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Welcome: Sinem Saka

Armed with pandemic-survival chocolate ice-cream and her molecular light-SABER, new EMBL group leader Sinem Saka embraces the role of molecular puzzle master

Woman with long brown hair stands in front of snow scene with arms crossed in front of her.
Sinem Saka, a new EMBL group leader in the Genome Biology Unit, takes puzzles to a whole new level, where finding a solution often means creating new molecular tools and methods. Credit: Massimo Del Prete/EMBL

For Sinem Saka, coming to EMBL for the next phase of her research career means a return to the country where she completed her PhD training. Sinem describes her research group’s role as creatively solving biological puzzles by developing tools and methods to unlock molecular information. They will harness multiple technologies, such as microscopy and single-cell analyses like single-cell omics, to become molecular puzzle masters.

Tell me about your research.

Biology is full of interconnected small puzzles, and we need to solve them without knowing what all the pieces are and which ones belong to each puzzle. In our new group, we focus on developing molecular tools and methods to increase the density of data and depth of information we acquire from our experiments. Integrating imaging with multiple complementary techniques for single-cell analysis, we hope to understand the phenotypic manifestations of a cell’s state and how spatial features in biology contribute to the function and organisation of subcellular compartments, cells, and tissues.  In other words, we want to capture the end-states (reached by integrating internal and external factors) of single cells much more comprehensively and unbiased than before, so that we can follow how they change under disease or stress conditions or in response to therapeutic interventions and identify what components drive these changes. This way we can discover the previously unknown pieces of the puzzles underlying cellular function and dysfunction.

How will EMBL and its facilities help your research?

EMBL is world famous for its collaborative atmosphere and the resources and expertise of its core facilities. Because we will use and integrate multiple technologies, these factors will be tremendously important to push our research forward. For me, direct access to diverse instruments and talent in EMBL’s Advanced Light Microscopy Facility and Genomics Core Facility will be particularly valuable. Similarly, I have no doubt that the interactions we are starting to have with EMBL’s dynamic groups will spark many new ideas and novel applications.

You developed a technique called Immuno-SABER in your research. What is it, how does it make your research better, and how sharp is it?

Immuno-SABER allows us to image multiple proteins in a given biological sample with improved sensitivity. We’ve demonstrated substantial improvements in the signal level, and have been able to detect more than 10 targets in the same sample, including clinical specimens. Known as multiplexing, this kind of capability, enabled by Immuno-SABER and other new methodologies, will help us uncover how structure and context relate to mechanisms behind health and dysfunction. With multiplexing we can discern the local environment surrounding our molecules or cells of interest. We hope that one day these methods will also have clinical applications, especially in the case of personalised medicine.

What’s your secret for staying focused and happy during the difficult times of the COVID-19 pandemic?

Frequent video chats with friends, family, and colleagues have been crucial to feel less isolated. To keep my mood up, I have been treating myself to homemade dinners and lots of chocolate ice-cream. Especially during extended periods of working from home, taking long walks outside when the sun is up and limiting the number of times I check the world news have been helpful for staying focused.

What was the last good book or movie that you enjoyed?

I recently saw the documentary series Our Planet. The ‘Jungles’ episode includes an amazing scene of a dancing male bird of paradise. Sometimes in the lab we focus on really specialised questions and don’t fully appreciate how those fine mechanisms come together at the organismal scale and create wonders like the amazing choreography of a bird of paradise. The episode was a good reminder that, thanks to evolution, nothing in biology is simple. A lot of perseverance and serendipity are needed to uncover its marvels, let alone the underlying molecular mechanisms behind those marvels.

What excites you most about your research?

I enjoy it when findings of seemingly unrelated research fields inspire a whole new approach for answering biological questions. I’m particularly excited when we can come up with a new method that could be used to solve problems in multiple different areas and eventually create value in other people’s lives.


Tags: advanced light microscopy, genome biology, phenotype, single-cell genomics, welcome

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