Optical control of ultrafast structural dynamics in a fluorescent protein

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling

Exciton transport can be enhanced in the strong coupling regime where excitons hybridize with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments indicate that organic polaritons propagate in a diffusive manner and more slowly than their group velocity. Here, we resolve this controversy by means of molecular dynamics simulations of Rhodamine molecules in a Fabry-Pérot cavity. Our results suggest that polariton propagation is limited by the cavity lifetime and appears diffusive due to reversible population transfers between polaritonic states that propagate ballistically at their group velocity, and dark states that are stationary. Furthermore, because long-lived dark states transiently trap the excitation, propagation is observed on timescales beyond the intrinsic polariton lifetime. These insights not only help to better understand and interpret experimental observations, but also pave the way towards rational design of molecule-cavity systems for coherent exciton transport.

Examination of critical factors influencing ruminant disease dynamics in the Black Sea Basin

Introduction

Ruminant production in the Black Sea basin (BSB) is critical for national economies and the subsistence of rural populations. Yet, zoonoses and transboundary animal diseases (TADs) are limiting and threatening the sector. To gain a more comprehensive understanding, this study characterizes key aspects of the ruminant sector in nine countries of the BSB, including Armenia, Azerbaijan, Belarus, Bulgaria, Georgia, Moldova, Romania, Türkiye, and Ukraine.

Methods

We selected six priority ruminant diseases (anthrax, brucellosis, Crimean Congo haemorrhagic fever (CCHF), foot-and-mouth disease (FMD), lumpy skin disease (LSD), and peste des petits ruminants (PPR)) that are present or threaten to emerge in the region. Standardized questionnaires were completed by a network of focal points and supplemented with external sources. We examined country and ruminant-specific data such as demographics, economic importance, and value chains in each country. For disease-specific data, we analysed the sanitary status, management strategies, and temporal trends of the selected diseases.

Results and discussion

The shift from a centrally planned to a market economy, following the collapse of the Soviet Union, restructured the ruminant sector. This sector played a critical role in rural livelihoods within the BSB. Yet, it faced significant challenges such as the low sustainability of pastoralism, technological limitations, and unregistered farms. Additionally, ruminant health was hindered by informal animal trade as a result of economic factors, insufficient support for the development of formal trade, and socio-cultural drivers. In the Caucasus and Türkiye, where diseases were present, improvements to ruminant health were driven by access to trading opportunities. Conversely, European countries, mostly disease-free, prioritized preventing disease incursion to avoid a high economic burden. While international initiatives for disease management are underway in the BSB, there is still a need for more effective local resource allocation and international partnerships to strengthen veterinary health capacity, protect animal health and improve ruminant production.

Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic Proteins from First Principles: The Fenna-Matthews-Olson Complex Example

Multiscale molecular modeling is utilized to predict optical absorption and circular dichroism spectra of two single-point mutants of the Fenna-Matthews-Olson photosynthetic pigment-protein complex. The modeling approach combines classical molecular dynamics simulations with structural refinement of photosynthetic pigments and calculations of their excited states in a polarizable protein environment. The only experimental input to the modeling protocol is the X-ray structure of the wild-type protein. The first-principles modeling reproduces changes in the experimental optical spectra of the considered mutants, Y16F and Q198V. Interestingly, the Q198V mutation has a negligible effect on the electronic properties of the targeted bacteriochlorophyll a pigment. Instead, the electronic properties of several other pigments respond to this mutation. The molecular modeling demonstrates that a single-point mutation can induce long-range effects on the protein structure, while extensive structural changes near a pigment do not necessarily lead to significant changes in the electronic properties of that pigment.

Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements.

Ibrutinib in combination with rituximab is highly effective in treatment of chronic lymphocytic leukemia patients with steroid refractory and relapsed autoimmune cytopenias

Autoimmune hemolytic anemia (AIHA) and pure red cell aplasia (PRCA) are common complications of CLL. The optimal treatment of steroid refractory AIHA/PRCA is not well established. We conducted a multicenter study of ibrutinib and rituximab in patients with relapsed/refractory to steroids AIHA/PRCA and underlying CLL. Protocol included induction (ibrutinib 420 mg/day and rituximab, 8 weekly and 4 monthly infusions) and maintenance phase with ibrutinib alone until progression or unacceptable toxicity. Fifty patients were recruited (44-warm AIHA, 2-cold AIHA, 4-PRCA). After the induction 34 patients (74%) have achieved complete response, 10 (21.7%) partial response. Median time to hemoglobin normalization was 85 days. With regards to CLL response 9 (19%) patients have achieved CR, 2 (4%) patients-stabilization and 39 (78%)-PR. The median follow-up was 37.56 months. In AIHA group 2 patients had a relapse. Among 4 patients with PRCA 1 patient did not respond, and 1 patient had a relapse after CR, 2 remained in CR. The most common adverse events were neutropenia (62%), infections (72%), gastrointestinal complications (54%). In conclusion ibrutinib in combination with rituximab is an active second-line treatment option for patients with relapsed or refractory AIHA/PRCA and underlying CLL.

Natural Products/Bioactive Compounds as a Source of Anticancer Drugs

Cancer is one of the major deadly diseases globally. The alarming rise in the mortality rate due to this disease attracks attention towards discovering potent anticancer agents to overcome its mortality rate. The discovery of novel and effective anticancer agents from natural sources has been the main point of interest in pharmaceutical research because of attractive natural therapeutic agents with an immense chemical diversity in species of animals, plants, and microorganisms. More than 60% of contemporary anticancer drugs, in one form or another, have originated from natural sources. Plants and microbial species are chosen based on their composition, ecology, phytochemical, and ethnopharmacological properties. Plants and their derivatives have played a significant role in producing effective anticancer agents. Some plant derivatives include vincristine, vinblastine, irinotecan, topotecan, etoposide, podophyllotoxin, and paclitaxel. Based on their particular activity, a number of other plant-derived bioactive compounds are in the clinical development phase against cancer, such as gimatecan, elomotecan, etc. Additionally, the conjugation of natural compounds with anti-cancerous drugs, or some polymeric carriers particularly targeted to epitopes on the site of interest to tumors, can generate effective targeted treatment therapies. Cognizance from such pharmaceutical research studies would yield alternative drug development strategies through natural sources which could be economical, more reliable, and safe to use.

Identifying Vibrations that Control Non-adiabatic Relaxation of Polaritons in Strongly Coupled Molecule-Cavity Systems

The strong light-matter coupling regime, in which excitations of materials hybridize with excitations of confined light modes into polaritons, holds great promise in various areas of science and technology. A key aspect for all applications of polaritonic chemistry is the relaxation into the lower polaritonic states. Polariton relaxation is speculated to involve two separate processes: vibrationally assisted scattering (VAS) and radiative pumping (RP), but the driving forces underlying these two mechanisms are not fully understood. To provide mechanistic insights, we performed multiscale molecular dynamics simulations of tetracene molecules strongly coupled to the confined light modes of an optical cavity. The results suggest that both mechanisms are driven by the same molecular vibrations that induce relaxation through nonadiabatic coupling between dark states and polaritonic states. Identifying these vibrational modes provides a rationale for enhanced relaxation into the lower polariton when the cavity detuning is resonant with specific vibrational transitions.

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization

Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling

Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While Agp1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes suggest the use of light-controllable histidine kinases and phosphatases for optogenetics.

New imaging tools to measure nephron number in vivo: opportunities for developmental nephrology

The mammalian kidney is a complex organ, requiring the concerted function of up to millions of nephrons. The number of nephrons is constant after nephrogenesis during development, and nephron loss over a life span can lead to susceptibility to acute or chronic kidney disease. New technologies are under development to count individual nephrons in the kidney in vivo. This review outlines these technologies and highlights their relevance to studies of human renal development and disease.

Helix Inversion Controlled by Molecular Motors in Multistate Liquid Crystals

Unravelling the rules of molecular motion is a contemporary challenge that promises to support the development of responsive materials and is likely to enhance the understanding of functional motion. Advances in integrating light-driven molecular motors in soft matter have led to the design and realization of chiral nematic (cholesteric) liquid crystals that can respond to light with modification of their helical pitch, and also with helix inversion. Under illumination, these chiral liquid crystals convert from one helical geometry to another. Here, a series of light-driven molecular motors that feature a rich configurational landscape is presented, specifically which involves three stable chiral states. The succession of chiral structures involved in the motor cycle is transmitted at higher structural levels, as the cholesteric liquid crystals that are formed can interconvert between helices of opposite handedness, reversibly. In these materials, the dynamic features of the motors are thus expressed at the near-macroscopic, functional level, into addressable colors that can be used in advanced materials for tunable optics and photonics.

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.

Plants adapt to the availability of light throughout their lives because it regulates so many aspects of their growth and reproduction. To detect the level of light, plant cells use proteins called phytochromes, which are also found in some bacteria and fungi. Phytochrome proteins change shape when they are exposed to red light, and this change alters the behaviour of the cell. The red light is absorbed by a molecule known as chromophore, which is connected to a region of the phytochrome called the PHY-tongue. This region undergoes one of the key structural changes that occur when the phytochrome protein absorbs light, turning from a flat sheet into a helix.

Claesson, Wahlgren, Takala et al. studied the structure of a bacterial phytochrome protein almost immediately after shining a very brief flash of red light using a laser. The experiments revealed that the structure of the protein begins to change within a trillionth of a second: specifically, the chromophore twists, which disrupts its attachment to the protein, freeing the protein to change shape. Claesson, Wahlgren, Takala et al. note that this structure is likely a very short-lived intermediate state, which however triggers more changes in the overall shape change of the protein.

One feature of the rearrangement is the disappearance of a particular water molecule. This molecule can be found at the core of many different phytochrome structures and interacts with several parts of the chromophore and the phytochrome protein. It is unclear why the water molecule is lost, but given how quickly this happens after the red light is applied it is likely that this disappearance is an integral part of the reshaping process.

Together these events disrupt the interactions between the chromophore and the PHY-tongue, enabling the PHY-tongue to change shape and alter the structure of the phytochrome protein. Understanding and controlling this process could allow scientists to alter growth patterns in plants, such as crops or weeds.

Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked

Photoactivation in the Photoactive Yellow Protein, a bacterial blue-light photoreceptor, proceeds via photoisomerization of the double C═C bond in the covalently attached chromophore. Quantum chemistry calculations, however, have suggested that in addition to double-bond photoisomerization, the isolated chromophore and many of its analogues can isomerize around a single C-C bond as well. Whereas double-bond photoisomerization has been observed with X-ray crystallography, experimental evidence of single-bond photoisomerization is currently lacking. Therefore, we have synthesized a chromophore analogue, in which the formal double bond is covalently locked in a cyclopentenone ring, and carried out transient absorption spectroscopy experiments in combination with nonadiabatic molecular dynamics simulations to reveal that the locked chromophore isomerizes around the single bond upon photoactivation. Our work thus provides experimental evidence of single-bond photoisomerization in a photoactive yellow protein chromophore analogue and suggests that photoisomerization is not restricted to the double bonds in conjugated systems. This insight may be useful for designing light-driven molecular switches or motors.

Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex

High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding quantum mechanics/molecular mechanics with the effective fragment potentials, we computed the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild-type and mutated photosynthetic pigment-protein complexes.

Two-photon quantum interference and entanglement at 2.1 μm

Quantum-enhanced optical systems operating within the 2- to 2.5-μm spectral region have the potential to revolutionize emerging applications in communications, sensing, and metrology. However, to date, sources of entangled photons have been realized mainly in the near-infrared 700- to 1550-nm spectral window. Here, using custom-designed lithium niobate crystals for spontaneous parametric down-conversion and tailored superconducting nanowire single-photon detectors, we demonstrate two-photon interference and polarization-entangled photon pairs at 2090 nm. These results open the 2- to 2.5-μm mid-infrared window for the development of optical quantum technologies such as quantum key distribution in next-generation mid-infrared fiber communication systems and future Earth-to-satellite communications.

Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. Here we briefly outline the challenges associated with such computations and review the progress made in this field.

Photon counting LIDAR at 2.3µm wavelength with superconducting nanowires

In this work, we show a proof-of-principle benchtop single-photon light detection and ranging (LIDAR) depth imager at 2.3µm, utilizing superconducting nanowire single-photon detectors (SNSPDs). We fabricate and fiber-couple SNSPDs to exhibit enhanced photon counting performance in the mid-infrared. We present characterization results using an optical parametric oscillator source and deploy these detectors in a scanning LIDAR setup at 2.3µm wavelength. This demonstrates the viability of these detectors for future free-space photon counting applications in the mid-infrared where atmospheric absorption and background solar flux are low.

Tracking Polariton Relaxation with Multiscale Molecular Dynamics Simulations

When photoactive molecules interact strongly with confined light modes in optical cavities, new hybrid light-matter states form. They are known as polaritons and correspond to coherent superpositions of excitations of the molecules and of the cavity photon. The polariton energies and thus potential energy surfaces are changed with respect to the bare molecules, such that polariton formation is considered a promising paradigm for controlling photochemical reactions. To effectively manipulate photochemistry with confined light, the molecules need to remain in the polaritonic state long enough for the reaction on the modified potential energy surface to take place. To understand what determines this lifetime, we have performed atomistic molecular dynamics simulations of room-temperature ensembles of rhodamine chromophores strongly coupled to a single confined light mode with a 15 fs lifetime. We investigated three popular experimental scenarios and followed the relaxation after optically pumping (i) the lower polariton, (ii) the upper polariton, or (iii) uncoupled molecular states. The results of the simulations suggest that the lifetimes of the optically accessible lower and upper polaritons are limited by (i) ultrafast photoemission due to the low cavity lifetime and (ii) reversible population transfer into the "dark" state manifold. Dark states are superpositions of molecular excitations but with much smaller contributions from the cavity photon, decreasing their emission rates and hence increasing their lifetimes. We find that population transfer between polaritonic modes and dark states is determined by the overlap between the polaritonic and molecular absorption spectra. Importantly, excitation can also be transferred "upward" from the lower polariton into the dark-state reservoir due to the broad absorption spectra of the chromophores, contrary to the common conception of these processes as a "one-way" relaxation from the dark states down to the lower polariton. Our results thus suggest that polaritonic chemistry relying on modified dynamics taking place within the lower polariton manifold requires cavities with sufficiently long lifetimes and, at the same time, strong light-matter coupling strengths to prevent the back-transfer of excitation into the dark states.

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra.

Design and Characterisation of Titanium Nitride Subarrays of Kinetic Inductance Detectors for Passive Terahertz Imaging

We report on the investigation of titanium nitride (TiN) thin films deposited via atomic layer deposition (ALD) for microwave kinetic inductance detectors (MKID). Using our in-house ALD process, we have grown a sequence of TiN thin films (thickness 15, 30, 60 nm). The films have been characterised in terms of superconducting transition temperature T c , sheet resistance R s and microstructure. We have fabricated test resonator structures and characterised them at a temperature of 300 mK. At 350 GHz, we report an optical noise equivalent power NEP opt ≈ 2.3 × 10 - 15 W / Hz , which is promising for passive terahertz imaging applications.

Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila

Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.

Hypoxic renal injury in newborns with abdominal compartment syndrome (clinical and experimental study)

BackgroundSurgical treatment for gastroschisis and congenital diaphragmatic hernia (CDH) commonly leads to abdominal compartment syndrome (ACS) associated with hypoxic renal injury. We hypothesized that measurement of urinary and serum concentrations of vascular endothelial growth factor (VEGF), π-glutathione S-transferase (π-GST), and monocyte chemoattractant protein-1 (MCP-1) may serve for noninvasive detection of hypoxic renal injury in such patients.MethodsIntra-abdominal pressure (IAP), renal excretory function, and the biomarker levels were analyzed before, 4, and 10 days after surgery. Association between the biomarker levels and renal histology was investigated using an original model of ACS in newborn rats.ResultsFour days after surgery, IAP increased, renal excretory function decreased, and the levels of VEGF, π-GST, and MCP-1 increased, indicating renal injury. Ten days after surgery, IAP partially decreased, renal excretory function completely restored, but the biomarker levels remained elevated, suggesting the ongoing kidney injury. In the model of ACS, increase in the biomarker levels was associated with progressing kidney morphological alteration.ConclusionSurgical treatment for gastroschisis and CDH is associated with prolonged hypoxic kidney injury despite complete restoration of renal excretory function. Follow-up measurement of VEGF, π-GST, and MCP-1 levels may provide a better tool for noninvasive assessment of renal parenchyma in newborns with ACS.

Urinary cytokines as markers of latent inflammation in children with chronic pyelonephritis and anorectal malformations

INTRODUCTION

Anorectal malformations (ARMs) comprise a range of defects in the development of the lowest portion of the intestinal tract that are often associated with anomalies of the urinary tract. We hypothesize that ARMs may specifically predispose the patients to prolonged urinary tract infection (UTI) and transition from a state of active (clinically apparent) inflammation to a state of latent inflammation following antibiotic treatment. Yet diagnosis of latent inflammation in the urinary tract is problematic.

OBJECTIVE

The aim was to investigate the urinary levels of proinflammatory (IL-1β, IL-6, IL-8, and MCP-1), anti-inflammatory (IL-10), and proangiogenic (VEGF) cytokines in the clinical course of chronic pyelonephritis (CP) as potential biomarkers of latent inflammation in the urinary tract in children with ARM.

PATIENTS AND METHODS

A total of 34 children (age range 4-120 months) with CP in the active phase of inflammation were divided into two groups: CP with ARM group included 20 patients and CP without ARM group included 14 patients. The control group included 20 healthy children similar by age and gender. Urine samples were collected at the time of enrollment, 5-7 days after institution of antibiotic treatment, and 1.5 months after enrollment. Cytokine concentrations were measured by ELISA.

RESULTS

Upon enrollment, we detected increased urinary levels of IL-10 and MCP-1 and normal levels of IL-1β, IL-6, IL-8, and VEGF in CP with ARM patients as well as normal levels of all of these cytokines in CP without ARM patients. After 5-7 days of antibiotic treatment, despite significant clinical and laboratory improvement observed in both patient groups, we documented a prominent increase in the urinary concentrations of all measured cytokines indicating ongoing inflammation in the urinary tract. Following 1.5 months of enrollment, in CP without ARM patients, IL-8 and MCP-1 were increased, IL-1, IL-6, and VEGF were close to control, and IL-10 was below the control level, indicating partial resolution of the inflammatory process. In contrast, in CP with ARM patients, IL-1β, IL-6, IL-8, MCP-1, and VEGF were increased suggesting persistent inflammation in the urinary tract (Table).

CONCLUSION

Based on the urinary cytokine profile, we conclude that presence of ARM may be associated with transition from active to latent inflammation in the urinary tract after antibiotic treatment for UTI. Follow-up monitoring of the urinary cytokines may provide a better assessment of inflammatory activity in the urinary tract in children with combined urological and anorectal pathologies.

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

Optical performance of an ultra-sensitive horn-coupled transition-edge-sensor bolometer with hemispherical backshort in the far infrared

The next generation of far infrared space observatories will require extremely sensitive detectors that can be realized only by combining extremely low intrinsic noise with high optical efficiency. We have measured the broad-band optical response of ultra-sensitive transtion edge sensor (TES) bolometers (NEP≈2aW/Hz) in the 30-60-μm band where radiation is coupled to the detectors with a few-moded conical feedhorn and a hemispherical backshort. We show that these detectors have an optical efficiency of 60% (the ratio of the power detected by the TES bolometer to the total power propagating through the feedhorn). We find that the measured optical efficiency can be understood in terms of the modes propagating through the feedhorn with the aid of a spatial mode-filtering technique.

Observation of Transverse Spin-Dependent Azimuthal Correlations of Charged Pion Pairs in p^{↑}+p at sqrt[s]=200 GeV

We report the observation of transverse polarization-dependent azimuthal correlations in charged pion pair production with the STAR experiment in p^{↑}+p collisions at RHIC. These correlations directly probe quark transversity distributions. We measure signals in excess of 5 standard deviations at high transverse momenta, at high pseudorapidities η>0.5, and for pair masses around the mass of the ρ meson. This is the first direct transversity measurement in p+p collisions.

Preliminary Analysis of the Surgical Treatment of Anorectal Malformations in Russia

The article provides the analysis of a survey of the professional community of Russian pediatric surgeons, dedicated to the treatment of anorectal malformations (ARM). The authors evaluated the differences and similarities in classification, surgical procedures, time of definitive repair, and postoperative management of ARM in different hospitals and centers. This was done by a survey upon specialists and experts in Russia followed by a symposium with live surgery, open discussion, and vote. Overall, 85% of the delegates supported the idea to create several regional centers of pediatric coloproctology as the way to improve the treatment of ARM in Russia. Moreover, 80% of delegates agreed to create a universal database of ARM information. The development of neonatal surgery and videoendoscopic surgical methods in the treatment of patients with ARM requires creation of a national guideline by the Russian Association of Pediatric Surgeons. Next step will concern standardization of the diagnosis and surgical treatment of children with ARM. This study is a collaborative effort to provide Russian Consensus on treatment of ARM.

Augmented Topological Descriptors of Pore Networks for Material Science

One potential solution to reduce the concentration of carbon dioxide in the atmosphere is the geologic storage of captured CO2 in underground rock formations, also known as carbon sequestration. There is ongoing research to guarantee that this process is both efficient and safe. We describe tools that provide measurements of media porosity, and permeability estimates, including visualization of pore structures. Existing standard algorithms make limited use of geometric information in calculating permeability of complex microstructures. This quantity is important for the analysis of biomineralization, a subsurface process that can affect physical properties of porous media. This paper introduces geometric and topological descriptors that enhance the estimation of material permeability. Our analysis framework includes the processing of experimental data, segmentation, and feature extraction and making novel use of multiscale topological analysis to quantify maximum flow through porous networks. We illustrate our results using synchrotron-based X-ray computed microtomography of glass beads during biomineralization. We also benchmark the proposed algorithms using simulated data sets modeling jammed packed bead beds of a monodispersive material.