Biology subjects

Voitiuk, K.

Publications and source records attributed to Voitiuk, K..

14 recordsLinked to original sources

bioRxiv2026

Servo-Actuated 3D-Printed Disposable Microvalves for Automated, Scalable Organoid Culture in Standard Incubators

Automation of organoid and cell culture processes is essential for achieving scalable and standardized experimentation in regenerative medicine and stem cell research. However, existing microfluidic platforms often rely on complex setups, limiting their integration within standard incubator environments. To address these challenges, we developed a compact, scalable multi-well platform featuring 3D-printed, servo-actuated disposable microvalves for fully automated media and drug exchange. This design eliminates the need for external pressure sources and control channels, providing a simplified and cost-effective solution for organoid culture. The platform integrates an internet-connected microscopy module with a motorized XYZ stage, allowing continuous, real-time imaging of individual wells directly within the incubator. It supports precise and reliable fluid handling under physiological conditions, improving throughput, reproducibility, and accessibility. We validate the platform through bench-top testing and in both mouse and human organoid models. Morphological analysis, immunohistochemistry (IHC), and qPCR demonstrate comparable viability, growth, and gene expression profiles between automated and manual culture conditions. These results establish a robust and scalable framework for fully automated organoid culture, offering a simplified and accessible alternative to conventional microfluidic systems with broad applications in regenerative medicine, drug discovery, and scalable biological screening. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/732526v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@10297f1org.highwire.dtl.DTLVardef@1458d48org.highwire.dtl.DTLVardef@13e7eeeorg.highwire.dtl.DTLVardef@1ff4e5c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

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

Self-Organizing Neural Networks in Organoids Reveal Principles of Forebrain Circuit Assembly

The mouse cortex is a canonical model for studying how functional neural networks emerge, yet it remains unclear which topological features arise from intrinsic cellular organization versus external regional cues. Mouse forebrain organoids provide a powerful system to investigate these intrinsic mechanisms. We generated dorsal (DF) and ventral (VF) forebrain organoids from mouse pluripotent stem cells and tracked their development using longitudinal electrophysiology. DF organoids showed progressively stronger network-wide correlations, while VF organoids developed more refined activity patterns, enhanced small-world topology, and increased modular organization. These differences emerged without extrinsic inputs and may be driven by the increased generation of Pvalb+ interneurons in VF organoids. Our findings demonstrate how variations in cellular composition influence the self-organization of neural circuits, establishing mouse forebrain organoids as a tractable platform to study how neuronal populations shape cortical network architecture.

neuroscience↗

bioRxiv2024

Calcium dynamics tune developmental tempo to generate evolutionarily divergent axon tract lengths

The human brain has undergone an evolutionary expansion in size, both in terms of cell numbers and the size of cellular structures, including axon tracts. Human brain development also progresses slowly and takes particularly long. However, the functional relevance of slowed timing, and whether it is responsible for these changes in size, remains unknown. Here, we investigate this by studying axon tract development in human and mouse brain organoids. We demonstrate that human axon tracts grow [~]2x more slowly than those of mice, reflecting their slowed tempo, but that this actually leads to shorter human axons, not longer. To overcome the effect of slowed tempo, human axons have a more prolonged growth duration that enables them to project farther despite their slower growth rate. Using a combination of single-cell RNA sequencing and live imaging, we demonstrate that the prolonged duration involves a different mechanism to that controlling tempo and is driven by calcium dynamics. Human axons exhibit a reduced calcium influx compared to mouse, mediated by L-Type voltage-gated calcium channels. Stimulating this calcium influx in human neurons triggers earlier cessation of growth, leading to shorter axon tracts similar to those of mouse. We further show that increasing calcium speeds up the transition to the synaptogenesis stage. Thus, calcium regulation sets the timing of transitions to disproportionately extend developmental duration, thereby enabling evolutionary expansion of human neurons.

developmental biology↗

bioRxiv2024

Goal-Directed Learning in Cortical Organoids

Experimental neuroscience techniques are advancing rapidly, with major recent developments in high-density electrophysiology and targeted electrical stimulation. In combination with these techniques, cortical organoids derived from pluripotent stem cells show great promise as in vitro models of brain development and function. Although sensory input is vital to neurodevelopment in vivo, few studies have explored the effect of meaningful input to in vitro neural cultures over time. In this work, we demonstrate the first example of goal-directed learning in brain organoids. We developed a closed-loop electrophysiology framework to embody mouse cortical organoids into a simulated dynamical task (the inverted pendulum problem known as Cartpole) and evaluate learning through high-frequency training signals. Longitudinal experiments enabled by this framework illuminate how different methods of selecting training signals enable improvement on the tasks. We found that for most organoids, training signals chosen by artificial reinforcement learning yield better performance on the task than randomly chosen training signals or the absence of a training signal. This systematic approach to studying learning mechanisms in vitro opens new possibilities for therapeutic interventions and biological computation.

neuroscience↗

bioRxiv2024

Pathological microcircuits initiate epileptiform events in patient hippocampal slices

How seizures begin at the level of microscopic neuronal circuits remains unknown. Advancements in high-density CMOS-based microelectrode arrays can be harnessed to study neuronal network activity with unprecedented spatial and temporal resolution. We use high-density electrophysiology recordings to probe the network activity of human hippocampal brain slices from six patients with mesial temporal lobe epilepsy. Two slices from the dentate gyrus exhibited epileptiform activity in the presence of low magnesium media with kainic acid. Both slices exhibit network oscillations indicative of a reciprocally connected circuit, which is unexpected under normal physiological conditions. Future studies may apply this approach to elucidate the network signals that underlie seizure initiation.

neuroscience↗

bioRxiv2024

Multiscale Cloud-based Pipeline for Neuronal Electrophysiology Analysis and Visualization

Electrophysiology offers a high-resolution method for real-time measurement of neural activity. Longitudinal recordings from high-density microelectrode arrays (HD-MEAs) can be of considerable size for local storage and of substantial complexity for extracting neural features and network dynamics. Analysis is often demanding due to the need for multiple software tools with different runtime dependencies. To address these challenges, we developed an open-source cloud-based pipeline to store, analyze, and visualize neuronal electrophysiology recordings from HD-MEAs. This pipeline is dependency agnostic by utilizing cloud storage, cloud computing resources, and an Internet of Things messaging protocol. We containerized the services and algorithms to serve as scalable and flexible building blocks within the pipeline. In this paper, we applied this pipeline on two types of cultures, cortical organoids and ex vivo brain slice recordings to show that this pipeline simplifies the data analysis process and facilitates understanding neuronal activity.

neuroscience↗

bioRxiv2024

A feedback-driven IoT microfluidic, electrophysiology, and imaging platform for brain organoid studies

The analysis of tissue cultures, particularly brain organoids, requires a sophisticated integration and coordination of multiple technologies for monitoring and measuring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Our approach enables continuous, communicative, non-invasive interactions within an Internet of Things (IoT) architecture among various sensing and actuation devices, achieving precisely timed control of in vitro biological experiments. The framework integrates microfluidics, electrophysiology, and imaging devices to maintain cerebral cortex organoids while measuring their neuronal activity. The organoids are cultured in custom, 3D-printed chambers affixed to commercial microelectrode arrays. Periodic feeding is achieved using programmable microfluidic pumps. We developed a computer vision fluid volume estimator used as feedback to rectify deviations in microfluidic perfusion during media feeding/aspiration cycles. We validated the system with a set of 7-day studies of mouse cerebral cortex organoids, comparing manual and automated protocols. The automated protocols were validated in maintaining robust neural activity throughout the experiment. The automated system enabled hourly electrophysiology recordings for the 7-day studies. Median neural unit firing rates increased for every sample and dynamic patterns of organoid firing rates were revealed by high-frequency recordings. Surprisingly, feeding did not affect firing rate. Furthermore, performing media exchange during a recording showed no acute effects on firing rate, enabling the use of this automated platform for reagent screening studies.

neuroscience↗

bioRxiv2023

Internet-connected cortical organoids for project-based stem cell and neuroscience education

The introduction of internet-connected technologies to the classroom has the potential to revolutionize STEM education by allowing students to perform experiments in complex models that are unattainable in traditional teaching laboratories. By connecting laboratory equipment to the cloud, we introduce students to experimentation in pluripotent stem cell-derived cortical organoids in two different settings: Using microscopy to monitor organoid growth in an introductory tissue culture course, and using high density multielectrode arrays to perform neuronal stimulation and recording in an advanced neuroscience mathematics course. We demonstrate that this approach develops interest in stem cell and neuroscience in the students of both courses. All together, we propose cloud technologies as an effective and scalable approach for complex project-based university training. HIGHLIGHTS- Development of cortical organoids as pedagogical tools for undergraduate education. - Organoids implemented in a tissue culture course through cloud-enabled microscopy. - Multielectrode arrays allow for live organoid manipulation in a mathematics course. - Students self-report increased interest in neuroscience and stem cells topics.

scientific communication and education↗

bioRxiv2023

Modulation of neuronal activity in cortical organoids with bioelectronic delivery of ions and neurotransmitters

Precise modulation of brain activity is fundamental for the proper establishment and maturation of the cerebral cortex. To this end, cortical organoids are promising tools to study circuit formation and the underpinnings of neurodevelopmental disease. However, the ability to manipulate neuronal activity with high temporal resolution in brain organoids remains limited. To overcome this challenge, we introduce a bioelectronic approach to control cortical organoid activity with the selective delivery of ions and neurotransmitters. Using this approach, we sequentially increased and decreased neuronal activity in brain organoids with the bioelectronic delivery of potassium ions (K+) and {gamma}-aminobutyric acid (GABA), respectively, while simultaneously monitoring network activity. This works highlights bioelectronic ion pumps as tools for high-resolution temporal control of brain organoid activity toward precise pharmacological studies that can improve our understanding of neuronal function.

bioengineering↗

bioRxiv2022

Cloud-controlled microscopy enables remote project-based biology education in Latinx communities in the United States and Latin America

Project-based learning (PBL) has long been recognized as an effective way to teach complex biology concepts. However, not all institutions have the resources to facilitate effective project-based coursework for students. We have developed a framework for facilitating PBL using remote-controlled internet-connected microscopes. Through this approach, one lab facility can host an experiment allowing simultaneous interaction by many students worldwide. Experiments on this platform can be run on long timescales and with materials that are typically unavailable to high school classrooms. This allows students to perform novel research projects rather than just repeat standard classroom experiments. To investigate the impact of this program, we designed and ran six user studies with students worldwide. All experiments were executed in Santa Cruz and San Francisco, California, with observations and decisions made remotely by the students using their personal computers and cellphones. In surveys gathered after the experiments conclusion, students reported increased excitement for science and a greater desire to pursue a career in STEM. This framework represents a novel, scalable, and effective PBL approach that has the potential to democratize biology and STEM education around the world.

scientific communication and education↗

bioRxiv2021

Internet of Things Architecture for High Throughput Biology

The Internet of Things (IoT) provides a simple framework to easily control online devices. IoT is now a commonplace tool used by technology companies, but it is rarely used in biology experiments. IoT can benefit research through alarm notifications, automation, and the real-time monitoring of experiments. We developed and implemented an IoT architecture to control biological devices used in experiments. We developed our own electrophysiology, microscopy, and microfluidic devices so that may be controlled through a unified IoT architecture. The system allows each device to be monitored and controlled through an online web tool. We present our IoT architecture so other labs may replicate it for their own experiments.

bioengineering↗

bioRxiv2021

Development of a Low-Cost System for Simultaneous Longitudinal Biological Imaging

Simultaneous longitudinal imaging across multiple conditions and replicates has been crucial for scientific studies aiming to understand biological processes and disease. Yet, imaging systems capable of accomplishing these tasks are economically unattainable for most academic and teaching laboratories around the world. Here we propose the Picroscope, which is the first low cost system for simultaneous longitudinal biological imaging made primarily using off-the-shelf and 3D-printed materials. The Picroscope is compatible with standard 24-well cell culture plates and captures 3D z-stack image data. The Picroscope can be controlled remotely, allowing for automatic imaging with minimal intervention from the investigator. Here we use this system in a range of applications. We gathered longitudinal whole organism image data for frogs, zebrafish and planaria worms. We also gathered image data inside an incubator to observe 2D monolayers and 3D mammalian tissue culture models. Using this tool, we can measure the behavior of entire organisms or individual cells over long time periods.

bioengineering↗