Nicolas Liem

Biophysical and biochemical characterization of enzymes (Rhodopsin phosphodiesterases) for Optogenetics: • Generated protein structures using LLM-based tools (AlphaFold2/3) in combination with classic homology modelling • Used and optimized ELISA / CLIA immunoassays to quantify small molecule antigens • Method development on RP-HPLC to develop an enzyme kinetic assay for 8 nucleotides • Aseptic techniques in mammalian cell cultures (HEK293T, ND7/23) for delicate proteins • Transient transfection to reduce build-test-learn cycles down to 7 days • Recombinant protein expression in 2 different prokaryotic systems (E. coli, P. pastoris) for high yield • Purified membrane proteins using affinity-tags (His6x, 1D4, StrepII) and SEC (ÄKTA pure) • Protein analysis by electrophoresis (SDS-PAGE) and western blotting • Used UV/Vis spectroscopy for stationary spectra and kinetic analysis • Optical assays using fluorescence, FRET, and luminescence in whole cells • Patch-clamp electrophysiology and improvement of optoelectronic systems • Molecular cloning (Quikchange, Gibson, restriction cloning) • General wet lab work, i.e. preparation of buffers and media • Conducted AI-supported literature research (Perplexity) to screen publications at large, extract findings, and assess them manually in my capacity as a reviewer. Paralleling my experimental research, I presented my results at internal and cross-team meetings, and at international conferences. I learned to communicate my findings through scientific writing and published a peer-reviewed paper as a first author. I coordinated collaboration projects and supervised students and technicians. This position was kindly supported by a scholarship for the BIG-NSE graduate school, funded by unisyscat/Einstein-Stiftung.

Initial phase in the unisyscat Graduate School (BIG-NSE) covering intercultural and softskill seminars.

For my master thesis, I switched to Hegemann lab, where I focused on color tuning of anion channelrhodopsins by rational design. • Homology modeling and sequence alignments to tailor point mutations • Molecular cloning (Quikchange) for mutant generation • Functional characterization (action spectra) using patch-clamp electrophysiology (HEK293) • Improved optical setups using custom-built devices, accelerating a routine task in calibration 6-fold I learned patch-clamp electrophysiology for HEK293 cells, and established an automated readout system for fast calibration of a state of the art monochromator (Cairn Optoscan).

To work on recently developed NIR voltage indicators, I joined Prof. Thomas Knöpfel's group (Laboratory for Neuronal Circuit Dynamics). • Aseptic cell culture (HEK293 cells) • Patch-clamp electrophysiology and the parallel readout of fluorescent voltage indicators (FRET) • Spectral multiplexing in all-optical electrophysiology experiments • Optimization approaches: illumination parameters, genetical engineering, transfection parameters. A great opportunity to have worked in a multinational, multidisciplinary team! Funded by the Erasmus+ internship programme.

I covered the fields of Physical Chemistry and Biophysics (e.g. fluid dynamics in biology and bioanalytics). For these, I prepared teaching material and taught undergrad seminars. A new professor had taken over the lecture, restructured it, and I redesigned the accompanying seminar. With my subsequential internship abroad planned, this on-site job was set up as a temporary position.

For my bachelor thesis, I investigated the motile pseudo amoeba D.discoideum during cAMP chemotaxis. • Fabrication of microfluidic chips using soft lithography • Lab-on-a-chip experiments using photouncaging. • Quantitative fluorescent microscopy of actin distributions using confocal microscopy • Image analysis using custom-written image segmentation algorithms (MATLAB)

I covered the fields of Physical Chemistry and Biophysics (e.g. fluid dynamics in biology and bioanalytics). For these, I prepared teaching material and taught undergrad seminars.

In my PhD studies, I specialized in enzyme research within cyclic nucleotide Optogenetics. • functional, spectral, and structural investigations with relevant methods • analytic skills: Critical thinking, pragmatic decision-making under uncertainty, interpretation of complex data • organizational/social skills: project management, crossfunctional teamwork, exchanging opinions in expert teams

Focus on experimental biophysics, molecular photobiophysics, photoreceptor research. Engineering of optogenetic actuators.