Biology subjects

Doganyigit, K.

Publications and source records attributed to Doganyigit, K..

3 recordsLinked to original sources

bioRxiv2026

A Modular In-Incubator Microscope for Longitudinal Live Cell Microscopy

Longitudinal live cell imaging is valuable for characterizing dynamic morphological and phenotypic changes in biological systems. However, conventional approaches rely on manual microscope operation, which is labor-intensive, limits imaging frequency, and disrupts the cellular environment. These constraints reduce scalability, increase experimental variability, and restrict both the duration and temporal resolution of continuous imaging. Although automated imaging platforms partially address these limitations, existing solutions are often constrained by the cost, footprint, and inflexibility of in-incubator microscopes or stage-top incubators. Here, we present an automated in-incubator epifluorescence microscope designed for long-term operation. The system features a modular architecture with optional multi-fluorescence imaging, automated plate scanning, configurable light sources, and compatibility with multiple plate formats, including integration with fluidic automation devices. By positioning the light sources and control electronics outside the incubator, the platform improves thermal stability and long-term operational reliability. This approach enables continuous, high-frequency imaging over extended durations, providing a source of rich data for quantifying time-dependent tissue phenotypes, morphological remodeling, and transient biological processes.

bioengineering↗

bioRxiv2026

Cloud-Connected Pluripotent Stem Cell Platform Enhances Scientific Identity in Underrepresented Students

Stem cell research offers unique opportunities for authentic scientific engagement, yet infrastructure requirements have confined participation to elite institutions, perpetuating workforce disparities. We developed an integrated framework combining engineered biology, cloud-connected microscopy, and validated psychometric assessment to make pluripotent stem cell (PSC) experimentation widely accessible. The framework comprises three components: a doxycycline-inducible NGN2 mouse embryonic stem cell line for rapid neuronal specification, low-cost cloud microscopy for remote observation, and the validated Stem Cell Research Identity Scale (SCRIS) for quantifying educational outcomes. Implementation across a Title I high school and urban community college demonstrated significant increases in scientific identity. Students using differentiating PSCs showed broader science identity development than those using neuroblastoma cells, particularly in competence, research readiness, and recognition. High school students showed enhanced research competence gains compared to community college students despite equivalent intervention duration. Demographic analyses revealed enhanced effectiveness for Hispanic and first-generation college students. This framework provides a scalable model for broadening participation in advanced biomedical research.

scientific communication and education↗

bioRxiv2025

Incubator-Free Organoid Culture in a Sealed Recirculatory System

Discovery in human biology is pivoting toward high-dimensional computational analysis of 3D in vitro models, but this progress is limited by reliance on conventional cell culture techniques. Realism and data collection are hindered by the environmental instabilities and accessibility constraints of standard incubators. We introduce an automated, sealed recirculatory system that eliminates these barriers, enabling unconstrained instrument integration and infrastructure-independent scalability. By employing gas-tight sealing, a liquid-phase gas buffer and a non-porous plastic gas exchanger, our technology maintains biological stability without the compromises of open-air vessels. This design eliminates the need for CO2 incubators and prevents the evaporative drift that typically plagues conventional open-culture vessels. Operating on the benchtop outside the cell culture suite, we demonstrate that our system supports continuous, multi-week live imaging of vascular organoids while maintaining metabolic viability, structural fidelity and electrophysiological activity in brain organoids comparable to traditional in-incubator cultures. TeaserA sealed benchtop device enables data-rich organoid culture beyond the constraints of the cell culture laboratory.

bioengineering↗