Large Structural Changes Research Articles

Characterization on Lead-Free Hybrid Perovskite [NH3(CH2)5NH3]CuCl4: Thermodynamic Properties and Molecular Dynamics.

It is essential to develop novel zero- and two-dimensional hybrid perovskites to facilitate the development of eco-friendly solar cells. In this study, we investigated the structure and dynamics of [NH3(CH2)5NH3]CuCl4 via various characterization techniques. Nuclear magnetic resonance (NMR) results indicated that the crystallographic environments of 1H in NH3 and 13C on C3, located close to NH3 at both ends of the cation, were changed, indicating a large structural change of CuCl6 connected to N–H···Cl. The thermal properties and structural dynamics of the [NH3(CH2)nNH3] cation in [NH3(CH2)nNH3]CuCl4 (n = 2, 3, 4, and 5) crystals were compared using thermogravimetric analysis (TGA) and NMR results for the methylene chain. The 1H and 13C spin-lattice relaxation times (T1ρ) exhibited similar trends upon the variation of the methylene chain length, with n = 2 exhibiting shorter T1ρ values than n = 3, 4, and 5. The difference in T1ρ values was related to the length of the cation, and the shorter chain length (n = 2) exhibited a shorter T1ρ owing to the one closest to the paramagnetic Cu2+ ions.

Bifurcation drives the evolution of assembly-line biosynthesis

Reprogramming biosynthetic assembly-lines is a topic of intense interest. This is unsurprising as the scaffolds of most antibiotics in current clinical use are produced by such pathways. The modular nature of assembly-lines provides a direct relationship between the sequence of enzymatic domains and the chemical structure of the product, but rational reprogramming efforts have been met with limited success. To gain greater insight into the design process, we wanted to examine how Nature creates assembly-lines and searched for biosynthetic pathways that might represent evolutionary transitions. By examining the biosynthesis of the anti-tubercular wollamides, we uncover how whole gene duplication and neofunctionalization can result in pathway bifurcation. We show that, in the case of the wollamide biosynthesis, neofunctionalization is initiated by intragenomic recombination. This pathway bifurcation leads to redundancy, providing the genetic robustness required to enable large structural changes during the evolution of antibiotic structures. Should the new product be non-functional, gene loss can restore the original genotype. However, if the new product confers an advantage, depreciation and eventual loss of the original gene creates a new linear pathway. This provides the blind watchmaker equivalent to the design, build, test cycle of synthetic biology.

Tumor protein D54 binds intracellular nanovesicles via an extended amphipathic region

Tumor protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54, and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical (e.g., COPI and COPII) transport vesicles. Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by four amphipathic helices (AH1-4), which could fold upon binding to lipid membranes. Limited proteolysis, CD spectroscopy, tryptophan fluorescence, and cysteine mutagenesis coupled to covalent binding of a membrane-sensitive probe showed that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. Furthermore, site-directed mutagenesis indicated that AH2 and AH3 have a predominant role in TPD54 binding to membranes both in cells and using model liposomes. We found that AH3 has the physicochemical features of an amphipathic lipid packing sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Accordingly, we observed that binding of TPD54 to liposomes is very sensitive to membrane curvature and lipid unsaturation. We conclude that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and ALPS-independent mechanisms.

Temporary employment in Europe: stagnating rates and rising risks

ABSTRACT There is a perception that temporary employment is rising in Europe but there is little evidence to support this. If one takes the position that temporary employment should be rising due to large structural changes in European labor markets, then stagnating trends represents something of a puzzle. I examine the puzzle by applying a life-course approach to understand the distribution and trends in temporary employment among prime-age workers in 31 European countries. I compare and contrast changes in the temporary employment rate in a single period of time using cross-sectional data from the European Labour Force Survey (LFS), with changes in the risk of experiencing temporary employment in multiple periods of time using longitudinal data from the European Survey of Income and Living Conditions (SILC). Results from cross-sectional data suggest that between 1996 and 2007, the temporary employment rate increased in Europe by 28%, but between 2007 and 2019, there was little change. By contrast, results from panel data suggest that between 2013 and 2019, the risk of experiencing at least one temporary employment contract rose 36%. Over time, the temporary employment rate stagnated, but the temporary employment risk rose. The contribution provides insight into the nature of employment experiences associated with insecurity.

Prion protein gene mutation detection using long-read Nanopore sequencing

Prion diseases are fatal neurodegenerative conditions that affect humans and animals. Rapid and accurate sequencing of the prion gene PRNP is paramount to human prion disease diagnosis and for animal surveillance programmes. Current methods for PRNP genotyping involve sequencing of small fragments within the protein-coding region. The contribution of variants in the non-coding regions of PRNP including large structural changes is poorly understood. Here, we used long-range PCR and Nanopore sequencing to sequence the full length of PRNP, including its regulatory region, in 25 samples from blood and brain of individuals with inherited or sporadic prion diseases. Nanopore sequencing detected the same variants as identified by Sanger sequencing, including repeat expansions/deletions. Nanopore identified additional single-nucleotide variants in the non-coding regions of PRNP, but no novel structural variants were discovered. Finally, we explored somatic mosaicism of PRNP’s octapeptide repeat region, which is a hypothetical cause of sporadic prion disease. While we found changes consistent with somatic mutations, we demonstrate that they may have been generated by the PCR. Our study illustrates the accuracy of Nanopore sequencing for rapid and field prion disease diagnosis and highlights the need for single-molecule sequencing methods for the detection of somatic mutations.

Modifying soil properties with herbaceous plants for natural flood risk-reduction

Background and aimNature-based solutions to engineering challenges are essential to limit climate change impacts on the urban environment. Quantitative understanding of multiple “engineering functions” provided by soil-plant interactions of different species is needed for species selection and re-establishing natural processes affected by urbanisation. MethodsContrasting herbaceous species (legumes, grasses, and forbs) were selected and grown as monoculture or species mix in soil columns for a five-month growing season. Saturated hydraulic conductivity was initially tested for each column, and then the columns were monitored for three-weeks of evapotranspiration. Water loss, matric suction, and penetrometer resistance were measured. Finally, soil was tested for aggregate stability and water retention. ResultsSaturated hydraulic conductivity of vegetated soil was generally larger than that of fallow soil (6.9e−6 ± 1.4e−6 m/s in fallow soil). Saturated hydraulic conductivity was significantly different between species (e.g., from 9.9e−6 ± 1.3e−6 m/s in Festuca ovina to 3.9e−5 ± 1.2e−6 m/s in Lotus corniculatus) and was negatively correlated with specific root length. The water stored in the soil was efficiently removed by plant transpiration (> 60% of evapotranspiration). Large changes in soil structure were observed in vegetated soil, with significant increases in soil strength, aggregate stability, and alteration of water retention properties. ConclusionsMultiple soil-plant interactions influence species selection for optimising nature-based solutions (e.g., bioretention barriers). Substantial scope exists to choose species mixes to manipulate soil hydro-mechanical properties. Enhanced biodiversity did not compromise the engineering services of nature-based solutions (e.g., water removal), and may have multiple benefits.

Support Vector Machine-Based Nonlinear Model and Its Application in Regional Economic Forecasting

The regional economic potential is affected by too many entities and large dynamic changes in the economic structure, resulting in large errors in the prediction obtained by the traditional economic potential development prediction method. Therefore, this paper puts forward the regional economic development potential prediction model with the concept of decision domain, solves the nonlinear characteristics of regional economic impact indicators by using the traditional support vector machine, and obtains the economic prediction data. The decision domain method is introduced in the decision-making process to construct the decision domain of training economic-related data sets. The experimental results show that compared with other prediction models, the model proposed in this paper has higher regional economic prediction accuracy, 2% higher than the baseline method, can quickly and accurately predict the potential trend of regional economic development, and has important application value.

Production of chitin nanoparticles by bottom-up approach from alkaline chitin solution

Most of the series of nanochitins have been produced by the break-down process. In this study, chitin nanoparticles were prepared by a bottom-up process. Chitin was treated with sodium hydroxide to obtain an alkaline chitin aqueous solution. The alkaline chitin was regenerated by neutralization and then vigorously stirred to obtain chitin nanoparticles. The average particle size of the chitin nanoparticles was 7 nm. The individual particles were stably dispersed in water. Chitin nanoparticles had lower crystallinity than the raw material chitin and the surface of the chitin nanoparticles regenerated in water were presumed to be hydrophilic. The low crystallinity and the high hydrophilicity of the surface contributed to the high dispersibility of the chitin nanoparticles in water. Chitin nanoparticles had higher heat resistance than the raw material chitin, suggesting a large change in the higher-order structure associated with dissolution and subsequent regeneration of chitin. Since chitin nanoparticles interact with each other less than chitin nanofibers produced by mechanical treatment, the viscosity of nanoparticles was smaller than that of nanofibers. Therefore, it can be prepared at a high concentration. In addition, the chitin nanoparticles can be easily redispersed in water after being concentrated by centrifugation.

A state-space approach to time-varying reduced-rank regression

We propose a new approach to reduced-rank regression that allows for time-variation in the regression coefficients. The Kalman filter based estimation allows for usage of standard methods and easy implementation of our procedure. The EM-algorithm ensures convergence to a local maximum of the likelihood. Our estimation approach in time-varying reduced-rank regression performs well in simulations, with amplified competitive advantage in time series that experience large structural changes. We illustrate the performance of our approach with a simulation study and two applications to stock index and Covid-19 case data.

Contingency and selection in mitochondrial genome dynamics.

High frequencies of mutant mitochondrial DNA (mtDNA) in human cells lead to cellular defects that are associated with aging and disease. Yet much remains to be understood about the dynamics of the generation of mutant mtDNAs and their relative replicative fitness that informs their fate within cells and tissues. To address this, we utilize long-read single-molecule sequencing to track mutational trajectories of mtDNA in the model organism Saccharomyces cerevisiae. This model has numerous advantages over mammalian systems due to its much larger mtDNA and ease of artificially competing mutant and wild-type mtDNA copies in cells. We show a previously unseen pattern that constrains subsequent excision events in mtDNA fragmentation in yeast. We also provide evidence for the generation of rare and contentious non-periodic mtDNA structures that lead to persistent diversity within individual cells. Finally, we show that measurements of relative fitness of mtDNA fit a phenomenological model that highlights important biophysical parameters governing mtDNA fitness. Altogether, our study provides techniques and insights into the dynamics of large structural changes in genomes that we show are applicable to more complex organisms like humans.

Operando structure observation of pyroelectric ceramics during power generation cycle

The microscopic origin of the pyroelectric power generation using ferroelectric ceramics for energy harvesting from time-varying waste heat can be understood by conducting operando neutron diffraction measurements. The behavior of the domain orientation and lattice strain in the lead zirconate titanate-based ceramics with a tetragonal structure during the novel power generation cycle combining the electric field and the temperature change were investigated. The [001] domains and the lattice strain of the (111) plane in the direction parallel to the electric field increase in the process of simultaneous rise in the electric field and temperature and rapidly decrease in the process of the field drop. Furthermore, larger structural changes were found in the material and cycle condition, giving higher power density. The alignment of the domain orientation by the electric field and its randomization by the higher temperature during the cycle are critical features of the current power generation system.

Cu doping modified FeCO3 microspheres with enhanced Li+ storage performance

Ferrous carbonate as an anode material for lithium ion batteries has been extensively investigated due to its facile synthesis and high theoretical capacity. However, the low intrinsic electronic conductivity and large structural changes are the main reasons for the poor electrochemical performance of ferrous carbonate. To solve above the issues, we design a novel method (copper doping) to enhance the lithium ion storage capability (718.2 mAh g−1 at 0.2 A g−1 after 100 cycles) and interface dynamics of ferrous carbonate. This work may provide a promising strategy for improving the electrochemical performance of transition metal carbonates.

Essential oil content of Rhododendron tomentosum responds strongly to manipulation of ecosystem resources in Arctic Alaska

The essential oils of the widely distributed boreal/Arctic dwarf shrub, Rhododendron tomentosum ssp. subarcticum (Harmaja) G.D. Wallace, have important ecological, cultural, medicinal, and commercial roles. To understand the relationship between resource limitation and essential oil content of this species we measured the amount and diversity of terpenes from shoots of plants exposed to a 14-year ecosystem resource manipulation experiment in Arctic Alaska. Treatments tested interactive effects of nitrogen (N) and phosphorus (P) addition, warming and N + P fertilization, and shading and N + P fertilization. The controls and NP fertilization had the highest essential oil content, whereas shading and P addition had less than 20% of the control content. Warming reduced essential oil content to <65% of that of the controls. Essential oil components varied greatly among the treatments, with significant differences in the expression of specific essential oil components. Large changes in plant community composition and ecosystem structure in response to treatments likely played a large role in the response of R. tomentosum. Our data suggest that resource changes in response to climate warming and its secondary effects on light and nutrient availability have the potential to change the profiles of essential oils in R. tomentosum, with important ecological and cultural impacts.

Charge and Lattice Dynamics in Excitonic Insulator Ta2NiSe5 Investigated Using Ultrafast Reflection Spectroscopy

An excitonic insulator, in which an optical gap is formed by exciton condensation, is expected to exhibit large photoresponses. Here, we report the results of femtosecond reflection spectroscopy covering a wide infrared region on a typical excitonic insulator, Ta2NiSe5, which gives direct information not only about a change of excitonic gap but also a metallization. With a weak excitation, the excitonic gap decreases due to the weakening of excitonic effect by photocarriers. With a strong excitation, a Drude-like high-reflection band appears, showing an excitonic-insulator-to-metal transition. Analyses of spectral and temporal changes of reflectivity revealed that the metallization is accompanied by large structural changes. This demonstrates an important role of electron–lattice interaction on the stabilization of excitonic phase.

Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.

RNA molecules fold as they are transcribed. Cotranscriptional folding of RNA plays a critical role in RNA functions in vivo. Present computational strategies focus on simulations where large structural changes may not be completely sampled. Here, we describe an alternative approach to predicting cotranscriptional RNA folding by zooming in and out of the RNA folding energy landscape. By classifying the RNA structural ensemble into "partitions" based on long, stable helices, we zoom out of the landscape and predict the overall slow folding kinetics from the interpartition kinetic network, and for each interpartition transition, we zoom in on the landscape to simulate the kinetics. Applications of the model to the 117-nucleotide E. coli SRP RNA and the 59-nucleotide HIV-1 TAR RNA show agreements with the experimental data and new structural and kinetic insights into biologically significant conformational switches and pathways for these important systems. This approach, by zooming in/out of an RNA folding landscape at different resolutions, might allow us to treat large RNAs in vivo with transcriptional pause, transcription speed, and other in vivo effects.

A Mechanism for Nitrogenase Including Loss of a Sulfide.

Nitrogenase is the only enzyme in nature that can fix N2 from the air. The active cofactor of the leading form of this enzyme contains seven irons and one molybdenum connected by sulfide bridges. In several recent experimental studies, it has been suggested that the cofactor is very flexible, and might lose one of its sulfides during catalysis. In this study, the possible loss of a sulfide has been investigated by model calculations. In previous studies, we have shown that there should be four activation steps before catalysis starts, and this study is based on that finding. It was found here that, after the four reductions in the activation steps, a sulfide will become very loosely bound and can be released in a quite exergonic step with a low barrier. The binding of N2 has no part in that release. In our previous studies, we suggested that the central carbide should be protonated three times after the four activation steps. With the new finding, there will instead be a loss of a sulfide, as the barrier for the loss is much lower than the ones for protonating the carbide. Still, it is suggested here that the carbide will be protonated anyway, but only with one proton, in the E3 to E4 step. A very complicated transition state for H2 formation involving a large structural change was obtained. The combined step, with a loss of H2 and binding of N2, is calculated to be endergonic by +2.3 kcal mol−1; this is in excellent agreement with experiments in which an easily reversible step has been found.

501Y.V2 spike protein resists the neutralizing antibody in atomistic simulations

SARS-CoV-2 outbreaks worldwide caused COVID-19 pandemic, which is related to several million deaths. In particular, SARS-CoV-2 Spike (S) protein is a major biological target for COVID-19 vaccine design. Unfortunately, recent reports indicated that Spike (S) protein mutations can lead to antibody resistance. However, understanding the process is limited, especially at the atomic scale. The structural change of S protein and neutralizing antibody fragment (FAb) complexes was thus probed using molecular dynamics (MD) simulations. In particular, the backbone RMSD of the 501Y.V2 complex was significantly larger than that of the wild-type one implying a large structural change of the mutation system. Moreover, the mean of Rg, CCS, and SASA are almost the same when compared two complexes, but the distributions of these values are absolutely different. Furthermore, the free energy landscape of the complexes was significantly changed when the 501Y.V2 variant was induced. The binding pose between S protein and FAb was thus altered. The FAb-binding affinity to S protein was thus reduced due to revealing over steered-MD (SMD) simulations. The observation is in good agreement with the respective experiment that the 501Y.V2 SARS-CoV-2 variant can escape from neutralizing antibody (NAb).

Crystallographic Studies of Rhodopsins: Structure and Dynamics.

Crystal structures have provided detailed insight in the architecture of rhodopsin photoreceptors. Of particular interest are the protein-chromophore interactions that govern the light-induced retinal isomerization and ultimately induce the large structural changes important for the various biological functions of the family. The reaction intermediates occurring along the rhodopsin photocycle have vastly differing lifetimes, from hundreds of femtoseconds to milliseconds. Detailed insight at high spatial and temporal resolution can be obtained by time-resolved crystallography using pump-probe approaches at X-ray free-electron lasers. Alternatively, cryotrapping approaches can be used. Both the approaches are described, including illumination and sample delivery. The importance of appropriate photoexcitation avoiding multiphoton absorption is stressed.

The State in Feminist Theory: Hopes and a Critique of Governance Feminism

Contemporary feminist theory rarely engages with the discussion of political strategies and the issue of the state. Feminist philosophers tend to interpret the state as an omnipotent institution continuously governing women’s lives and bodies, while defining women as rather passive objects of state politics. The new global wave of feminist protests against domestic violence and sexual harassment that has erupted in the last four years inspired a new cycle of theoretical debates about the meaning of gender equality and the role of the state in the feminist liberation project. The increasing power of feminist movements coupled with new feminist attempts to infuence political institutions raise new questions about the dominant feminist political strategies and engagements with the state. How should feminist movements view the state? What does the state mean, and what role do women play in it? The article discusses the state as a major feminist theoretical issue. It argues that feminist thinkers and activists need to engage with state issues if we are to achieve such large scale and structural changes as gender equality, the end of female poverty, or abolition of unpaid reproductive labor. The paper reconstructs the political theory of carceral feminism, i.e., the dominant form of political feminism in today’s world, developed by Catherine A. Mackinnon’s reviewing its recent critique formulated by Janet Halley. It concludes by posing the question about other alternative and non-carceral forms of feminist governance.

Bridging the sexual health gap for black adolescent females: why social work practitioners should consider father–daughter relationships

ABSTRACT Current sexual health outcomes disproportionately represent Black adolescent and young adult females. The significance of this conceptual review is to first highlight reduced access to traditional forms of sexual health resources and the urgency for innovative social work intervention. Secondly, I present an overview of fatherhood literature that points to the value of Black father–daughter relationships pertaining to sexual health. Recent policies have insufficiently addressed the sexual health needs of many young Black females, and the Black father, despite historically damaging images of his engagement, may offer immediate support to a daughter’s sexual health decision making processes. While large scale structural changes are needed for developing effective health policies, in the interim, benefits of Black father engagement through sexual communication training and education may support the healthy sexual decisions of daughters.