Rafiqi Lab
Work areas
Ecological Evolutionary Developmental Biology, Endosymbiosis, Major Transitions
PI. Ab. Matteen Rafiqi
Dr. Rafiqi has had extensive experience in insects' development and evolution. He initially studied the flies (Diptera: Phoridae and Syrphidae) where he explored the major steps in the evolution of extraembryonic membranes. He then switched to the ants (Hymenoptera: Formicidae) where he studied the evolution of endosymbiosis. Now he works with ants as well as true bugs (Hemiptera: Cicadellidae). He is broadly interested in exploring how development integrates genetic and environmental inputs into the phenotype - the primary target of natural selection. The working idea in the lab is that endosymbiosis must be seen not as a relationship between two individual organisms but a phenomenon where the endosymbiont must integrate into the host developmental gene regulatory network such that they act as a single organism. He uses insects because they are the most speciose eukaryotic organisms on the planet and possess a remarkable degree of morphological, physiological and behavioral diversity. Dr. Rafiqi expands upon the rapid advances in the field of evolutionary developmental biology (evo-devo) in the past few decades wherein the developmental genetic basis of this diversity in insects was studied in detail. Taking inspiration from the classical studies in embryology of insects done from the mid-19th to the mid-20th century, he wants to understand how genetic accommodation, genetic assimilation, developmental plasticity, and developmental endosymbiosis can be integrated into the study of evolution.
Currently the lab works on two model organisms and several projects. Broadly these projects are aimed at understanding the mechanisms of major evolutionary transitions and the molecular genetic interactions between the endosymbiont and the host genes.
State of the art facilities and expertise for imaging, transgenesis, and genetic manipulation of insect embryos.
Dr. Rafiqi came to Turkiye from the University of Chicago and McGill with a vision to expand the availability of state-of-the-art scientific training beyond the developed countries. In this regard, he believes that basic science shall play a pivotal role in minimizing the disparity in scientific training as well as attitudes towards science in general and biology in particular. While translational science provides quick returns, basic science treads on untrodden paths to discoveries, making it possible to make a higher impact in the societies where it is undertaken. Studying basic sciences also allows the trainees to ask creative and original questions in their fields, which deepens their understanding of these concepts.
PhD - The University of Chicago
MSc - Wageningen University
Molecular Biology, Biotechnology, Evolutionary Biology, Developmental Biology, Ecology.
2017 – present Bezmialem Vakif University
2010 -2016 McGill University
2009 – 2010 The University of Chicago
1. 2020 Rafiqi, A.M, Rajakumar, A. and Abouheif, E. "Origin and elaboration of a major evolutionary transition in individuality." Nature 585.7824 (2020): 239-244.
2. 2021 Alim Uysal, B. A., Kotan, G., Guneser, M. B., Dincer, A. N., Senturk, H., & Rafiqi, A. M. (2021). Investigation of the effect of different chelation solutions on penetration of resin-based and bioceramic sealers with a novel method. Microscopy res & tech, 10.1002/jemt.23717. Advance online publication. https://doi.org/10.1002/jemt.23717
3. 2021 Milat NS, Çelik M and Rafiqi A.M. Taxonomic classification analysis of human gut microbiota using Kraken 2 [version 1; not peer reviewed]. F1000Research 2021, 10:695 (poster) (https://doi.org/10.7490/f1000research.1118672.1)
4. 2022 Rafiqi A.M, Polo P.G., Milat N.S., Durmuş Z.Ö, Çolak-Al B., Alarcón M.E., Çağıl F.Z., Rajakumar A. (2022) Developmental Integration of Endosymbionts in Insects. Fron in Ecol & Evol
5. 2022 Alarcon, M.E., Polo, P.G., Akyüz, S.N., Rafiqi, A.M. (2022) Evolution and ontogeny of bacteriocytes in insects. Front in Phys, 13, 2482
6. 2022 Polo, P.G., Çolak-Al, B., Şentürk, H., Rafiqi A.M. (2022) Gut bacteria after recovery from COVID-19: a pilot study, Eur Rev for Med & Phar Sci, 26: 8599-8611
7. 2023 Akyuz, S.N., Kina, U.Y., Aly, A.S.I, Palabiyik, B. (2023) Iron affects localization of Ght5 in fission yeast. FEMS Microbiology Letters, 17;370:fnad022
8. 2023 Kina, U.Y., Kamil, M., Deveci G., Rafiqi A.M., Aly A.S.I (2023) A Candidate Bacterial-Type Amino Acid Decarboxylase Is Essential for Male Gamete Exflagellation and Mosquito Transmission of the Malaria Parasite. ASM Infection & Immunity, 18;91(7):e0016723.
9. 2023 Kianifard, L., Rafiqi, A.M., Akcakir, O. et al. A recombinant Aspergillus oryzae fungus transmitted from larvae to adults of Anopheles stephensi mosquitoes inhibits malaria parasite oocyst development. Sci Rep 13, 12177 (2023). https://doi.org/10.1038/s41598-023-38654-0
10. 2024 Fatma Zehra Çağıl, Koray Ak, Ab Matteen Rafiqi, Ayten Saraçoğlu, Gamze Nur Öter, Şermin Tetik Determination of Early Diagnostic Biomarkers of Renal Dysfunction After Cardiopulmonary Bypass: miR-21 and miR10a Mediated Postoperative Inflammation Clin Exp Health Sci 2024; 14: 245-252
- Understanding the Emergence of Cells Housing Endosymbionts using Leafhoppers. TÜBİTAK 1001
- Use of transcriptome to study the effects of antibiotics on the development of the leafhopper, Anaceratagallia ribauti (Hemiptera: Cicadellidae) BVU-BAP
- Investigating interactions between multiple gene regulatory networks during ant development BVU-BAP
- Genome editing of Hox gene region by CRISPR/Cas9 system in ants BVU-BAP
- Completed grants/projects
- Establishment of insect colonies for the study of obligate endosymbiosis in insects BVU-BAP 6.2018/20
- Experimental studies on the effect of antibiotics on early development of Cicadellidae BVU-BAP 9.2019/5
- Identification of gut microbiome of individuals who live in Turkey, pilot study BVU-BAP 11.2018/16
- Development of microorganisms against vector borne diseases by biotechnological and paratransgenetic methods TÜBİTAK 1001 218S724
- Mechanism of segregation of endosymbiont between midgut epithelium and gonad BVU-BAP 20200822
- Characterization of fungal endosymbionts of bumble bees (Bombus terrestris) and their relation with pathogens. BVU-BAP 20200610
- The Developmental Genetics of Obligate Endosymbiosis and Its Effect on the Evolution of Insects TÜBİTAK 2247-A 120C157
- Potential role of alternative transcript isoforms in developmental genes in ants TÜBİTAK 2209-A
- BMP signaling in Camponotus floridanus and its alteration in the presence of obligate endosymbionts İÜ-BAP FYL-2021-37348
Lab Achievements
In recent years, our lab has made tremendous progress, particularly with the development of two insect model systems designed for experimental use. The successful completion of the Turkish Leadership Researcher (TÜBİTAK 2232) project has been a key achievement, propelling us into new and exciting research directions within the field of ecological evolutionary developmental biology (eco-evo-devo). Through this journey, we've also had the honor of mentoring two promising scientists—one now pursuing graduate studies at the University of Chicago, and the other serving as a faculty member at Syracuse University.
One of the most significant intellectual contributions of our team is the creation of the “developmental integration" framework in endosymbiosis. This innovative approach redefines how we think about the interactions between hosts and their symbiotic partners, and we have shared these ideas in a recent review. Our lab is also at the forefront of using system-level transcriptomics and enhancer studies to explore these interactions. In addition, we're pioneering new methods like PNA-based gene knockdown with plasmid-based rescue, which will shed new light on the mechanisms of endosymbiont gene function.
Mentorship Philosophy & Role of BILSAB
As a principal investigator, I'm committed to cultivating an environment of open access and inclusive mentorship. While many academic programs require formal training prerequisites, I strongly believe that talented students often remain untapped due to rigid educational systems. In our lab, we focus on hands-on engagement, giving students the chance to explore science through real-world research. Many of our current team members started as volunteers and, through guidance and personal growth, have transitioned into full-fledged scientists.
BILSAB has been an ideal environment for realizing this mentorship vision. The institute's flexibility and support for unconventional educational pathways have been crucial in allowing me to tailor mentoring practices to the unique needs of each student. This has made it possible to foster a scientific community where curiosity and collaboration drive progress, not rigid rules or hierarchies. BILSAB's openness to individualized learning and innovative training models has provided the perfect foundation to develop the next generation of researchers who are not only skilled but also driven by a passion for discovery.
Vision for the Future
I firmly believe that the future of science lies in inclusive, collaborative communities—where talent from all backgrounds is nurtured, and scientific inquiry is guided by curiosity rather than barriers. By offering equal opportunities for all, regardless of race, gender, or socioeconomic background, we can unite a diverse set of minds to tackle the most complex and urgent challenges facing the world today. My vision is to contribute to reducing global disparities in both the quality of science and the scientists producing it. This can only happen when we actively empower and uplift those who have been historically marginalized or overlooked in traditional academic structures.
At BILSAB, I'm excited to be part of a collective effort to build a more inclusive and impactful scientific future, where our research contributes not just to academia but to solving global problems and creating positive change in the world.
About the team:
Our team consists of PI, a postdoctoral scientist, and four PhD students.
- Number of the team members/students in lab
5
- Dr. Mauricio Alarcon Post-doctoral Researcher Bezmialem Vakıf University
- Zelal Özgür Durmuş Tübitak Scholar / PhD Candidate Hacettepe University
- Nihan Sultan Milat PhD Student / Research Assistant Bezmialem Vakıf University
- Birgül Çolak-Al PhD Student / Research Assistant Bezmialem Vakıf University
- Sevim Nur Akyüz PhD Student / Technician Bezmialem Vakıf University
- Elif Kurt Technician Bezmialem Vakıf University
Introduction of the team members. A line or two by the team members, as to why they recommend BILSAB.
Mauricio E. Alarcón, PhD, is a native of Chiguayante, Chile. Early in his research, he studied parasitic symbiosis through flea-rodent and cat flea-gregarine interactions. Currently, Dr. Alarcón's research focuses on mutualistic interactions between bacterial endosymbionts and insects, examining the ecology of the species, their embryological development, and their evolutionary history. His long-term goal is to decipher how phylogenetically distant organisms become fully integrated, ultimately functioning as a single unit. He is currently leading the TÜBİTAK 1001 project which aims to track the developmental trajectory of the cells that become bacteriocytes in a species of leafhoppers called Anaceratagallia ribauti.
Zelal Özgür Durmuş
I am writing my doctoral dissertation with Prof. Ergi Deniz Özsoy at Hacettepe University, the Department of Biology and I am working as a research assistant in a TUBİTAK project directed by Ab. Matteen Rafiqi at Beykoz Institute of Life Science and Biotechnology.
My main fields of interest are endosymbiosis and developmental genetics. I seek to approach these two subjects within the framework of ecological, evolutionary, developmental biology. Furthermore, I am curious about the alteration of traditional evolutionary views within the context of the philosophy of biology. On a personal level, sharing ideas, giving speeches, and writing popular columns about science and evolution are some of my outreach activities. I am also a passionate nature observer, whether the birds, the sky, or the underwater.
I'm Nihan Sultan, a PhD candidate in the Rafiqi Lab. I'm fascinated by the complex question of obligate endosymbiosis: how hosts and their symbiotic partners co-evolve and communicate at the molecular level. To investigate this, I focus on ants, a group that showcases incredible biological diversity and intriguing symbiotic associations. More specifically, I study how the BMP signaling pathway shapes these endosymbiotic interactions and contributes to key developmental processes. By examining gene expression and pathway dynamics, I aim to uncover how molecular signaling governs the intricate crosstalk between the host and its endosymbionts. One of my favorite aspects of my scientific work is also a bit of an exploration: capturing the hidden beauty of endosymbiosis through microscopy, blending science with art, and I love every moment of it!
Beyond the lab, I love exploring new countries and immersing myself in different cultures. Science has also taken me on journeys around the world, allowing me to attend conferences, share ideas, and collaborate with researchers from diverse backgrounds. These experiences fuel my curiosity and passion for discovery!
Birgül Çolak Al
I am a PhD student with a background in Molecular Biology and Genetics, having completed my bachelor's and master's degrees in this field. This year, I started the PhD programme in the Laboratory of Ecological Evolutionary Developmental Biology at the Beykoz Institute of Life Sciences and Biotechnology to explore fundamental questions about the evolutionary and developmental biology of ants.
My research focuses on Camponotus floridanus, a model ant species that harbors the obligate endosymbiont Blochmannia. I study the Hox genes within the bithorax complex (BX-C), which are highly conserved transcription factors that determine segmental identity during embryogenesis in bilaterian animals. In ants, these genes have evolved beyond their canonical homeotic functions, exhibiting maternal expression that influences posterior development and germline formation. My work aims to uncover how the regulatory mechanisms of BX-C genes have evolved in ants.
Sevim Nur Akyüz
I am a PhD student and research technician with a background in Molecular Biology and Genetics, currently pursuing my PhD in Biotechnology at BILSAB. My work explores the metabolism of Blochmannia, the obligate endosymbiont of the Carpenter ant Camponotus floridanus.
My research focuses on Blochmannia's genes and metabolic pathways using advanced molecular tools to uncover how this bacterium supports its host and sustains the intricate metabolic interdependence between the symbiont and ant.
The lab attended two major conference this year, one in Helsinki, which was attended by four of the members including the PI and one in Çanakkale, which was attended by five of the members including the PI. The conferences were a great opportunity to share our work and ideas with the wider global and Turkish community of scientists.
Rafiqi Lab Projects
- Ab. Matteen Rafiqi Establishment of insect colonies for the study of obligate endosymbiosis in insects Ongoing
- Ab. Matteen Rafiqi Identification of gut microbiome of individuals who live in Turkey, pilot study Ongoing
- Ab. Matteen Rafiqi Mechanism of segregation of endosymbiont between midgut epithelium and gonad Ongoing
- Ab. Matteen Rafiqi The Developmental Genetıcs of Obligate Endosymbiosis and Its Effect on the Evolutıon of Insects Ongoing
- Ab. Matteen Rafiqi Investigating interactions between multiple gene regulatory networks during ant development Ongoing
- Ab. Matteen Rafiqi Genome editing of Hox gene region by CRISPR/Cas9 system in ants Ongoing
- Ab. Matteen Rafiqi Camponotus karıncalarında BMP ve Hox gen düzenleyici ağ bağlantılarının araştırılması Ongoing
- Koray Kasan Potential role of alternative transcript isoforms in developmental genes in ants Ongoing
- Mauricio Ernesto Alarcon Alvarez Understanding the Emergence of Cells Housing Endosymbionts using Leafhoppers Ongoing
- Mauricio Ernesto Alarcon Alvarez Use of transcriptome to study the effects of antibiotics on the development of the leafhopper, Anaceratagallia ribauti (Hemiptera: Cicadellidae) Ongoing
- Nihan Sultan Milat BMP signaling in Camponotus floridanus and its alteretion in the presence of obligate endosymbionts Completed
- Priscila Gomez Polo Experimental studies on the effect of antibiotics on early development of Cicadellidae Completed
- Priscila Gomez Polo Characterization of fungal endosymbionts of bumble bees (Bombus terrestris) and their relation with pathogens. Completed
Lab alumni. Their current status.
- Hilal Şentürk (Istinye Üniversitesi)
- Esra Taylan (Dora Vocational High School of Health)
- Koray Kasan (The University of Chicago)
- Fatma Zehra Çağıl (Syracuse University)
- Yeşim Erol (İstanbul Technical University)
- Priscila Gomez-Polo (Ruykus University Japan)
Testimonies by Alumni. Waiting for the response from the alumni.
