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Lanthanide nitride ( Ln N) materials have garnered significant interest in recent years due to their promising potential as heterogeneous catalysts for green ammonia synthesis under low temperature and pressure reaction conditions. Here, we report on the synthesis of an extended series of lanthanide ( Ln ) nitride powders ( Ln = lanthanum, cerium, neodymium, samarium, gadolinium, terbium, dysprosium, erbium, lutetium) and their structural and vibrational properties. Polycrystalline powders were fabricated using a ball milling mechanochemical process, and their structural properties were assessed by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The experimental lattice constants deduced from XRD and TEM were compared with density functional theory-based calculated lattice constants using the Perdew-Burke-Ernzerhof exchange-correlation functional. We show that the calculated lattice constants are within 1-1.5% of the experimental values for the majority of the Ln N species-a notable increase in accuracy over prior computational approaches. The frequencies of Raman scattering from the LO(Γ) phonon are reported across the series and compare well with published thin-film data on a smaller selection of the series. As expected, there is a linear relationship between the LO(Γ) phonon frequency and atomic number. Finally, we demonstrate that Raman spectroscopy can be used to detect the presence of a nanoscale oxide layer on the surface of ErN powders., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

This work presents a general chemical reaction network theory for olfactory sensing processes that employ G-protein-coupled receptors as olfactory receptors (ORs). The theory can be applied to general mixtures of odorants and an arbitrary number of ORs. Reactions of ORs with G-proteins, in both the presence and absence of odorants, are explicitly considered. A unique feature of the theory is the definition of an odor activity vector consisting of strengths of odorant-induced signals from ORs relative to those due to background G-protein activity in the absence of odorants. It is demonstrated that each component of the odor activity defined this way reduces to a Michaelis-Menten form capable of accounting for cooperation or competition effects between different odorants. The main features of the theory are illustrated for a two-odorant mixture. Known and potential mixture effects, such as suppression, shadowing, inhibition, and synergy, are quantitatively described. Effects of relative values of rate constants, basal activity, and G-protein concentration are also demonstrated.

Flexible and easy-to-use microfluidic systems are suitable options for point-of-care diagnostics. Here, we investigate liquid transport in fluidic channels produced by stencil printing on flexible substrates as a reproducible and scalable option for diagnostics and paper-based sensing. Optimal printability and flow profiles were obtained by combining minerals with cellulose fibrils of two different characteristic dimensions, in the nano- and microscales, forming channels with ideal wettability. Biomolecular ligands were easily added by inkjet printing on the channels, which were tested for the simultaneous detection of glucose and proteins. Accurate determination of clinically relevant concentrations was possible from linear calibration, confirming the potential of the introduced paper-based diagnostics. The results indicate the promise of simple but reliable fluidic channels for drug and chemical analyses, chromatographic separation, and quality control., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

This paper presents pySBOL, a software library for computer-aided design of synthetic biological systems in the Python scripting language. This library provides an easy-to-use, object-oriented, application programming interface (API) with low barrier of entry for synthetic biology application developers. The pySBOL library enables reuse of genetic parts and designs through standardized data exchange with biological parts repositories and software tools that communicate using the Synthetic Biology Open Language (SBOL). In addition, pySBOL supports data management of design-build-test-learn workflows for individual laboratories as well as large, distributed teams of synthetic biologists. PySBOL also lets users add custom data to SBOL files to support the specific data requirements of their research. This extensibility helps users integrate software tool chains and develop workflows for new applications. These features and others make the pySBOL library a valuable tool for supporting engineering practices in synthetic biology. Documentation and installation instructions can be found at pysbol2.readthedocs.io .

Kaede, an analogue of green fluorescent protein (GFP), is a green-to-red photoconvertible fluorescent protein used as an in vivo "optical highlighter" in bioimaging. The fluorescence quantum yield of the red Kaede protein is lower than that of GFP, suggesting that increasing the conjugation modifies the electronic relaxation pathway. Using a combination of anion photoelectron spectroscopy and electronic structure calculations, we find that the isolated red Kaede protein chromophore in the gas phase is deprotonated at the imidazole ring, unlike the GFP chromophore that is deprotonated at the phenol ring. We find evidence of an efficient electronic relaxation pathway from higher-lying electronically excited states to the S 1 state of the red Kaede chromophore that is not accessible in the GFP chromophore. Rapid autodetachment from high-lying vibrational states of S 1 is found to compete efficiently with internal conversion to the ground electronic state.

BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto-enol tautomerization induced by electronic excitation of the flavin ring are considered.

Acinetobacter baumannii is an important human pathogen that can form biofilms and persist under harsh environmental conditions. Biofilm formation and virulence are modulated by blue light, which is thought to be regulated by a BLUF protein, BlsA. To understand the molecular mechanism of light sensing, we have used steady-state and ultrafast vibrational spectroscopy to compare the photoactivation mechanism of BlsA to the BLUF photosensor AppA from Rhodobacter sphaeroides . Although similar photocycles are observed, vibrational data together with homology modeling identify significant differences in the β5 strand in BlsA caused by photoactivation, which are proposed to be directly linked to downstream signaling.

Living systems are fundamentally dependent on the ability of proteins to respond to external stimuli. The mechanism, the underlying structural dynamics, and the time scales for regulation of this response are central questions in biochemistry. Here we probe the structural dynamics of the BLUF domain found in several photoactive flavoproteins, which is responsible for light activated functions as diverse as phototaxis and gene regulation. Measurements have been made over 10 decades of time (from 100 fs to 1 ms) using transient vibrational spectroscopy. Chromophore (flavin ring) localized dynamics occur on the pico- to nanosecond time scale, while subsequent protein structural reorganization is observed over microseconds. Multiple time scales are observed for the dynamics associated with different vibrations of the protein, suggesting an underlying hierarchical relaxation pathway. Structural evolution in residues directly H-bonded to the chromophore takes place more slowly than changes in more remote residues. However, a point mutation which suppresses biological function is shown to 'short circuit' this structural relaxation pathway, suppressing the changes which occur further away from the chromophore while accelerating dynamics close to it.

Photochromic proteins, such as Dronpa, are of particular importance in bioimaging and form the basis of ultraresolution fluorescence microscopy. The photochromic reaction involves switching between a weakly emissive neutral trans form of the chromophore (A) and its emissive cis anion (B). Controlling the rates of switching has the potential to significantly enhance the spatial and temporal resolution in microscopy. However, the mechanism of the switching reaction has yet to be established. Here we report a high signal-to-noise ultrafast transient infrared investigation of the photochromic reaction in the mutant Dronpa2, which exhibits facile switching behavior. In these measurements we excite both the A and B forms and observe the evolution in the IR difference spectra over hundreds of picoseconds. Electronic excitation leads to bleaching of the ground electronic state and instantaneous (subpicosecond) changes in the vibrational spectrum of the protein. The chromophore and protein modes evolve with different kinetics. The chromophore ground state recovers in a fast nonsingle-exponential relaxation, while in a competing reaction the protein undergoes a structural change. This results in formation of a metastable form of the protein in its ground electronic state (A'), which subsequently evolves on the time scale of hundreds of picoseconds. The changes in the vibrational spectrum that occur on the subnanosecond time scale do not show unambiguous evidence for either proton transfer or isomerization, suggesting that these low-yield processes occur from the metastable state on a longer time scale and are thus not the primary photoreaction. Formation of A', and further relaxation of this state to the cis anion B, are relatively rare events, thus accounting for the overall low yield of the photochemical reaction.

Misfolding and aggregation of α-synuclein (α-syn) is associated with the development of a number of neurodegenerative diseases including Parkinson's disease (PD). Analyses of post mortem tissues revealed the presence of molecular chaperones within α-syn aggregates, suggesting that chaperones play a role in α-syn misfolding and aggregation. In fact, inhibition of chaperone activity aggravates α-syn toxicity, and the overexpression of chaperones, particularly 70-kDa heat shock protein (Hsp70), protects against α-syn-induced toxicity. In this study, we investigated the effect of carbenoxolone (CBX), a glycyrrhizic acid derivative previously reported to upregulate Hsp70, in human neuroglioma cells overexpressing α-syn. We report that CBX treatment lowers α-syn aggregation and prevents α-syn-induced cytotoxicity. We demonstrate further that Hsp70 induction by CBX arises from activation of heat shock factor 1 (HSF1). The Hsp70 inhibitor MAL3-101 and the Hsp70 enhancer 115-7c led to an increase or decrease in α-syn aggregation, respectively, in agreement with these findings. In summary, this study provides a proof-of-principle demonstration that chemical modulation of the Hsp70 machine is a promising strategy to prevent α-syn aggregation.

Co/ZnO and Co/ZnAlO films were prepared by depositing ultrathin cobalt layers and semiconductor layers on glass substrates at room temperature. The films consist of metallic Co particles, semiconductor matrix, and an interfacial magnetic semiconductor with the substitution of Co(2+) for Zn(2+) in the ZnO lattice at the interface between Co particles and the semiconductor matrix. Large room temperature negative tunneling magnetoresistance was observed in the films. In addition, the magnetism and magnetoresistance were obviously enhanced by adding aluminum to the ZnO, and in one Co/ZnAlO sample, the room temperature negative magnetoresistance value reaches -12.3% at 18 kOe (compared with -8.4% of the corresponding Co/ZnO film) and the spin polarization of the tunneling electrons is about 37.5% which is characteristic of metallic Co. This enhancement of the tunneling spin polarization has been ascribed to the tunneling through an interfacial magnetic semiconductor, which causes the robust spin injection from cobalt metal into the semiconductors at room temperature resulting from the spin filter effect of the interfacial magnetic semiconductors.

Protein aggregation is the hallmark of a number of neurodegenerative diseases including Parkinson's and Huntington's diseases. There is a significant interest in understanding the molecular mechanisms involved in the self-association and fibrillization of monomeric soluble proteins into insoluble deposits in vivo and in vitro. Probes with novel properties, such as red-shifted emission, large Stokes shifts, and high photostability, are desirable for a variety of protein aggregation studies. To respond to the increasing need for aggregation-responsive compounds suitable to cellular studies, we present a ruthenium(II) dipyridophenazine derivative, [Ru(phen)(2)dppz](2+) (phen =1,10-phenanthroline, dppz = dipyrido[3,2-a:2'.3'-c]phenazine), to study aggregation of α-synuclein (αS), which is associated with the development of Parkinson's disease. We demonstrated the use of [Ru(phen)(2)dppz](2+) to monitor αS fibril formation in real-time and to detect and quantify αS aggregates in neuroglioma cells, thereby providing a novel molecular tool to study protein deposition diseases in vitro and in vivo.

Cis-trans photoisomerization is proposed as a key process in the photoswitching of some photoactivatable fluorescent proteins. Here we present ultrafast fluorescence measurements of the model GFP chromophore (HBDI) in the cis state and in a mixture of the cis and trans states. Our results demonstrate that the mean lifetimes of the cis and trans states are remarkably similar. Therefore, the specific isomer of the chromophore cannot be solely responsible for the different photophysics of the bright and dark states of photoactive proteins, which must therefore be due to differential interactions between the different isomers of the chromophore and the protein.

An efficient synthesis of NP25302 is presented that relies on 5-endo-dig N-cyclization to establish the bicyclic core and Curtius rearrangement to install the N-acyl vinylogous urea functionality.

We analyzed perfluorinated surfactants (PFSs) in 20 river samples and 5 wastewater secondary effluent samples in Japan to reveal their occurrence and sources. Nine PFS species were determined: perfluorooctanesulfonate (PFOS), perfluorooctane sulfonamide (FOSA), perfluoroheptanoate (PFHpA), perfluorooctanoate (PFOA), perfluorononanoate (PFNA), perfluorodecanoate (PFDA), perfluoroundecanoate (PFUA), perfluorododecanoate (PFDDA), and perfluorotridecanoate (PFTDA). PFSs were detected in all rivers, revealing nationwide contamination of rivers. In particular, 11 out of 20 river samples exceeded New Jersey guidance for PFOA in drinking water (40 ng/L). PFOS, PFHpA, PFOA, and PFNA were major species in Japan. Concentrations of PFOS, PFHpA, and PFNA in rivers were strongly correlated with population density, suggesting that the chemicals were derived from urban activities. PFOA showed a significant but weak correlation. We used crotamiton, a marker of sewage effluent, for further source analysis. Concentrations of PFOS, PFHpA, and PFNAwere strongly correlated with those of crotamiton, and plots of secondary effluents fell near the regression lines of rivers, indicating that the PFOS, PFHpA, and PFNA in rivers were derived from sewage effluent. On the other hand, PFOA was found at remarkably high levels (54-192 ng/L) in seven river samples containing low levels of crotamiton, suggesting that it was derived from nonsewage point sources, as well as sewage effluent. The total fluxes of sewage-derived PFOS, PFHpA, PFOA, and PFNA from Japan were estimated to be 3.6, 2.6, 5.6, and 2.6 t/year, respectively. This is the first report to identify PFOA in several rivers, derived from nonsewage point sources, by using a marker of sewage effluent.

We examined the utility of 13 pharmaceuticals and personal care products (PPCPs) as molecular markers of sewage contamination in riverine, groundwater, and coastal environments. The PPCPs were crotamiton, ibuprofen, naproxen, ketoprofen, fenoprofen, mefenamic acid, thymol, triclosan, propyphenazone, carbamazepine, diethyltoluamide, ethenzamide, and caffeine. Measurements in 37 Japanese rivers showed positive correlations of riverine flux of crotamiton (r2 = 0.85), carbamazepine (r2 = 0.84), ibuprofen (r2 = 0.73), and mefenamic acid (r2 = 0.67) with the population in the catchments. In three surveys in the Tamagawa estuary, crotamiton, carbamazepine, and mefenamic acid behaved conservatively across seasons within a salinity range of 0.4-29 per thousand, suggesting their utility as molecular markers in coastal environments. Removal of ketoprofen and naproxen in the estuary was ascribed to photodegradation. Ibuprofen and thymol were removed from estuarine waters in summer by microbial degradation. Triclosan was removed by a combination of microbial degradation, photodegradation, and adsorption. These results were consistent with those of river water incubated for 8 d at 25 degrees C in the dark in order to examine the effects of biodegradation and photodegradation. Crotamiton was detected in groundwater from the Tokyo metropolitan area (12 out of 14 samples), suggesting wastewater leakage from decrepit sewers. Carbamazepine, ketoprofen, and ibuprofen (5/14), caffeine (4/14), and diethyltoluamide (3/14) were also detected in the groundwater, whereas the other carboxylic and phenolic PPCPs were not detected and were thought to be removed during their passage through soil. All the data demonstrated the utility of crotamiton and carbamazepine as conservative markers in freshwater and coastal environments. We recommend combining these conservative markers with labile PPCPs to detect inputs of poorly treated sewage.