A new analytical method, using the dark Fenton reaction as an OH radical source to study oxidations of unsaturated (di)aldehydes in the aqueous phase

<p>Anthropogenic and biogenic sources produce numerous primary emitted gases, organic compounds, and aerosols in the atmosphere. An important group of such compounds are α, β-unsaturated carbonyl molecules, which can be formed in the atmosphere due to their secondary origin, including oxidation of their precursors such as hydrocarbons with common atmospheric oxidants such as hydroxyl radicals (‧OH). Since those compounds contain at least one double bond and one carbonyl group, they are characterized as water-soluble molecules, which can diffuse on the cloud droplets’ surface and undergo a phase transfer from the gas phase to the atmospheric aqueous phase. In the latter, the oxidized organic compounds can contribute to aerosol mass production through in-cloud processes, yielding aqueous phase secondary organic aerosols (aqSOA). Due to their strong photochemical behavior, the development of a new analytical approach for evaluating the OH radical kinetics in the aqueous phase under dark conditions was essential. One of the most studied non-photolytic reactions is Fenton chemistry (Fe(II)/H<sub>2</sub>O<sub>2</sub>), which serves as an OH radical source in the dark in the atmospheric aqueous phase after catalytic decomposition of H<sub>2</sub>O<sub>2</sub> in the presence of Fe(II) at acidic pH values. In a typical experiment, temperature-dependent second-order rate constants of OH radicals with unsaturated dialdehydes, such as (1) crotonaldehyde, and (2) 1,4-butenedial, were determined in a bulk reactor by using the competition kinetics method. In the newly developed method, the role of radical scavenger was performed by isotopically labeled 2-propanol (d8), while the OH-initiated oxidation produces deuterated acetone (d6), being analyzed with GC-MS after derivatization. The findings from our research will be incorporated in the CAPRAM model to explain discrepancies between experimentally observed and predicted aqSOA properties.</p>

A Contrast Calibration Protocol for X-ray Speckle Visibility Spectroscopy

X-ray free electron lasers, with their ultrashort highly coherent pulses, opened up the opportunity of probing ultrafast nano- and atomic-scale dynamics in amorphous and disordered material systems via speckle visibility spectroscopy. However, the anticipated count rate in a typical experiment is usually low. Therefore, visibility needs to be extracted via photon statistics analysis, i.e., by estimating the probabilities of multiple photons per pixel events using pixelated detectors. Considering the realistic X-ray detector responses including charge cloud sharing between pixels, pixel readout noise, and gain non-uniformity, speckle visibility extraction relying on photon assignment algorithms are often computationally demanding and suffer from systematic errors. In this paper, we present a systematic study of the commonly-used algorithms by applying them to an experimental data set containing small-angle coherent scattering with visibility levels ranging from below 1% to ∼60%. We also propose a contrast calibration protocol and show that a computationally lightweight algorithm can be implemented for high-speed correlation evaluation.

High-Resolution Ion-Flux Imaging of Proton Transport Through Graphene|Nafion Membranes

In 2014, it was reported that protons can traverse between aqueous phases separated by nominally pristine monolayer graphene and hexagonal boron nitride (h-BN) films (membranes) under ambient conditions. This “intrinsic proton conductivity” of the one-atom-thick crystals, with proposed through-plane conduction, challenged the notion that graphene is impermeable to atoms, ions and molecules. More recent evidence points to a defect-facilitated transport mechanism, analogous to transport through conventional ion-selective membranes based on graphene and h-BN. To clarify the nature of proton transmission through graphene, local ion-flux imaging is performed herein on graphene|Nafion membranes using an “electrochemical ion (proton) pump cell” mode of scanning electrochemical cell microscopy (SECCM). Targeting regions that are free from visible macroscopic defects (e.g., cracks, holes etc.), and assessing hundreds to thousands of different sites across the graphene surfaces in a typical experiment, most of the graphene|Nafion membrane is impermeable to proton transport, with transmission typically occurring at only ≈20 – 60 localized sites across a ≈0.003 mm2 area of membrane (>5000 measurements, total). When localized proton transport occurs, it can be a highly dynamic process, with new transmission sites “opening” and a small number of sites “closing” under an applied electric field, on the seconds timescale. Applying a simple equivalent circuit model of ion-transport through a cylindrical nanopore, the local transmission sites are estimated to possess dimensions (radii) on the (sub)nanometer-scale, implying that rare atomic defects are responsible for proton conductance through monolayer graphene. Overall, this work reinforces SECCM as a premier tool for the structure−property mapping of microscopically complex (electro)materials, with the local ion-flux mapping configuration introduced herein being widely applicable for functional membrane characterization and beyond, e.g., for diagnosing failure mechanisms in protective surface coatings.

An Efficient Synthesis Of α, β Unsaturated Ketones Via Claisen–Schmidt Condensation Reaction Using Amino Acid Based Ionic Liquids

: Synthesis of chalcone by Claisen–Schmidt condensation using recyclable L- aspartic acid coupled imidazolium-based ionic liquid as a green synthetic approach has been developed. Present work offers significant advantages such as high yield, enhanced reaction speed even at room temperature, catalyst reusability, and the involvement of non-toxic reagents. Background: Chalcones are a flavonoid family and have pharmacological and biological activities. It includes antibacterial, antifungal, immunosuppressive, and anti-nociceptive properties. Objective: Ionic liquid has emerged as a powerful tool for molecular organic solvents and wide liquid range, ease of recovery and reuse, and making them a greener alternative to volatile organic solvents. Thus, our objective was to employ them as dual catalyst and solvent systems to synthesize chalcone via CS condensation in the present work. Method: In a typical experiment, benzaldehyde (10 mmol), acetophenone (10 mmol), and 2.5 mol% (L-AAIL) ionic liquid were mixed in a 50 mL round-bottom flask. The reaction was preceded quickly at room temperature with stirring, the resulting mixture became a biphasic system with the residue at the bottom and the upper phase containing some unreacted substrate separated from the catalyst by filtration and decantation. The catalyst was extracted with CH2Cl2 and split for the next cycle. Results: Claisen–Schmidt condensation accomplished with reasonable to good yields, ranged from 78 to 95% at room temperature in the presence of the [L-AAIL], as compared to the traditional route at more than 100O C. Conclusion: [L-AAIL] are found a highly efficient and eco-friendly catalyst for synthesizing chalcone derivatives at room temperature. [L-AAIL] as a solvent and catalyst will exhibit real advantages by providing a ‘green’ process with the safer operation, Short reaction periods, mild reaction conditions, easier separation, and reusability of ionic liquid made this methodology valuable for synthetic organic chemists as well as industry.

O-157 Micro-Computed Tomography of the adult mouse ovary: an in-silico 3D reconstruction of folliculogenesis

Study question Which are the spatial dynamics of follicles recruitment and growth inside the ovary? Summary answer 3D micro-Computed Tomography (microCT) shows a simultaneous and homogeneous distribution of follicle recruitment all-over the cortex,and subsequent growth within the same ovarian region. What is known already In the mouse ovary, folliculogenesis progresses from the primordial type 1 (T1) to the fully-grown T8 follicle. Most of our knowledge of the folliculogenetic process has been obtained by disaggregating the ovary into its functional units (i.e., follicles and oocytes), thus losing the complexity of the whole histo-functional context. To date, few studies employed 3D imaging approaches to gain information on the inside 3D ovary organisation. MicroCT is the only technique that combines a high spatial resolution (down to ∼1 µm) with the production of a true 3D organ reconstruction, with cubic voxels and isotropic resolution. Study design, size, duration Three ovaries of three different adult mice were treated with the contrast agent and then imaged with microCT. A typical experiment required a total of 35 man/h from ovaries isolation to completion of X-ray scanning, and 24 man/h for follicles classification and mapping. Participants/materials, setting, methods Three ovaries of three different 8-week-old CD1 mice were fixed in 4% Paraformaldehyde and treated with Lugol’s solution for 3 hr at RT. Ovaries were scanned with Skyscan 1172 (Bruker) using a 1.5 µm/pixel resolution. MicroCT sections were processed with Fiji ImageJ (NIH), and 3D rendering of follicles and blood vessels were obtained with Avizo-9 (Thermo Fisher Scientific). ANOVA and Bonferroni post-­hocstatistical analyses were performed with RStudio, considering data significantly different when p < 0.05. Main results and the role of chance Using microCT we built the first in silico3D reconstruction of the tiny mouse ovary, identifying, mapping and counting follicles,from pre-antral secondary T4 (53.2 + 12.7 µm in diameter) to fully-grown antral T8 (321.0 + 21.3 µm), and the corpora lutea.MicroCTbrought up the main functional compartments of the growing follicle, i.e., granulosa and cumulus cells, the antrum, the zona pellucida, and the oocyte with its nucleus. Instead, primordial and primary follicles (T1–T3) could not be observed, perhaps due to the reduced size of their enclosed oocyte and to the absence of a well-formed zona pellucida around the germ cell. In addition, our analysis allowed the visualisation and 3D modelling of the main ovarian vasculature, from the largest vessel that enters the organ at the hilum site (∼150 µm size in diameter)to smaller branches present in the medulla region (∼35 µm). These results show that each of the eight ovarian sectors, virtually segmented along the dorsal-ventral axis,houses an equal number of each follicle type, suggesting a simultaneous and homogeneous distribution of follicle recruitment all-over the cortex,and subsequent growth within the same ovarian region. Limitations, reasons for caution To strengthen the results, the number of ovaries/individuals analysed should be increased. Wider implications of the findings This 3D mapping of follicles and vessels could contribute our understanding of folliculogenesis dynamics, not only under normal conditions, but also during ageing, after hormones or drugs administration, or in the presence of ovarian pathologies. Trial registration number not applicable

Molecular Biomechanics Controls Protein Mixing and Segregation in Adherent Membranes

Cells interact with their environment by forming complex structures involving a multitude of proteins within assemblies in the plasma membrane. Despite the omnipresence of these assemblies, a number of questions about the correlations between the organisation of domains and the biomechanical properties of the involved proteins, namely their length, flexibility and affinity, as well as about the coupling to the elastic, fluctuating membrane, remain open. Here we address these issues by developing an effective Kinetic Monte Carlo simulation to model membrane adhesion. We apply this model to a typical experiment in which a cell binds to a functionalized solid supported bilayer and use two ligand-receptor pairs to study these couplings. We find that differences in affinity and length of proteins forming adhesive contacts result in several characteristic features in the calculated phase diagrams. One such feature is mixed states occurring even with proteins with length differences of 10 nm. Another feature are stable nanodomains with segregated proteins appearing on time scales of cell experiments, and for biologically relevant parameters. Furthermore, we show that macroscopic ring-like patterns can spontaneously form as a consequence of emergent protein fluxes. The capacity to form domains is captured by an order parameter that is founded on the virial coefficients for the membrane mediated interactions between bonds, which allow us to collapse all the data. These findings show that taking into account the role of the membrane allows us to recover a number of experimentally observed patterns. This is an important perspective in the context of explicit biological systems, which can now be studied in significant detail.

Parametric instability of a magnetic pendulum in the presence of a vibrating conducting plate

A pendulum with an attached permanent magnet swinging in the vicinity of a conductor is a typical experiment for the demonstration of electromagnetic braking and Lenz’ law of induction. When the conductor itself moves, it can transfer energy to the pendulum. An exact analytical model of such an electromagnetic interaction is possible for a flat conducting plate. The eddy currents induced in the plate by a moving magnetic dipole and the resulting force and torque are known analytically in the quasistatic limit, i.e., when the magnetic diffusivity is sufficiently high to ensure an equilibrium of magnetic field advection and diffusion. This allows us to study a simple pendulum with a magnetic dipole moment in the presence of a horizontal plate oscillating in vertical direction. Equilibrium of the pendulum in the vertical position can be realized in three cases considered, i.e., when the magnetic moment is parallel to the rotation axis, or otherwise, its projection onto the plane of motion is either horizontal or vertical. The stability problem is described by a differential equation of Mathieu type with a damping term. Instability is only possible when the vibration amplitude and the distance between plate and magnet satisfy certain constraints related to the simultaneous excitation and damping effects of the plate. The nonlinear motion is studied numerically for the case when the magnetic moment and rotation axis are parallel. Chaotic behavior is found when the eigenfrequency is sufficiently small compared to the excitation frequency. The plate oscillation typically has a stabilizing effect on the inverted pendulum.

Segmentation and analysis of mother machine data: SAM

Time-lapse imaging of bacteria growing in micro-channels in a controlled environment has been instrumental in studying the single cell dynamics of bacterial growth. This kind of a microfluidic setup with growth chambers is popularly known as mother machine [1]. In a typical experiment with such a set-up, bacterial growth can be studied for numerous generations with high resolution and temporal precision using image processing. However, as in any other experiment involving imaging, the image data from a typical mother machine experiment has considerable intensity fluctuations, cell intrusion, cell overlapping, filamentation etc. The large amount of data produced in such experiments makes it hard for manual analysis and correction of such unwanted aberrations. We have developed a modular code for segmentation and analysis of mother machine data (SAM) for rod shaped bacteria where we can detect such aberrations and correctly treat them without manual supervision. We track cumulative cell size and use an adaptive segmentation method to avoid faulty detection of cell division. SAM is currently written and compiled using MATLAB. It is fast (∼ 15 min/GB of image) and can be efficiently coupled with shell scripting to process large amount of data with systematic creation of output file structures and graphical results. It has been tested for many different experimental data and is publicly available in Github.

RNA Conformation Capture by Proximity Ligation

RNA proximity ligation is a set of molecular biology techniques used to analyze the conformations and spatial proximity of RNA molecules within cells. A typical experiment starts with cross-linking of a biological sample using UV light or psoralen, followed by partial fragmentation of RNA, RNA–RNA ligation, library preparation, and high-throughput sequencing. In the past decade, proximity ligation has been used to study structures of individual RNAs, networks of interactions between small RNAs and their targets, and whole RNA–RNA interactomes, in models ranging from bacteria to animal tissues and whole animals. Here, we provide an overview of the field, highlight the main findings, review the recent experimental and computational developments, and provide troubleshooting advice for new users. In the final section, we draw parallels between DNA and RNA proximity ligation and speculate on possible future research directions.

Performance of Typical and Superior Face Recognisers on a Novel Interactive Face Matching Procedure

Unfamiliar simultaneous face matching is error prone. Reducing incorrect identification decisions will positively benefit forensic and security contexts. The absence of view-independent information in static images likely contributes to the difficulty of unfamiliar face matching. We tested whether a novel interactive viewing procedure that provides the user with 3D structural information as they rotate a facial image to different orientations would improve face matching accuracy. We tested the performance of ‘typical’ (Experiment 1) and ‘superior’ (Experiment 2) face recognisers, comparing their performance using high quality (Experiment 3) and pixelated (Experiment 4) Facebook profile images. In each trial, participants responded whether two images featured the same person with one of these images being either a static face, a video providing orientation information, or an interactive image. Taken together, the results show that fluid orientation information and interactivity prompt shifts in criterion and support matching performance. Because typical and superior face recognisers both benefited from the structural information provided by the novel viewing procedures, our results point to qualitatively similar reliance on pictorial encoding in these groups. This also suggests that interactive viewing tools can be valuable in assisting face matching in high performing practitioner groups.