

ATU BAP

30000 TL

2012-

Nano-sized drug carriers (NC) increases the therapeutic effectiveness of drugs while reducing the systemic toxicity, hence, improve the patient’s life quality and expectancy; reduce the costs reflected to patients, healthcare-providers and pharmaceutical industry. -Alginate-NCs (ANC) are biodegradable polymeric NCs, and produced with Calcium cross-binders (CB) mostly at micro-sizes. For the first time, this project showed that low nanosized ANCs can be produced with different metal CBs are advantageous by providing  lowest toxicity than other CBs available in literature. It is still in-progress to evaluate their comparative drug-release capabilities, and their efficacy to facilitate absorption of therapeutics loaded.

Poster Presentation : Umran Aydemir Sezer, Yasemin G. Isgor, Belgin S. Isgor, “The Analysis Of Alginate Nanocarriers With Novel Cross-Linkers: The Effect Of Cross-Linker On Drug Release And Biological Activity” Applied to The world Materials Congress, September 2013, Izmir, Turkey.

Project Name

Relevant Institution/ Organization

Budget

Beginning Ending Date

The Analysis of Different Extracts Prepared from Some Wild Plants Grown Around Ankara for their antioxidant capacities and effects on antioxidant enzymes

Ankara University BAP

15.000

2013-2015

In support of the MSc project of Gulsah Merve Aslan (Co-advisor)

Project Name

Relevant Institution/ Organization

Budget

Beginning Ending Date

Evaluation of Medicinal Plant Extracts from Ankara Region to Determine Their Antioxidant and Anticancer Activities

Ankara University BAP

23.000

2013-2015

In support of the PhD project of Naznoosh Shomali (Co-advisor)