Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data.

The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOx complex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.

X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

Biophysical Techniques in Structural Biology.

Over the past six decades, steadily increasing progress in the application of the principles and techniques of the physical sciences to the study of biological systems has led to remarkable insights into the molecular basis of life. Of particular significance has been the way in which the determination of the structures and dynamical properties of proteins and nucleic acids has so often led directly to a profound understanding of the nature and mechanism of their functional roles. The increasing number and power of experimental and theoretical techniques that can be applied successfully to living systems is now ushering in a new era of structural biology that is leading to fundamentally new information about the maintenance of health, the origins of disease, and the development of effective strategies for therapeutic intervention. This article provides a brief overview of some of the most powerful biophysical methods in use today, along with references that provide more detailed information about recent applications of each of them. In addition, this article acts as an introduction to four authoritative reviews in this volume. The first shows the ways that a multiplicity of biophysical methods can be combined with computational techniques to define the architectures of complex biological systems, such as those involving weak interactions within ensembles of molecular components. The second illustrates one aspect of this general approach by describing how recent advances in mass spectrometry, particularly in combination with other techniques, can generate fundamentally new insights into the properties of membrane proteins and their functional interactions with lipid molecules. The third reviewdemonstrates the increasing power of rapidly evolving diffraction techniques, employing the very short bursts of X-rays of extremely high intensity that are now accessible as a result of the construction of free-electron lasers, in particular to carry out time-resolved studies of biochemical reactions. The fourth describes in detail the application of such approaches to probe the mechanism of the light-induced changes associated with bacteriorhodopsin's ability to convert light energy into chemical energy.

A multistep computational approach reveals a neuro-mesenchymal cell population in the embryonic hematopoietic stem cell niche.

The first hematopoietic stem and progenitor cells (HSPCs) emerge in the Aorta-Gonad-Mesonephros (AGM) region of the mid-gestation mouse embryo. However, the precise nature of their supportive mesenchymal microenvironment remains largely unexplored. Here, we profiled transcriptomes of laser micro-dissected aortic tissues at three developmental stages and individual AGM cells. Computational analyses allowed the identification of several cell subpopulations within the E11.5 AGM mesenchyme, with the presence of a yet unidentified subpopulation characterized by the dual expression of genes implicated in adhesive or neuronal functions. We confirmed the identity of this cell subset as a neuro-mesenchymal population, through morphological and lineage tracing assays. Loss of function in the zebrafish confirmed that Decorin, a characteristic extracellular matrix component of the neuro-mesenchyme, is essential for HSPC development. We further demonstrated that this cell population is not merely derived from the neural crest, and hence, is a bona fide novel subpopulation of the AGM mesenchyme.

Laser-driven noncontact bubble transfer printing via a hydrogel composite stamp.

Transfer printing that enables heterogeneous integration of materials into spatially organized, functional arrangements is essential for developing unconventional electronic systems. Here, we report a laser-driven noncontact bubble transfer printing via a hydrogel composite stamp, which features a circular reservoir filled with hydrogel inside a stamp body and encapsulated by a laser absorption layer and an adhesion layer. This composite structure of stamp provides a reversible thermal controlled adhesion in a rapid manner through the liquid-gas phase transition of water in the hydrogel. The ultrasoft nature of hydrogel minimizes the influence of preload on the pick-up performance, which offers a strong interfacial adhesion under a small preload for a reliable damage-free pick-up. The strong light-matter interaction at the interface induces a liquid-gas phase transition to form a bulge on the stamp surface, which eliminates the interfacial adhesion for a successful noncontact printing. Demonstrations of noncontact transfer printing of microscale Si platelets onto various challenging nonadhesive surfaces (e.g., glass, key, wrench, steel sphere, dry petal, droplet) in two-dimensional or three-dimensional layouts illustrate the unusual capabilities for deterministic assembly to develop unconventional electronic systems such as flexible inorganic electronics, curved electronics, and micro-LED display.

Superradiant Thomson scattering from graphite in the extreme ultraviolet.

We study the Thomson scattering from highly oriented pyrolitic graphite excited by the extreme ultraviolet, coherent pulses of FERMI free electron laser (FEL). An apparent nonlinear behavior is observed and fully described in terms of the coherent nature of both exciting FEL beam and scattered radiation, producing an intensity-dependent enhancement of the Thomson scattering cross-section. The process resembles Dicke's superradiant phenomenon and is thus interpreted as the observation of superradiant Thomson scattering. The process also triggers the creation of coherent, low-q ([Formula: see text] 0.3 Å[Formula: see text]), low energy phonons. The experimental data and analysis provide quantitative information on the sample characteristics, absorption, scattering factor, and coherent phonon energies and populations and open the route for the investigation of the deep nature of complex materials.

Laser direct overall water splitting for H2 and H2O2 production.

Hydrogen (H2) and hydrogen peroxide (H2O2) play crucial roles as energy carriers and raw materials for industrial production. However, the current techniques for H2 and H2O2 production rely on complex catalysts and involve multiple intermediate steps. In this study, we present a straightforward, environmentally friendly, and highly efficient laser-induced conversion method for overall water splitting to simultaneously generate H2 and H2O2 at ambient conditions without any catalysts. The laser direct overall water splitting approach achieves an impressive light-to-hydrogen energy conversion efficiency of 2.1%, with H2 production rates of 2.2 mmol/h and H2O2 production rates of 65 µM/h in a limited reaction area (1 mm2) within a short real reaction time (0.36 ms/h). Furthermore, we elucidate the underlying physics and chemistry behind the laser-induced water splitting to produce H2 and H2O2. The laser-induced cavitation bubbles create an optimal microenvironment for water-splitting reactions because of the transient high temperatures (104 K) surpassing the chemical barrier required. Additionally, their rapid cooling rate (1010 K/s) hinders reverse reactions and facilitates H2O2 retention. Finally, upon bubble collapse, H2 is released while H2O2 remains dissolved in the water. Moreover, a preliminary amplification experiment demonstrates the potential industrial applications of this laser chemistry. These findings highlight that laser-based production of H2 and H2O2 from water holds promise as a straightforward, environmentally friendly, and efficient approach on an industrial scale beyond conventional chemical catalysis.

Mid-infrared trace detection with parts-per-quadrillion quantitation accuracy: Expanding frontiers of radiocarbon sensing.

Detection sensitivity is a critical characteristic to consider during selection of spectroscopic techniques. However, high sensitivity alone is insufficient for spectroscopic measurements in spectrally congested regions. Two-color cavity ringdown spectroscopy (2C-CRDS), based on intra-cavity pump-probe detection, simultaneously achieves high detection sensitivity and selectivity. This combination enables mid-infrared detection of radiocarbon dioxide ([Formula: see text]CO[Formula: see text]) molecules in room-temperature CO[Formula: see text] samples, with 1.4 parts-per-quadrillion (ppq, 10[Formula: see text]) sensitivity (average measurement precision) and 4.6-ppq quantitation accuracy (average calibrated measurement error for 21 samples from four separate trials) demonstrated on samples with [Formula: see text]C/C up to [Formula: see text]1.5[Formula: see text] natural abundance ([Formula: see text]1,800 ppq). These highly reproducible measurements, which are the most sensitive and quantitatively accurate in the mid-infrared, are accomplished despite the presence of orders-of-magnitude stronger, one-photon signals from other CO[Formula: see text] isotopologues. This is a major achievement in laser spectroscopy. A room-temperature-operated, compact, and low-cost 2C-CRDS sensor for [Formula: see text]CO[Formula: see text] benefits a wide range of scientific fields that utilize [Formula: see text]C for dating and isotope tracing, most notably atmospheric [Formula: see text]CO[Formula: see text] monitoring to track CO[Formula: see text] emissions from fossil fuels. The 2C-CRDS technique significantly enhances the general utility of high-resolution mid-infrared detection for analytical measurements and fundamental chemical dynamics studies.

Mechanosensor Piezo1 mediates bimodal patterns of intracellular calcium and FAK signaling.

Piezo1 belongs to mechano-activatable cation channels serving as biological force sensors. However, the molecular events downstream of Piezo1 activation remain unclear. In this study, we used biosensors based on fluorescence resonance energy transfer (FRET) to investigate the dynamic modes of Piezo1-mediated signaling and revealed a bimodal pattern of Piezo1-induced intracellular calcium signaling. Laser-induced shockwaves (LIS) and its associated shear stress can mechanically activate Piezo1 to induce transient intracellular calcium (Ca[i] ) elevation, accompanied by an increase in FAK activity. Interestingly, multiple pulses of shockwave stimulation caused a more sustained calcium increase and a decrease in FAK activity. Similarly, tuning the degree of Piezo1 activation by titrating either the dosage of Piezo1 ligand Yoda1 or the expression level of Piezo1 produced a similar bimodal pattern of FAK responses. Further investigations revealed that SHP2 serves as an intermediate regulator mediating this bimodal pattern in Piezo1 sensing and signaling. These results suggest that the degrees of Piezo1 activation induced by both mechanical LIS and chemical ligand stimulation may determine downstream signaling characteristics.

Tools to analyze the organization and formation of the germline cyst in zebrafish oogenesis.

Oocytes develop in the germline cyst, a cellular organization in which germ cells are tightly interconnected and surrounded by somatic cells. The cyst produces oocytes for follicle formation and is a hub for essential processes in meiosis and oocyte differentiation. However, the formation and organization of the cyst, and their contribution to oocyte production in vertebrates remain unclear. Here, we provide tools for three-dimensional and functional in vivo analyses of the germline cyst in the zebrafish ovary. We describe the use of serial block-face scanning electron microscopy (SBF-SEM) to resolve the three-dimensional architecture of cells and organelles in the cyst at ultrastructural resolution. We present a deep learning-based pipeline for high-throughput quantitative analysis of three-dimensional confocal datasets of cysts in vivo. We provide a method for laser ablation of cellular components for manipulating cyst cells in ovaries. These methods will facilitate the investigation of the cyst cellular organization, expand the toolkit for the study of the zebrafish ovary, and advance our understanding of female developmental reproduction. They could also be further applied to the investigation of other developmental systems.

Enhanced in situ spatial proteomics by effective combination of MALDI imaging and LC-MS/MS.

Highly specialized cells are fundamental for proper functioning of complex organs. Variations in cell-type specific gene expression and protein composition have been linked to a variety of diseases. Investigation of the distinctive molecular makeup of these cells within tissues is therefore critical in biomedical research. Although several technologies have emerged as valuable tools to address this cellular heterogeneity, most workflows lack sufficient in situ resolution and are associated with high cost and extremely long analysis times. Here, we present a combination of experimental and computational approaches that allows a more comprehensive investigation of molecular heterogeneity within tissues than by either shotgun LC-MS/MS or MALDI imaging alone. We applied our pipeline on mouse brain, which contains a wide variety of cell types that not only perform unique functions but also exhibit varying sensitivities to insults. We explored the distinct neuronal populations within the hippocampus, a brain region crucial for learning and memory that is involved in various neurological disorders. As an example, we identified the groups of proteins distinguishing the neuronal populations of dentate gyrus (DG) and the cornu ammonis (CA) in the same brain section. Most of the annotated proteins matched the regional enrichment of their transcripts, thereby validating the method. As the method is highly reproducible, the identification of individual masses through the combination of MALDI-IMS and LC-MS/MS methods can be used for the much faster and more precise interpretation of MALDI-IMS measurements only. This greatly speeds up spatial proteomic analyses and allows the detection of local protein variations within the same population of cells. The method's general applicability has the potential to be used to investigate different biological conditions and tissues and a much higher throughput than other techniques making it a promising approach for clinical routine applications.

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.

Suppressing transverse mode instability through multimode excitation in a fiber amplifier.

High-power fiber laser amplifiers have enabled an increasing range of applications in industry, science, and defense. The power scaling for fiber amplifiers is currently limited by transverse mode instability. Most techniques for suppressing the instability are based on single- or few-mode fibers in order to output a clean collimated beam. Here, we study theoretically using a highly multimode fiber amplifier with many-mode excitation for efficient suppression of thermo-optical nonlinearity and instability. We find that the mismatch of characteristic length scales between temperature and optical intensity variations across the fiber generically leads to weaker thermo-optical coupling between fiber modes. Consequently, the transverse mode instability (TMI) threshold power increases linearly with the number of equally excited modes. When the frequency bandwidth of a coherent seed laser is narrower than the spectral correlation width of the multimode fiber, the amplified light maintains high spatial coherence and can be transformed to any target pattern or focused to a diffraction-limited spot by a spatial mask at either the input or output end of the amplifier. Our method simultaneously achieves high average power, narrow spectral width, and good beam quality, which are required for fiber amplifiers in various applications.

Real-time imaging of acoustic waves in bulk materials with X-ray microscopy.

The dynamics of lattice vibrations govern many material processes, such as acoustic wave propagation, displacive phase transitions, and ballistic thermal transport. The maximum velocity of these processes and their effects is determined by the speed of sound, which therefore defines the temporal resolution (picoseconds) needed to resolve these phenomena on their characteristic length scales (nanometers). Here, we present an X-ray microscope capable of imaging acoustic waves with subpicosecond resolution within mm-sized crystals. We directly visualize the generation, propagation, branching, and energy dissipation of longitudinal and transverse acoustic waves in diamond, demonstrating how mechanical energy thermalizes from picosecond to microsecond timescales. Bulk characterization techniques capable of resolving this level of structural detail have previously been available on millisecond time scales-orders of magnitude too slow to capture these fundamental phenomena in solid-state physics and geoscience. As such, the reported results provide broad insights into the interaction of acoustic waves with the structure of materials, and the availability of ultrafast time-resolved dark-field X-ray microscopy opens a vista of new opportunities for 3D imaging of materials dynamics on their intrinsic submicrosecond time scales.

Imaging innate immunity.

Innate immunity is the first line of defense against infectious intruders and also plays a major role in the development of sterile inflammation. Direct microscopic imaging of the involved immune cells, especially neutrophil granulocytes, monocytes, and macrophages, has been performed since more than 150 years, and we still obtain novel insights on a frequent basis. Initially, intravital microscopy was limited to small-sized animal species, which were often invertebrates. In this review, we will discuss recent results on the biology of neutrophils and macrophages that have been obtained using confocal and two-photon microscopy of individual cells or subcellular structures as well as light-sheet microscopy of entire organs. This includes the role of these cells in infection defense and sterile inflammation in mammalian disease models relevant for human patients. We discuss their protective but also disease-enhancing activities during tumor growth and ischemia-reperfusion damage of the heart and brain. Finally, we provide two visions, one experimental and one applied, how our knowledge on the function of innate immune cells might be further enhanced and also be used in novel ways for disease diagnostics in the future.

Imaging the different timescales of germinal center selection.

Germinal centers (GCs) are the site of antibody affinity maturation, a fundamental immunological process that increases the potency of antibodies and thereby their ability to protect against infection. GC biology is highly dynamic in both time and space, making it ideally suited for intravital imaging. Using multiphoton laser scanning microscopy (MPLSM), the field has gained insight into the molecular, cellular, and structural changes and movements that coordinate affinity maturation in real time in their native environment. On the other hand, several limitations of MPLSM have had to be overcome to allow full appreciation of GC events taking place across different timescales. Here, we review the technical advances afforded by intravital imaging and their contributions to our understanding of GC biology.

Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems.

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/).

mBeRFP: a versatile fluorescent tool to enhance multichannel live imaging and its applications.

Cell and developmental biology increasingly require live imaging of protein dynamics in cells, tissues or living organisms. Thanks to the discovery and development of a panel of fluorescent proteins over the last decades, live imaging has become a powerful and commonly used approach. However, multicolor live imaging remains challenging. The generation of long Stokes shift red fluorescent proteins offers interesting new perspectives to bypass this limitation. Here, we provide a detailed characterization of mBeRFP for in vivo live imaging and its applications in Drosophila. Briefly, we show that a single illumination source is sufficient to stimulate mBeRFP and GFP simultaneously. We demonstrate that mBeRFP can be easily combined with classical green and red fluorescent proteins without any crosstalk. We also show that the low photobleaching of mBeRFP is suitable for live imaging, and that this protein can be used for quantitative applications, such as FRAP or laser ablation. Finally, we believe that this fluorescent protein, with the set of new possibilities it offers, constitutes an important tool for cell, developmental and mechano-biologists in their current research.

Species-specific function of conserved regulators in orchestrating rice root architecture.

Shoot-borne adventitious/crown roots form a highly derived fibrous root system in grasses. The molecular mechanisms controlling their development remain largely unknown. Here, we provide a genome-wide landscape of transcriptional signatures - tightly regulated auxin response and in-depth spatio-temporal expression patterns of potential epigenetic modifiers - and transcription factors during priming and outgrowth of rice (Oryza sativa) crown root primordia. Functional analyses of rice transcription factors from WUSCHEL-RELATED HOMEOBOX and PLETHORA gene families reveal their non-redundant and species-specific roles in determining the root architecture. WOX10 and PLT1 regulate both shoot-borne crown roots and root-borne lateral roots, but PLT2 specifically controls lateral root development. PLT1 activates local auxin biosynthesis genes to promote crown root development. Interestingly, O. sativa PLT genes rescue lateral root primordia outgrowth defects of Arabidopsis plt mutants, demonstrating their conserved role in root primordia outgrowth irrespective of their developmental origin. Together, our findings unveil a molecular framework of tissue transdifferentiation during root primordia establishment, leading to the culmination of robust fibrous root architecture. This also suggests that conserved factors have evolved their transcription regulation to acquire species-specific function.

A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology.

The emergence of multidrug-resistant bacteria is a critical global crisis that poses a serious threat to public health, particularly with the rise of multidrug-resistant Staphylococcus aureus. Accurate assessment of drug resistance is essential for appropriate treatment and prevention of transmission of these deadly pathogens. Early detection of drug resistance in patients is critical for providing timely treatment and reducing the spread of multidrug-resistant bacteria. This study aims to develop a novel risk assessment framework for S. aureus that can accurately determine the resistance to multiple antibiotics. The comprehensive 7-year study involved ˃20 000 isolates with susceptibility testing profiles of six antibiotics. By incorporating mass spectrometry and machine learning, the study was able to predict the susceptibility to four different antibiotics with high accuracy. To validate the accuracy of our models, we externally tested on an independent cohort and achieved impressive results with an area under the receiver operating characteristic curve of 0. 94, 0.90, 0.86 and 0.91, and an area under the precision-recall curve of 0.93, 0.87, 0.87 and 0.81, respectively, for oxacillin, clindamycin, erythromycin and trimethoprim-sulfamethoxazole. In addition, the framework evaluated the level of multidrug resistance of the isolates by using the predicted drug resistance probabilities, interpreting them in the context of a multidrug resistance risk score and analyzing the performance contribution of different sample groups. The results of this study provide an efficient method for early antibiotic decision-making and a better understanding of the multidrug resistance risk of S. aureus.