Journal: Molecular Systems Biology

Article Title: Abundant clock proteins point to missing molecular regulation in the plant circadian clock

doi: 10.1038/s44320-025-00086-5

Figure Lengend Snippet: Clock protein dissociation constants for DNA-binding, from models or data.

Article Snippet: The black, green and cyan arcs represent, respectively, the clock gene circuit models such as U2020 (schema from Urquiza-García and Millar, Supp Fig. ), the Framework Model version 2 for clock-controlled seedling and rosette growth in simple environments (FMv2; Chew et al, ), and the FM-life model for whole-lifecycle simulation under natural environments (Zardilis et al, ).

Techniques:

Journal: Molecular Systems Biology

Article Title: Abundant clock proteins point to missing molecular regulation in the plant circadian clock

doi: 10.1038/s44320-025-00086-5

Figure Lengend Snippet: Natural genetic variation in promoter sequences is predicted to alter the molecular phenotype (dynatype). ( A ) GI transcript levels under 10L:14D cycles were simulated in U2020.5 (white region, light interval; shaded region, dark interval). The K d for CCA1 binding to the promoter of GI was calculated using the EMA matrix (Fig. ), for all GI promoter sequences from the 1001 Genomes Project (dashed lines). The model retained the default GI gene (solid line, second highest peak), while a second copy that simulated only GI RNA production was tested with the K d for each promoter sequence and plotted (dashed lines). The range of dynamics shown reflects only altered GI transcription rates, without the effects of altered GI protein dynamics. ( B ) Connecting models (adapted from Millar, Fig. ). The central circuit represents the conceptual steps as a genome, in cells, builds organismal traits (upper arrow) in a given environment (green shading). Those traits and potentially management inputs (yellow), in populations, lead to selection on genome sequences (lower arrow). The black, green and cyan arcs represent, respectively, the clock gene circuit models such as U2020 (schema from Urquiza-García and Millar, Supp Fig. ), the Framework Model version 2 for clock-controlled seedling and rosette growth in simple environments (FMv2; Chew et al, ), and the FM-life model for whole-lifecycle simulation under natural environments (Zardilis et al, ). This paper illustrates how a clock gene circuit model can incorporate genome sequence data (dashed black arc), via promoter sequences that alter CCA1 binding, as in ( A ). Others might connect such models in future and add simulated genetic variation (pink), in order to explain and predict both the operation and the evolution of the plant clock genes.

Article Snippet: The black, green and cyan arcs represent, respectively, the clock gene circuit models such as U2020 (schema from Urquiza-García and Millar, Supp Fig. ), the Framework Model version 2 for clock-controlled seedling and rosette growth in simple environments (FMv2; Chew et al, ), and the FM-life model for whole-lifecycle simulation under natural environments (Zardilis et al, ).

Techniques: Binding Assay, Sequencing, Selection

Journal: Scientific Reports

Article Title: Ventilation and features of the lung environment dynamically alter modeled intrapulmonary aerosol exposure from inhaled electronic cigarettes

doi: 10.1038/s41598-024-81066-x

Figure Lengend Snippet: Ventilated artificial lung system and vaping exposure paradigm. ( a) The central component is a temperature-controlled and pressure-regulated artificial lung chamber (6-L volume) connected to a ventilator with independent controls for inspiratory time, respiratory rate, tidal volume, heating and humidification. A JUUL-pod holder with a regulated flow of filtered air and a programmable power supply is used to generate e-cig aerosols in individual puffs in coordination with the ventilator. ( b ) A normal resting breathing pattern was established by setting the ventilator to 10 breaths/min (BPM), tidal volume of 480 mL, and inspiratory time of 2 s, which created a 6 s respiratory cycle (2 s inhalation; 4 s exhalation). At the initiation of a vaping session, a puff of e-cig aerosol is delivered into the inspiratory limb at the end of exhalation, and inhaled into the lung chamber by the next inhalation. Dynamic pressure measurements within the lung exposure chamber document these repetitive breathing and vaping cycles. ( c) Particle number concentrations (PNCs) within the lung chamber over a 4-puff vaping session were measured in real time via the integrated sampling port. The lung chamber was continuously ventilated and 4 puffs of e-cig aerosols were delivered at 1-min intervals followed by a decay period for 10–12 min driven by the continued ventilation. A saw-tooth pattern (rise/fall) of recorded PNCs occurs with each breath due to the impact of symmetric inspiratory and expiratory pressure changes on flow rates to the water-based condensation particle counter (WCPC). Mean values ( ) represent actual diluted PNCs. The particle size distributions were measured using a Scanning Mobility Particle Sizer (SMPS) and Aerodynamic Particle Sizer (APS) at discrete time points: after the 1 st and 4 th puffs and following 5 min of ongoing ventilation.

Article Snippet: A ventilated artificial lung system was developed from three major components (Fig. a ) : 1) a temperature-controlled and pressure-regulated lung chamber; 2) a volume-controlled ventilator (EPV100, Allied Healthcare Inc., USA) with integrated heating and humidification (MR730, Fisher & Paykel Healthcare Ltd., New Zealand) and a single limb ventilator circuit (Model L599-130, Allied Healthcare Products Inc., USA); and 3) a programmable e-cig puffing apparatus.

Techniques: Aerosol, Sampling

Journal: Scientific Reports

Article Title: Ventilation and features of the lung environment dynamically alter modeled intrapulmonary aerosol exposure from inhaled electronic cigarettes

doi: 10.1038/s41598-024-81066-x

Figure Lengend Snippet: Visualization of e-cig aerosols within the artificial lung chamber under different ventilation and environmental conditions. Images of the artificial lung exposure chamber were captured immediately after the 4th puff with either the ventilator turned on (top row: 10 BPM; 480 mL/breath) or under static conditions (bottom row) and under three different environmental conditions.

Article Snippet: A ventilated artificial lung system was developed from three major components (Fig. a ) : 1) a temperature-controlled and pressure-regulated lung chamber; 2) a volume-controlled ventilator (EPV100, Allied Healthcare Inc., USA) with integrated heating and humidification (MR730, Fisher & Paykel Healthcare Ltd., New Zealand) and a single limb ventilator circuit (Model L599-130, Allied Healthcare Products Inc., USA); and 3) a programmable e-cig puffing apparatus.

Techniques: