Biology subjects

Jaiswal, B.

Publications and source records attributed to Jaiswal, B..

3 recordsLinked to original sources

bioRxiv2026

Fabrication and Use of a 32-Well LED-Embedded Microplate for Optogenetic Dynamic Control

SUMMARYThis protocol describes how to fabricate, program, and operate a 32-well LED-embedded microplate for optogenetic studies (LEMOS 2.0) inside a microplate reader to enable high-throughput optogenetic stimulation and quantitative gene expression measurements in microbial cultures. Optogenetic control enables light-actuated regulation of gene expression and provides a programmable interface between living cells and electronic systems. However, routine prototyping of optogenetic constructs remains limited by infrastructure. Existing closed-loop platforms often require chemostats, microfluidics, robotic handling, or custom optical sensors, which can increase cost, reduce accessibility, or constrain measurement performance. Here, we present LEMOS 2.0, an updated LED-Embedded Microplate for Optogenetic Studies, a low-cost device for optogenetic stimulation and gene-circuit characterization inside standard off-the-shelf microplate readers. LEMOS 2.0 builds on the original LEMOS platform by increasing throughput from 16 to 32 microwells and reducing light leakage between adjacent microwells, allowing dark conditions to be used as an additional illumination state. The device consists of a 3D-printed frame, individually addressable LEDs positioned next to each microwell, a rechargeable battery, and an onboard microcontroller for Bluetooth-based wireless communication. Biocompatible polydimethylsiloxane microwells are cast directly into the device by replica molding, allowing bacterial cultures to be stimulated while optical density and fluorescence are measured by the microplate reader. This protocol describes the full LEMOS 2.0 workflow, including device fabrication, circuit assembly, Arduino programming, PDMS microwell casting, plate-reader setup, strain and culture preparation, automated experiment execution, device cleanup, and fluorescence/OD600 data analysis. As a demonstration, the protocol uses the CcaSR optogenetic system, in which sfGFP expression is activated by green light and repressed by red light. LEMOS 2.0 is intended to make optogenetic perturbation and gene-expression characterization more accessible to wet-lab users, enabling faster design-build-test-learn cycles without requiring specialized bioreactor or microfluidic infrastructure.

synthetic biology↗

bioRxiv2025

TIP60, a key lysine acetyltransferase, acts as a wound-induced factor essential for efficient wound response in planaria

Chromatin modifiers are essential regulators of gene expression, DNA repair, replication, and cell division. Among them, histone acetyltransferases (HATs) such as TIP60 play a central role in modulating chromatin dynamics through acetylation of histone and non-histone proteins. TIP60, a member of the MYST family of HATs, is known to regulate key cellular processes, including transcriptional activation, DNA damage response, and cell cycle progression. Although TIP60s role in stem cell maintenance and differentiation is well established, its function in stem cell-driven regeneration has remained unexplored. In this study, we characterize the role of the TIP60 homolog, SMED-TIP60, in the planarian Schmidtea mediterranea, a model organism renowned for its regenerative capacity. Biochemical assays confirmed SMED-TIP60s acetyltransferase and auto-acetylation activity. RNAi-mediated knockdown of Smed-tip60 resulted in severe defects in tissue homeostasis, survival, and regeneration, including impaired blastema formation and failure to regenerate tissues. In situ hybridization and immunofluorescence analyses revealed a marked reduction in stem cell populations and mitotic activity. Western blotting showed a peak in SMED-TIP60 expression at 5 days post-amputation, suggesting a role during regeneration. RNA-seq analysis revealed widespread dysregulation of gene expression at both anterior and posterior wounds, correlating with increased TIP60 expression post-injury. Notably, wound-response gene expression was aberrant in Smed-tip60 RNAi animals, indicating TIP60s essential role in initiating wound responses and resetting positional cues. Together, these findings establish TIP60 as a critical regulator of stem cell-mediated regeneration and wound healing in planarians.

cell biology↗

bioRxiv2025

Closed-loop Optogenetic Control in a Microplate Reader

Optogenetics integrates living cells and electronics into powerful cell-silicon systems, but prototyping their dynamics remains challenging. Current tools either require robotic liquid transfers into flow cytometers or rely on custom sensors with narrow dynamic range that limit controller performance. Additionally, current successful optogenetic feedback controllers only operate in chemostats or microfluidic devices that enforce constant growth, because models for growth-aware controller design in batch culture are lacking. Here we present LEMOS, a low-cost LED-embedded microplate that runs inside a commercial microplate reader. Coupled to a growth-aware multiscale model of gene expression for controller tuning, this platform enables rapid design-build-test-learn cycles for cell-silicon systems. We demonstrate closed loop setpoint tracking of gene expression in batch cultures within a standard microplate reader and show how growth dynamics complicates controller selection and tuning. Together, this platform reduces setup overhead and speed up iteration, enabling accurate real-time optogenetic feedback control.

synthetic biology↗