Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening.

Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems.

Toward a complete understanding of quasi-static bubble growth and departure.

The distortion by gravity of a quasi-static bubble attached on an upward facing surface in a quiescent liquid is investigated. The contact angle evolution during the growth of such a bubble is studied, and the consequences on the motion of the contact line between the solid and the interface are discussed. From the initial case of a bubble attached to the rim of a nucleation site, the contact line can move inside the cavity for a highly wetting fluid, causing premature departure. For a higher wettability, the contact can either remain attached to the rim of the cavity or spread out of the cavity, depending on the cavity size and geometry. For the latter case, the bubble growth is investigated taking into account a contact angle hysteresis. Finally, a comprehensive map detailing various geometrical characteristics of bubbles is presented, ranging over several orders of magnitude of Bond numbers and normalized volumes. The map aims at being used as a tool for investigating bubble growth in a similar situation.

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation.

Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryoelectron microscopy to a unique transcription system using σ54 (σN), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promoter complex and an initial de novo transcribing complex at 3.4 and 3.7 Å, respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilization that involves coordinated, large-scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by σ54.

Rubber-like elasticity in laser-driven free surface flow of a Newtonian fluid.

The energy needed to deform an elastic solid may be recovered, while in Newtonian fluids, like water and glycerol, deformation energy dissipates on timescales of the intermolecular relaxation time [Formula: see text] . For times considerably longer than [Formula: see text] the existence of shear elasticity requires long-range correlations, which challenge our understanding of the liquid state. We investigated laser-driven free surface bubbles in liquid glycerol by analyzing their expansion and bursting dynamics, in which we found a flow-dominating, rubber-like elasticity unrelated to surface tension forces. In extension to findings of a measurable liquid elasticity at even very low deformation frequencies [L. Noirez, P. Baroni, J. Mol. Struct. 972, 16-21 (2010), A. Zaccone, K. Trachenko, Proc. Natl. Acad. Sci. U.S.A. 117, 19653-19655 (2020)], that is difficult to access under increased strain, we find a robust, strain rate driven elasticity. The recovery of deformation energy allows the bursting bubble to reach Taylor-Culick velocities 20-fold higher than expected. The elasticity is persistent for microseconds, hence four orders of magnitude longer than [Formula: see text] . The dynamic shows that this persistence cannot originate from the far tail of a distribution of relaxation times around [Formula: see text] but must appear by frustrating the short molecular dissipation. The longer time should be interpreted as a relaxation of collective modes of metastable groups of molecules. With strain rates of 106 s-1, we observe a metastable glycerol shell exhibiting a rubber-like solid behavior with similar elasticity values and characteristic tolerance toward large strains, although the molecular interaction is fundamentally different.

A general mechanism for transcription bubble nucleation in bacteria.

Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ70, nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ70. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σN-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σN, like σ70, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.

Submicron drops from flapping bursting bubbles.

Tiny water drops produced from bubble bursting play a critical role in forming clouds, scattering sunlight, and transporting pathogens from water to the air. Bubbles burst by nucleating a hole at their cap foot and may produce jets or film drops. The latter originate from the fragmentation of liquid ligaments formed by the centripetal destabilization of the opening hole rim. They constitute a major fraction of the aerosols produced from bubbles with cap radius of curvature (R) > ∼0.4 × capillary length (a). However, our present understanding of the corresponding mechanisms does not explain the production of most submicron film drops, which represent the main number fraction of sea spray aerosols. In this study, we report observations showing that bursting bubbles with R < ∼0.4a are actually mainly responsible for submicron film drop production, through a mechanism involving the flapping shear instability of the cap with the outer environment. With this proposed pathway, the complex relations between bubble size and number of drops produced per bubble can be better explained, providing a fundamental framework for understanding the production flux of aerosols and the transfer of substances mediated by bubble bursting through the air-water interface and the sensitivity of the process to the nature of the environment.

Spatially Resolved Quantum Sensing with High-Density Bubble-Printed Nanodiamonds.

Nitrogen-vacancy (NV-) centers in nanodiamonds have emerged as a versatile platform for a wide range of applications, including bioimaging, photonics, and quantum sensing. However, the widespread adoption of nanodiamonds in practical applications has been hindered by the challenges associated with patterning them into high-resolution features with sufficient throughput. In this work, we overcome these limitations by introducing a direct laser-writing bubble printing technique that enables the precise fabrication of two-dimensional nanodiamond patterns. The printed nanodiamonds exhibit a high packing density and strong photoluminescence emission, as well as robust optically detected magnetic resonance (ODMR) signals. We further harness the spatially resolved ODMR of the nanodiamond patterns to demonstrate the mapping of two-dimensional temperature gradients using high frame rate widefield lock-in fluorescence imaging. This capability paves the way for integrating nanodiamond-based quantum sensors into practical devices and systems, opening new possibilities for applications involving high-resolution thermal imaging and biosensing.

Laser-Induced Controllable Porosity in Additive Manufacturing Boosts Efficiency of Electrocatalytic Water Splitting.

In laser-based additive manufacturing (AM), porosity and unmelted metal powder are typically considered undesirable and harmful. Nevertheless in this work, precisely controlling laser parameters during printing can intentionally introduce controllable porosity, yielding a porous electrode with enhanced catalytic activity for the oxygen evolution reaction (OER). This study demonstrates that deliberate introduction of porosity, typically considered a defect, leads to improved gas molecule desorption, enhanced mass transfer, and increased catalytically active sites. The optimized P-93% electrode displays superior OER performance with an overpotential of 270 mV at 20 mA cm-2. Furthermore, it exhibits remarkable long-term stability, operating continuously for over 1000 h at 10 mA cm-2 and more than 500 h at 500 mA cm-2. This study not only provides a straightforward and mass-producible method for efficient, binder-free OER catalysts but also, if optimized, underscores the potential of laser-based AM driven defect engineering as a promising strategy for industrial water splitting.

High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.

Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence dependence of the local unzipping of double-stranded DNA, the first step towards replication initiation, is lacking. Here, utilizing a Markov chain model that was created to address the directional nature of DNA unzipping and replication, we model the sequence dependence of local melting of double-stranded linear DNA segments. We show that generalized palindromic sequences with high nucleotide skews have a low kinetic barrier for local melting near melting temperatures. This allows for such sequences to function as potential replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids.

TiO2 Nanotube Arrays Inside Ultrafine Ti Tubes with an Aspect Ratio of 2500 for Sensing Needles: The Bubble Effect in a Confined Space.

Capillary metal tubes have attracted considerable interest for flexible electronics, portable devices, trace sampling, and detection. Tailoring the microstructure and wettability inside the capillary tubes is of paramount importance, yet it presents great difficulty because of the spatial confinement. Here, the coupling effect is revealed between the fluidic and electric field induced by bubble motion in a confined space during anodic oxidation. By controlling the bubble regeneration and flow rate, uniform and superhydrophilic TiO2 nanotube arrays are developed throughout the inner surface of an ultrafine Ti tube with a diameter of 0.4 mm and length of 1000 mm, equivalent to an aspect ratio of 2500 that is the largest value being ever reported. The inner surface of a capillary tube is further coated with a polytetrafluoroethylene layer and explored as a sensing needle for liquid detection in terms of concentration and species. This study provides an innovative approach to tailor the microstructure and wettability in a confined space for functional capillary tubes.

Fabrication and Performance of Bubble-Containing Multicompartmental Particles: Novel Self-Orienting Carriers.

In this work, a class of bubble-containing multicompartmental particles with self-orienting capability is developed, where a single bubble is enclosed at the top of the super-segmented architecture. Such bubbles, driven by potential energy minimization, cause the particles to have a bubble-upward preferred orientation in liquid, enabling efficient decoding of their high-density signals in an interference-resistant manner. The particle preparation involves bubble encapsulation via the impact of a multicompartmental droplet on the liquid surface and overall stabilization via rational crosslinking. The conditions for obtaining these particles are systematically investigated. Methodological compatibility with materials is demonstrated by different hydrogel particles. Finally, by encapsulating cargoes of interest, these particles have found broad applications in actuators, multiplexed detection, barcodes, and multicellular systems.

Self-healable, Tolerant Superaerophobic Coating for Improving Electrochemical Hydrogen Production.

Gas-evolving electrodes often suffer from the blocking of catalytic active sites-due to unwanted and unavoidable adhesion of generated gas bubbles, which elevates the overpotential for the electrochemical hydrogen evolution reaction (HER)- by raising the resistance of the electrode. Here, a catalyst-free and self-healable superaerophobic coating having ultra-low bubble adhesion is introduced for achieving significantly depleted overpotentials of 209 and 506 mV at both low (50 mA cm-2) and high (500 mA cm-2) current densities, respectively, compared to a bare nickel-foam electrode. The optimized coating ensured an early detachment of the generated tiny (0.8 ± 0.1 mm) gas bubble-and thus, prevented the undesired rise in resistance of the coated electrode. The systematic association of physical (i.e., ionic interactions, H-bonding, etc.) cross-linkage, ß-amino ester type covalent cross-linkage and reinforced halloysite nano clay enables the design of such functional material embedded with essential characteristics-including improved mechanical (toughness of 63.7 kJ m-3, and tensile modulus of 26 kPa) property and chemical (extremes of pH (1 and 14), salinity, etc.) stability, rapid (<10 min) self-healing ability (even at alkaline condition) and desired bubble-wettability (bubble contact angle of 158.2 ± 0.2°) with ultralow force (4.2 ± 0.4 µN) of bubble adhesion.

Dual-Mode Imaging of Dynamic Interaction between Bubbles and Single Nanoplates during the Electrocatalytic Hydrogen Evolution Process.

Gas bubble formation at electrochemical interfaces can significantly affect the efficiency and durability of electrocatalysts. However, obtaining comprehensive details on bubble evolution dynamics, particularly their dynamic interaction with high-performance structured electrocatalysts, poses a considerable challenge. Herein, dual-mode interference/total internal reflection fluorescence microscopy is introduced, which allows for the simultaneous capture of the evolution pathway of bubbles and the 3D motion of nanoplate electrocatalysts, providing high-resolution and accurate spatiotemporal information. During the hydrogen evolution reaction, the dynamics of hydrogen bubble generation and their interactions with single nanoplate electrocatalysts at the electrochemical interface are observed. The results unveiled that, under constant potential, bubbles initially manifest as fast-moving nanobubbles, transforming into stationary microbubbles subsequently. The morphology of stationary nanoplates regulates the trajectories of these moving nanobubbles while the pinned microbubbles induce the motion of the electrocatalysts. The dual-mode microscopy can be employed to scrutinize numerous multiphase electrochemical interactions with high spatiotemporal resolution, which can facilitate the rational design of high-performance electrocatalysts.

A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging.

Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast imaging with gas chromatography in real time, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (two to three times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gasses remain unchanged. By coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications.

Real-time imaging of decompression gas bubble growth in the spinal cord of live rats.

PURPOSE: To observe the growth and resolution of decompression gas bubbles in the spinal cord of live rats in real time using MRI. METHODS: We constructed an MRI-compatible pressure chamber system to visualize gas bubble dynamics in deep tissues in real time. The system pressurizes and depressurizes rodents inside an MRI scanner and monitors their respiratory rate, heart rate, and body temperature while providing gaseous anesthesia under pressure during the experiments. RESULTS: We observed the formation of decompression gas bubbles in the spinal cord of rats after compression to 7.1 bar absolute and rapid decompression inside the MRI scanner while maintaining continuous gaseous anesthesia and vital monitoring. CONCLUSION: We have shown the direct observation of decompression gas bubble formation in real time by MRI in live, anesthetized rats.

"Bubble-Diode" Breathable Electrodes for Fast Gas Transport.

Bubbles arising from wild gas evolution commonly exist in electrochemical systems, particularly in water electrolysis and rechargeable aqueous batteries (e. g., Zn-air batteries). Substantial energy dissipation occurs due to the obstruction of active sites and ion-conducting pathways by evolving bubbles. Efforts are made to elucidate effective strategies for fast gas transport, most of which focus on minimizing bubble size and facilitating their timely detachment through complex techniques such as constructing super-hydrophilic nano-structure electrodes, flowing electrolytes, and ultrasonic oscillation. Recently, an innovative, facile, and highly efficient method utilizing a breathable electrode design to promote gaseous molecules to the external environment emerges as a promising approach since it avoids remarkable bubble accumulation while remaining free of additional accessories. This paper highlights the origin and evolution of this promising design. Starting with introducing the basic concept of traditional breathable electrodes based on hydrophobic polymer networks and discussing the current progress made in underlying mechanisms, a detailed description of the advanced design inspired by a "bubble-diode" concept with superior breathability follows. This Concept aims to contribute to a deep understanding of this technology and paves the way for further advancements in this renewable energy era.

Synthesis of Superelastic, Highly Conductive Graphene Aerogel/Liquid Metal Foam and its Piezoresistive Application.

Graphene aerogel (GA) has important application potential as piezoresistive sensors due to its low density, high conductivity, high porosity, and good mechanical properties. However, the fabrication of GA-based sensors with good mechanical properties and excellent sensing performance is still challenging. Herein, liquid- metal-modified GAs (GA/LM) are proposed for the development of an excellent GA-based sensor. GA/LM with three-dimensional interconnected layered structure exhibits excellent compressive stress of 41 KPa and fast response time (<20 ms). While generally flexible GA composites cannot be compressed beyond 80 % strain without plastic deformation, GA/LM demonstrates a high compressive strength of 60 kPa under a strain of 90 %. A real-time pressure sensor was fabricated based on GA/LM-2 to monitor swallowing, pulse beating, finger, wrist and knee bending, and even plantar pressure during walking. These excellent features enable potential applications in health detection.

Effect of Annealing on Visible-Bubble Formation and Stability Profiles of Freeze-Dried High Concentration Omalizumab Formulations.

In the clinical application of freeze-dried highly concentrated omalizumab formulations, extensive visible bubbles (VBs) can be generated and remain for a long period of time in the reconstitution process, which greatly reduces the clinical use efficiency. It is necessary to understand the forming and breaking mechanism of VBs in the reconstitution process, which is a key factor for efficient and safe administration of biopharmaceutical injection. The effects of different thermal treatments on the volume of VBs and stability of omalizumab, mAb-1, and mAb-2 were investigated. The internal microvoids of the cake were characterized by scanning electron microscopy and mercury intrusion porosimetry. Electron paramagnetic resonance was applied to obtain the molecular mobility of the protein during annealing. A large number of VBs were generated in the reconstitution process of unannealed omalizumab and remained for a long period of time. When annealing steps were added, the volume of VBs was dramatically reduced. When annealed at an aggressive temperature (i.e., -6 °C), although the volume of VBs decreased, the aggregation and acidic species increased significantly. Thus, our observations highlight the importance of setting an additional annealing step with a suitable temperature, which contributes to reducing the VBs while maintaining the stability of the high concentration freeze-dried protein formulation.

The use of bubble charts in analyzing second stage cesarean delivery rates.

BACKGROUND: The incidence of second stage cesarean delivery has been rising globally because of the failure or the anticipated difficulty of performing instrumental delivery. Yet, the best way to interpret the figure and its optimal rate remain to be determined. This is because it is strongly influenced by the practice of other 2 modes of birth, namely cesarean delivery performed before reaching the second stage and assisted vaginal birth during the second stage. In this regard, a bubble chart that can display 3-dimensional data through its x-axis, y-axis, and the size of each plot (presented as a bubble) may be a suitable method to evaluate the relationship between the rates of these 3 modes of births. OBJECTIVE: This study aimed to conduct an epidemiologic study on the incidence of second stage cesarean deliveries rates among >300,000 singleton term births in 10 years from 8 obstetrical units and to compare their second stage cesarean delivery rates in relation to their pre-second stage cesarean delivery rates and assisted vaginal birth rates using a bubble chart. STUDY DESIGN: The territory-wide birth data collected between 2009 and 2018 from all 8 public obstetrical units (labelled as A to H) were reviewed. The inclusion criteria were all singleton pregnancies with cephalic presentation that were delivered at term (≥37 weeks' gestation). Pre-second stage cesarean delivery rate was defined as all elective cesarean deliveries and those emergency cesarean deliveries that occurred before full cervical dilatation was achieved as a proportion of the total number of births. The second stage cesarean delivery rate and assisted vaginal birth rate were calculated according to the respective mode of delivery as a proportion of the number of cases that reached full cervical dilatation. The rates of these 3 modes of births were compared among the parity groups and among the 8 units. Using a bubble chart, each unit's second stage cesarean delivery rate (y-axis) was plotted against its pre-second stage cesarean delivery rate (x-axis) as a bubble. Each unit's second stage cesarean delivery to assisted vaginal birth ratio was represented by the size of the bubble. RESULTS: During the study period, a total of 353,434 singleton cephalic presenting term pregnancies were delivered in the 8 units, and 180,496 (51.1%) were from nulliparous mothers. When compared with the multiparous group, the nulliparous group had a significantly lower pre-second stage cesarean delivery rate (18.58% vs 21.26%; P<.001) but a higher second stage cesarean delivery rate (0.79% vs 0.22%; P<.001) and a higher assisted vaginal birth rate (17.61% vs 3.58%; P<.001). Using the bubble of their averages as a reference point in the bubble chart, the 8 units' bubbles were clustered into 5 regions indicating their differences in practice: unit B and unit H were close to the average in the center. Unit A and unit F were at the upper right corner with a higher pre-second stage cesarean delivery rate and second stage cesarean delivery rate. Unit D and unit E were at the opposite end. Unit C was at the upper left corner with a low pre-second stage cesarean delivery rate but a high second stage cesarean delivery rate, whereas unit G was at the opposite end. Unit C and unit G were also in the extremes in terms of pre-second stage cesarean delivery to assisted vaginal birth ratio (0.09 and 0.01, respectively). Although some units seemed to have very similar second stage cesarean delivery rates, their obstetrical practices were differentiated by the bubble chart. CONCLUSION: The second stage cesarean delivery rate must be evaluated in the context of the rates of pre-second stage cesarean delivery and assisted vaginal birth. A bubble chart is a useful method for analyzing the relationship among these 3 variables to differentiate the obstetrical practice between different units.