Elham Mirfazeli

ESR 14- Activated PI3 kinase delta in systemic lupus erythematosus (SLE)

Elham completed her bachelor’s and master’s degree at University of Tehran, Iran (2018) and during this time and after that experienced working in several different areas in biology. As her master’s thesis, she worked on the regulation of Wnt pathway during the process of dopaminergic neuron differentiation. She also contributed to a project regarding the function of SOXB1 proteins in pluripotent cells during her internship at University of Edinburgh. After graduation, she collaborated for establishing an NGS-based kit for the diagnosis of hereditary breast cancer in Dr. Zeinali's Medical Genetics Laboratory in Tehran.

Her scientific ambition, more specifically, is investigating how biological questions can be turned into computational questions and thereby addressed and further employing this approach for solving human health related problems. In this regard, she has started her work from the beginning of February 2020 in Prof. dr. Nejentsev lab at MCBI department in the O2 building of VU Medical Center. Her PhD project aims to address one of the major challenges in regard to treating systemic lupus erythematosus which is the high heterogeneity of the disease. She is studying the increased activity of PI3K delta pathway and the biomarkers that can be associated with this disturbance by analyzing the immune cell markers and transcriptome profile of these patients. Doing this research will hopefully help subgrouping lupus patients and open ways for personalized therapy of such patients as there are several FDA-approved drugs on the market that can inhibit this pathway. This puzzle solving with math but with this important implication to human health is what Elham enjoys about her work and makes her passionate about her field and what she is pursuing.

During her free time, Elham enjoys playing violin, swimming, traveling and exploring different cultures.

 

 

 

 

 

 

Dasha Balashova

Daria Balashova

ESR12 - Bioinformatics analysis of T-cell and B-cell repertoires

Daria Balashova received degree in mathematics with specialization in probability theory from Lomonosov Moscow State University (Moscow, Russia) in 2013 and since 2016 she continued research under the scientific supervision of Prof. Elena Yarovaya. Daria’s scientific interests are branching random walks, Markov processes, on which it is possible to construct a population-dynamic model of the reproduction and death of particles when they move along a multidimensional lattice.

In 2018 Daria graduated from Bioinformatics Institute (St. Petersburg, Russia). She took part in several projects, one of them was focused on analysis of gene expression by the use of algorithmic and statistical methods and hidden Markov chains and the goal of another one was to improve the quality of the ultra-low-input-NChIP-seq data with convolutional neural networks. Daria's keen interest was caused by the processes associated with adaptive immunity, the study of repertoires of immune receptors using machine and deep learning.

In her free time Daria spends time with friends and family, goes in for sports (hiking, skiing, snowboarding), attends a modern theater school and travels.

3 keywords:

branching random walk

machine/deep learning

computational immunology

Fatemeh Khodadust

Fatemeh Khodadustvaskasi

ESR18-  Molecular imaging of angiogenesis and therapeutic effects of anti-angiogenetic agents in rheumatoid arthritis

 

Studying radiology as my bachelor’s degree along with my master’s degree, radiopharmaceutical sciences, provide me with a comprehensive skills and broad view in wide variety of imaging modalities.

I have knowledge and experiences in radiopharmacy, radiolabeling, stability test, affinity assay,cell culture,biodistribution, human xenograft tumor mouse model, the preparation, quality control and supply of radiopharmaceuticals, biomolecules and labeled compounds, ability to work with analytical devices (TLC, HPLC) and also different imaging modalities, such as MRI, CT, X-ray tube, mammography, SPECT.

The title of my master’s thesis was “the influence of HYNIC chelator with Edda/Tricine as colignds on the specific uptake and the biodistribution of SSSLTVSPWYP peptide for imaging of ovarian cancer with overexpression of HER2”.

This developed peptide has been proven to exhibit high contrast tumor uptake both in biodistribution data and SPECT imaging which led to further examination by my knowledgeable research group to test it for clinical application. Simultaneously, I was involved in another project with the same peptide evaluating the influence of a co-ligand for improving the targeting and imaging of HER2 overexpression tumor. I have two publication related to my master thesis:

  • "An improved 99mTc-HYNIC-(Ser)3-LTVSPWY peptide with EDDA/tricine as co-ligands for targeting and imaging of HER2 overexpression tumor. " F. Khodadust, S. Ahmadpour, N. Aligholikhamseh, S.M. Abedi, S.J. Hosseinimehr, European Journal of Medicinal Chemistry, 2018. 144: p. 767-773.

DOI: https://doi.org/10.1016/j.ejmech.2017.12.037

Description: Overexpression of human epidermal receptor 2 (HER2) has given the opportunity for targeting delivery of anti-tumor drugs and radiotracers. The aim of this study was to evaluate the 99mTc-HYNIC-(EDDA/tricine)-(Ser3)-LTVSPWY peptide for tumor targeting and imaging of tumor with overexpression of HER2.

In our project, SSSLTVSPWY peptide was successfully labeled with 99mTc using HYNIC as chelator and EDDA/tricine co-ligands to overcome the problem of time-consuming double stage direct radiolabeling procedure, with an efficient output under the mild condition and improved in vitro and in vivo findings for tumor targeting compared to previously studied radiolabeled peptide (99mTc-Cys-Ser-Ser-Ser-LTVSPWY) by our research group. The proposed labeling method having advantages of a well-defined chemistry and the ability for post conjugation labeling in which the peptide is first conjugated with a BFCA and stored for later radiolabeling process. The result of my thesis turned out to be successful and became a subject for further experiment on clinical stage. For my project, radiolabeling, the in vitro stability, cellular affinity, animal biodistribution in

tumor bearing mice and imaging have been performed.

  • " 99mTc-HYNIC-(Ser)3-LTVPWY peptide bearing tricine as co-ligand for targeting and imaging of HER2 overexpression tumor." N. Aligholikhamseh, S. Ahmadpour, F. Khodadust, S.M. Abedi, S.J Hosseinimehr, Radiochimica Acta, 2018. 106(7), 601-609.

DOI: https://doi.org/10.1515/ract-2017-2868

Description: In other project with the same peptide (99mTc-HYNIC-(tricine)-(Ser)3-LTVSPWY peptide) labeling procedure have been evaluated with different coligand (tricine). It was investigated for HER2 binding affinity, targeting and imaging of HER2+ ovarian cancer. This radiolabeled peptide exhibited in vitro affinity and in vivo tumor targeting. The HYNIC-(Ser)3-LTVSPWY peptide was successfully labeled with 99mTc using tricine as a co-ligand at room temperature in order to make the radiolabeling procedure easier without the need for heating. Using tricine as coligand and tri-serine as spacer give a hydrophilic nature to this radiolabeled peptide which lead to fast clearance from kidneys and blood leading to rapid washout from non-targeted tissues in xenografted nude mice.The tumor/muscle ratio of 99mTc-HYNIC-peptide was lower than cysteine based peptide and tumor uptake was visualized at 4 h after injection of 99mTc-HYNIC-tricine-(Ser)3 LTVSPWY in SPECT imaging. For labeling of this peptide with 99mTc , practicing other co-ligands and chelators to achieve better tumor targeting and imaging is recommended.

My academic background:

September2015- May 2018

Master's Degree in Radiopharmaceutical Sciences

Mazandaran University of Medical Sciences

Sari, Mazandaran Province, Iran

 

Thesis title: The Influence of HYNIC Chelator with EDDA/Tricine as Colignds on the Specific Uptake and the Biodistribution of SSSLTVSPWYP Peptide for Imaging of Ovarian Cancer with Overexpression of HER2

Thesis Supervisor: Prof. Seyed Jalal Hosseinimehr

February 2013- February 2015

Bachelor's Degree in Radiology

Mazandaran University of Medical Sciences

Sari, Mazandaran Province, Iran

September2007-July 2009

Associate's Degree in Radiology

Mazandaran University of Medical Sciences

Sari, Mazandaran Province, Iran

 

 

Andrew Morrison

Andrew Morrison

ESR20- Development of immune competent lymph node on chip model including lymph node stromal cells, lymphocytes, and dendritic cells.

Andrew was born in Scotland and studied at the University of Aberdeen, graduating in June 2018 with a First Class MSci in Immunology & Pharmacology. Here, he was awarded the Immunology/Pharmacology prize for outstanding academic achievement. 

During his degree, Andrew completed an industrial placement with Novartis in Basel, Switzerland, where he worked in the Autoimmunity, Transplantation and Inflammation (ATI) department. His research efforts were focused on investigating IL-17A signalling events. After finishing university, he returned to Basel and the ATI department on a further postgraduate internship, this time uncovering mechanisms behind the cGAS/STING pathway. With almost two years in industry, Andrew decided the next step of his scientific career was to pursue a PhD at the Amsterdam UMC. 

Andrew started his PhD in April 2020 under the supervision of Prof. Dr. Reina Mebius & Prof. Dr. Sue Gibbs. His PhD project aims to develop a functional 3D organotypic lymph node with integrated lymphatics that mimic adaptive immune responses. Combining research on lymph node stromal cells and current in-house expertise of tissue engineering & microfluidic devices, the overall objective of the project is to design an organ-on-chip model that features lymphatic drainage of an immune competent gut into a lymph node. The immunosurveillance capability of the potential model will then be assessed by inducing an inflammatory response, followed by utilizing this next generation technology for testing of RA drugs.

Keywords: autoimmunity, adaptive immunity, organ-on-chip

Melis Asal small

Melis Asal 

ESR19- A human gut and -lymphatics on chip to model functional immune surveillance and activation; development of immune competent gut on chip model

 

Education

2017-2020 Master of Science

The Dokuz Eylul University, Izmir International Biomedicine and Genome Institute, Department of Molecular Biology and Genetics, Therapeutic Bioengineering Group, Izmir, Thesis title: Development of Lacrimal Gland from Human Induced Pluripotent Stem Cells Using Tissue Engineering Approaches

My thesis focuses on differentiation of hiPSCs in a microfluidic system in 3D to offer a treatment method for dry eye syndrome. In order to achieve this, I have developed the strategy to differentiate hiPSCs into cells that are capable of developing the lacrimal gland by following different methods and making modifications. I have monitored the differentiation by checking the expression of markers through ICC, IHC and qPCR. I am currently working on transferring the maturation process into a microfluidic system.

Student Supervision: Effect of potential therapeutic agent on breast cancer cells under dynamic conditions

I supervised a high school project that took place in our lab where we investigated the apoptotic effect of CAPE in a breast cancer cell line by objecting the cells to flow. I contributed to the experimental setup of this project and showed the students the principles of cell culture, microfluidic chip fabrication and cell staining studies.

2013-2017     Bachelor of Engineering (High Honor Student)

Manisa Celal Bayar University, Faculty of Engineering, Department of Bioengineering, Manisa, Turkey

Title: Independent research activity (Funded by The Scientific and Technological Research Council of Turkey: The Effect of Mesenchymal Stem Cells and Thyme Oil in Wound Healing

This project aimed investigating the use of thyme oil to increase the therapeutic effect of MSC in wound healing. I created wound models on Wistar rats and treated with different combinations of rat adipose mesenchymal stem cells, thyme oil and Madecassol. The synergistic effect of the combination was analyzed morphologically, histologically and immunohistochemically.

Bachelor’s Thesis: The Effect of Different Seed Extracts on Microbial Quality of Meat Products

The aim of this project was to increase the microbial safety of meat products by incorporating plant extracts. I assessed the antibacterial effects of hot ethanol extracts of dog rose, firethorn and grape seeds using disc diffusion assay and spectrophotometric analysis on model organisms Staphylococcus aureus and Bacillus subtilis. Then I applied the extracts to meat samples and analyzed their effects on microbial growth.

Professional Experiences and Internships

July-August 2018      Department of Physical Microfluidics and Bioengineering, Institut Pasteur, Paris, France, Erasmus Internship

Achievements: I worked on making collagen, fibrin and GelMA gels, I learned soft lithography chip fabrication and carried out 3D cell culture by encapsulating HUVEC, 3T3 and C2C12 cell lines in collagen and fibrin gels both conventionally and by forming droplets inside chips, and followed the migration of cells in 3D through live cell imaging

July-August 2017     Department of Bacterial Genome Plasticity, Institut Pasteur, Paris, France, Erasmus Internship

Achievements: Protein characterization through construction of mutants and doing viability studies under DNA damaging conditions to study the SOS induction in Vibrio cholera. Doing pathogenic bacteria culture, various PCR applications, competent cell preparation, electroporation, transformation, growth curve analysis and sample preparation for FACS analysis

August 2016             Department of Genomics, Izmir International Biomedicine and Genome Institute, Turkey. 

Achievements: Optimization of Gateway cloning, gel purification

July 2016                   Department of Microbiology and Quality Assurance, Pinar Integrated Meat Company                        

Achievements: Microbiological analysis on meat products (Listeria monocytogenes, Salmonella, Escherichia coli, Lactobacilli, mold and yeast analyses), doing pathogenic bacteria culture, qPCR analyses

July 2015                  Department of Molecular Biology and Genetics, GENMAR Diagnostic Company

Achievements: PCR primer synthesis, PCR applications and Sanger/Next Generation Sequencing

2012                       Student Science Projects Team, Izmir Private Çamlaraltı High School

Achievements: Conduction of the project “Measuring the Avidity of Monoclonal Antibodies Produced Against Toxoplasma gondii with ELISA using NaSCN”. Doing Enzyme Linked Immunosorbent Assay (ELISA) studies, result analysis

2012                          Student Science Projects Team, Izmir Private Çamlaraltı High School

Achievements: Conduction of the project “Biosorption of Pb+2 and Cd+2 Ions from Aqueous Solutions Using Phaeodactylum tricornutum, Chlorella vulgaris and Scenedesmus dimorphus”. Carrying out microalgae culture, biosorption experiments, FTIR measurements, applying the data to isotherms

2011                        Student Science Projects Team, Izmir Private Çamlaraltı High School

Achievements: Conduction of the project “The Antibacterial Effect of Montmorillonite Modified with Ag+1”. Adsorption, Volhard Titration and disc diffusion experiments, data interpretation

Professional Experiences and Internships

Laboratory Skills

 

Bioengineering: Design and fabrication of microfluidic systems, photolithograpy, softlithography

Biomaterials: Synthesis of photocrosslinkable hydrogels, 3D cell culture systems using fibrin, GelMA, PEG, collagen…

Cell Culture: Differentiation and protocol development for iPSCs, 3D cell culture under both static and dynamic micro environments/devices, culture of primary mammalian cells, cell lines, bacteria and microalgae

Genetic and Molecular Biology: Plasmid transformation, Nucleic acid isolation, PCR primer design and synthesis, qPCR, ELISA

Imaging and Histology: Live cell imaging, Confocal microscopy (Zeiss LSM 880), ICC, IHC

Lab animals: Certified user of mice and rats

Chemistry: Adsorption/biosorption, titration, FTIR

Computer Skills

MS Office (Word, PowerPoint, Excel)

GraphPad

CorelDraw

Adobe Photoshop

Matlab (beginner)

Scholarships and Awards

2018

3rd Place in the Best Poster Award Biomedical Science and Technology Symposium

2018

Scholarship for Outstanding Master’s Students, The Scientific and Technological Research Council of Turkey

2017

‘The Effect of Thyme Oil to Stem Cell Therapy in Experimental Wound Healing Model’, 3rd Place in the Engineering Category of Manisa Celal Bayar University 24th Science and Spring Festival Science Projects Contest

2017

‘The Effect of Mesenchymal Stem Cells and Thyme Oil in Wound Healing’ Undergrad Research Project Funding, The Scientific and Technological Research Council of Turkey

2012

‘Measuring the Avidity of mAbs Produced Against Toxoplasma gondii with ELISA Using NASCN’ Finalist of Acibadem University Project Olympiad, 2012

2012

‘Biosorption of Pb+2 And Cd+2 Ions From Aqueous Solutions Using Phaeodactylum  Tricornutum, Chlorella Vulgaris and Scenedesmus Dimorphus’ Honorable Mention, International Sustainable World Energy Engineering Environment Project Olympiad, Houston, TX

2011

‘The Antibacterial Effect Of Montmorillonite Modified With Ag+1‘ The Best Project of 13th Expo Sciences International, Bratislava, Slovakia

 

Publications

Asal, M., Güven, S. (2019) ‘Stem Cells: Sources, Properties and Cell Types’, Vrana, N., Knopf-Marques, H., Barthes, J. (ed.) Biomaterials for Organ and Tissue Regeneration: New Technologies and Future Prospects. Elsevier [book chapter submitted]

Asal, M., Özen, Ö., Şahinler, M., Baysal, H. and Polatoğlu, İ. (2018). An Overview of Biomolecules, Immobilization Methods and Support Materials of Biosensors. Sensor Review, 39(3), pp. 377-386.

Asal, M., Özen, Ö., Şahinler, M., Polatoğlu, İ. (2018). Recent Developments in Enzyme, DNA and Immuno-Based Biosensors. Sensors (Basel), 18(6).

Erbay, İ., Baş, A., Asal, M., Yanık, H., Güven, S., (2018). ‘Microfluidic Systems and Tissue Engineering’, Kuralay, F. (ed.) Advanced Materials: Biomaterial and Nanomaterial Applications. Palme Yayınları (in Turkish)

International Conference Proceedings

Asal, M., Yıldırım, C.A., Güven, S. ‘Induced Pluripotent Stem Cells (iPSC) Derived Lacrimal Gland’ 24th International Biomedical Science and Technology Symposium, İzmir, 17-20 October 2019

Baş, A.K., Asal, M., Kasal., K., Akbulud, O.B., Yıldırım, C.A., Güven, S. ‘Bioengineering of Lacrimal Gland in Microfludics’ 24th International Biomedical Science and Technology Symposium, İzmir, 17-20 October 2019

Sönmez Kılıçarslan P., Toros P., Asal M., Şahinler M., Tuğlu., İ. M. ‘Effects of stem cells and thyme oil in rat wound healing models’ 2nd International Graduate Education Congress, Manisa, 12-14 May 2017 (in Turkish)

Özen Ö., Baysal H.T., Asal M., Şahinler M. ‘The in vitro Effects of Stem Cells and Thyme Oil in Wound Healing Models in L929 Cell Line’ 2nd Life Sciences Congress, Kayseri, 23-25 February 2017

National Conference Proceedings

Baş, A.K., Asal, M., Kasal., K., Akbulud, O.B., Yanık, H., Yıldırım, C.A., Güven, S. 2018 ‘Lacrimal Tissue Engineering’ 23rd Biomedical Science and Technology Symposium, İstanbul, 15-16 December (in Turkish)

Baş, A.K., Asal, M., Kasal., K., Akbulud, O.B., Yanık, H., Yıldırım, C.A., Güven, S. 2018 ‘Development of Lacrimal Gland From Stem Cells Using the Tissue Engineering Approach’ 5th Biomaterial Days, İstanbul, 22-23 October (in Turkish)

Certificates

Certificate of Experimental Animal Use (80 hours)

Therapeutic mAb Engineering and Production Workshop (10 hours)

Extra-Curricular Activities

2018-…              Dokuz Eylül University, Faculty of Fine Arts, Department of Stage Arts, Acting

2018-…              Yol Sahne Theatre Troupe, Acting and Dramaturgy

2016-2018         Muradiye Campus Theater Club, Management and Membership

2016-…              LÖSEV (Children with Leukemia Foundation) Volunteer

2016-2018         Izmir Tarz Dance Academy, Classical Ballet Student

2015-2017         Izmir Tango Academy, Argentine Tango Student

Languages

Turkish (Native)

English (Excellent): IELTS Score 8

German (Beginner)

Spanish (Beginner)