Ajdari, A. | Search bioRxiv

bioRxiv2026

A synthetic biology approach to bacterial transcription initiation: RNA aptamer based in vitro transcription assay for rapidly testing bacterial RNA polymerases, promoters and inhibitors.

We present a robust and versatile in vitro transcription (IVT) assay based on an optimized Broccoli RNA aptamer sequence. When paired with the fluorophore DFHBI-1T, this system enables real-time monitoring of multi-round transcription over several hours. To facilitate streamlined promoter analysis, we developed the pIVT3 plasmid backbone. The system was validated using both the single-subunit T7 RNA polymerase and the multi-subunit Escherichia coli RNA polymerase; notably, the activity of the E. coli enzyme remained strictly dependent on the presence of a {sigma} factor and a cognate promoter. To optimize the signal-to-noise ratio, we incorporated two rrnBT1 terminators upstream of the promoter of interest. This modification effectively eliminated background transcription for weak promoters (PlivJ) and prevented interference from read-through transcription in strong synthetic promoters (Ptrc*). Furthermore, we demonstrated the assays utility for drug discovery by characterizing the time- and dose-dependent inhibitory kinetics of rifampicin. Collectively, these results establish the Broccoli-based IVT system as a highly adaptable platform for quantifying promoter strength and screening small-molecule inhibitors of bacterial transcription. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/744185v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1632360org.highwire.dtl.DTLVardef@1a77977org.highwire.dtl.DTLVardef@1780c9org.highwire.dtl.DTLVardef@1082e05_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

Neuromuscular Basis of Kinematic Adaptations During Bidirectional Walking

1BackgroundHuman locomotion is a highly adaptive motor skill that adjusts to new environmental demands through learning. Split-belt treadmill paradigms have advanced our understanding of gait adaptation. Most studies have examined gait when the belts move at different speeds in the same direction. We are studying muscle activation patterns during an asymmetric gait, when the treadmill belts move at equal speed in opposite directions, i.e., bidirectional walking (BDW). MethodsTwelve healthy volunteers performed a single session on a split-belt treadmill. We simultaneously collected ground reaction forces via treadmill force plates, joint kinematics via motion capture, and surface electromyography (EMG) from bilateral soleus (SOL) and tibialis anterior (TA) muscles. Participants started with 2 min of forward walking (FW), followed with four 5-min blocks of BDW separated by 1-min standing rest intervals, and finished the session with 2 min of FW (washout). ResultsAll participants successfully completed the protocol. We analyzed EMG signals for temporal activation patterns (rhythm generation) and amplitude characteristics (pattern formation). EMG recordings revealed antiphasic activation of SOL and TA muscles bilaterally throughout all trials. During BDW, the backward-moving legs TA showed prolonged activation patterns that persisted during washout FW, suggesting retention of adaptive changes. Burst-to-cycle duration ratios showed transient changes during early adaptation but remained relatively stable across conditions, demonstrating robust rhythm generation despite adaptive modulation of activation patterns during BDW. DiscussionThese findings demonstrate that BDW induces asymmetric adjustments in muscle activation patterns. Rhythm generation (timing) did not significantly differ between BDW and FW. However, we did observe changes in pattern formation (i.e., EMG profiles) during FW pre- and post-BDW training. Burst-to-cycle duration ratios, as a measure of rhythm generation, showed changes during early adaptation, particularly the increase in right SOL and right TA during block 1, though these changes did not reach statistical significance and largely returned to baseline during washout. The underlying pattern formation structure, was maintained across all conditions, with selective amplitude modulations rather than fundamental reorganization of activation patterns. The substantial temporal adjustments in the backward-moving legs SOL and phase shifts in TA provide the neuromuscular mechanism driving the bilateral step-length reduction, altered inter-limb phasing, and asymmetric double stance timing. These results extend our understanding of locomotor control by suggesting how the central nervous system (CNS) dynamically recalibrates muscle timing and amplitude to maintain satisfactory locomotion under new environmental demands.

neuroscience↗