Cycles of satellite and transposon evolution in Arabidopsis centromeres.

Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation.

Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation.

The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host-pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.

Modeling the spatiotemporal patterns and drivers of Dungeness crab fishing effort to inform whale entanglement risk mitigation on the U.S. West Coast.

Understanding and characterizing the spatiotemporal dynamics of fishing fleets is crucial for ecosystem-based fisheries management (EBFM). EBFM must not only account for the sustainability of target species catches, but also for the collateral impacts of fishing operations on habitats and non-target species. Increased rates of large whale entanglements in commercial Dungeness crab fishing gear have made reducing whale-fishery interactions a current and pressing challenge on the U.S. West Coast. While several habitat models exist for different large whale species along the West Coast, less is known about the crab fishery and the degree to which different factors influence the intensity and distribution of aggregate fishing effort. Here, we modeled the spatiotemporal patterns of Dungeness crab fishing effort in Oregon and Washington as a function of environmental, economic, temporal, social, and management related predictor variables using generalized linear mixed effects models. We then assessed the predictive performance of such models and discussed their usefulness in informing fishery management. Our models revealed low between-year variability and consistent spatial and temporal patterns in commercial Dungeness crab fishing effort. However, fishing effort was also responsive to multiple environmental, economic and management cues, which influenced the baseline effort distribution pattern. The best predictive model, chosen through out-of-sample cross-validation, showed moderate predictive performance and relied upon environmental, economic, and social covariates. Our results help fill the current knowledge gap around Dungeness crab fleet dynamics, and support growing calls to integrate fisheries behavioral data into fisheries management and marine spatial planning.

Performance of various 3D-printed monolith geometries as an alternative to expanded bed adsorption for protein purification.

Here, we compare the performance of various three-dimensional-printed Monolith Adsorption (PMA) columns designed from a triply periodic minimal surface geometry, the Schoen gyroid. The structures examined had designed hydraulic diameters between 203 and 458 µm and voidages of 40%-60%. We compare column efficiency, porosity, static binding capacity and dynamic binding capacity for various load volumes and flow rates. The results show that all structures allowed efficient passage of yeast cells (>97%) over a wide range of interstitial velocities (191 to 1911 cm/h) while maintaining a low pressure drop (<0.1 MPa). The structure with a voidage of 40% and a hydraulic diameter of 203 µm showed the best performance in all aspects evaluated. Bovine serum albumin (BSA) recoveries for all structures (27%-91% when the loaded volume was 180 mL) were significantly affected by hydraulic diameter, mean channel wall thickness, velocity and voidage. Moreover, biomass addition resulted in a decrease in BSA recovery, which became more obvious at high velocities. However, this did not lead to a dramatic reduction in saturated binding capacity, significant changes in axial dispersion, or blockage of channels and could be compensated for by recirculation of the feed, even at high velocity. PMA thus potentially provides an appealing alternative to Expanded Bed Adsorption, retaining the latter's advantages, while eliminating fluidization issues and minimizing both processing time and buffer consumption.

Accurate measurements of self-diffusion coefficients with benchtop NMR using a QM model-based approach.

The measurement of self-diffusion coefficients using pulsed-field gradient (PFG) nuclear magnetic resonance (NMR) spectroscopy is a well-established method. Recently, benchtop NMR spectrometers with gradient coils have also been used, which greatly simplify these measurements. However, a disadvantage of benchtop NMR spectrometers is the lower resolution of the acquired NMR signals compared to high-field NMR spectrometers, which requires sophisticated analysis methods. In this work, we use a recently developed quantum mechanical (QM) model-based approach for the estimation of self-diffusion coefficients from complex benchtop NMR data. With the knowledge of the species present in the mixture, signatures for each species are created and adjusted to the measured NMR signal. With this model-based approach, the self-diffusion coefficients of all species in the mixtures were estimated with a discrepancy of less than 2 % compared to self-diffusion coefficients estimated from high-field NMR data sets of the same mixtures. These results suggest benchtop NMR is a reliable tool for quantitative analysis of self-diffusion coefficients, even in complex mixtures.

Well-Being and Help-Seeking Among Assemblies of God Ministers in the USA.

This study examined Assemblies of God pastors in the USA (n = 874) on role identity, well-being, religious coping, and attitudes toward seeking professional counseling. Overall, 14.1% had depression at moderate or higher severity based on the PHQ-9 scale (score of 10 or above), with an additional 25.7% in the mild category (score of 5-9). On the Clergy Spiritual Well-Being scale, 9.2% had poor spiritual well-being in everyday life, while 18.1% showed poor spiritual well-being in ministry (score below 15 on each respective subscale). About 20% of the sample scored in the high range (above 10) on the Clergy Occupational Distress Index. Male role norms, occupational distress, and positive religious coping were predictive of help-seeking attitudes. Those who were married, younger, more highly educated, female, or had more close friends had more positive attitudes toward seeking counseling.

The effects of population synchrony, life history, and access constraints on benefits from fishing portfolios.

Natural resources often exhibit large interannual fluctuations in productivity driven by shifting environmental conditions, and this translates to high variability in the revenue resource users earn. However, users can dampen this variability by harvesting a portfolio of resources. In the context of fisheries, this means targeting multiple populations, though the ability to actually build diverse fishing portfolios is often constrained by the costs and availability of fishing permits. These constraints are generally intended to prevent overcapitalization of the fleet and ensure populations are fished sustainably. As linked human-natural systems, both ecological and fishing dynamics influence the specific advantages and disadvantages of increasing the diversity of fishing portfolios. Specifically, a portfolio of synchronous populations with similar responses to environmental drivers should reduce revenue variability less than a portfolio of asynchronous populations with opposite responses. We built a bioeconomic model based on the Dungeness crab (Metacarcinus magister), Chinook salmon (Oncorhynchus tshawytscha), and groundfish fisheries in the California Current, and used it to explore the influence of population synchrony and permit access on income patterns. As expected, synchronous populations reduced revenue variability less than asynchronous populations, but only for portfolios including crab and salmon. Synchrony with the longer-lived groundfish population was not important because environmentally driven changes in groundfish recruitment were mediated by growth and natural mortality over the full population age structure, and overall biomass was relatively stable across years. Thus, building a portfolio of diverse life histories can buffer against the impacts of poor environmental conditions over short time scales. Increasing access to all permits generally led to increased revenue stability and decreased inequality of the fleet, but also resulted in less revenue earned by an individual from a given portfolio because more vessels shared the available biomass. This means managers are faced with a trade-off between the average revenue individuals earn and the risk those individuals accept. These results illustrate the importance of considering connections between social and ecological dynamics when evaluating management options that constrain or facilitate fishers' ability to diversify their fishing.

A comparison of non-uniform sampling and model-based analysis of NMR spectra for reaction monitoring.

Nuclear magnetic resonance (NMR) spectroscopy is widely used for applications in the field of reaction and process monitoring. When complex reaction mixtures are studied, NMR spectra often suffer from low resolution and overlapping peaks, which places high demands on the method used to acquire or to analyse the NMR spectra. This work presents two NMR methods that help overcome these challenges: 2D non-uniform sampling (NUS) and a recently proposed model-based fitting approach for the analysis of 1D NMR spectra. We use the reaction of glycerol with acetic acid as it produces five reaction products that are all chemically similar and, hence, challenging to distinguish. The reaction was measured on a high-field 400 MHz NMR spectrometer with a 2D NUS-heteronuclear single quantum coherence (HSQC) and a conventional 1D 1 H NMR sequence. We show that comparable results can be obtained using both 2D and 1D methods, if the 2D volume integrals of the 2D NUS-HSQC NMR spectra are calibrated. Further, we monitor the same reaction on a low-field 43 MHz benchtop NMR spectrometer and analyse the acquired 1D 1 H NMR spectra with the model-based approach and with partial least-squares regression (PLS-R), both trained using a single, calibrated data set. Both methods achieve results that are in good quantitative agreement with the high-field data. However, the model-based method was found to be less sensitive to the training data set used than PLS-R and, hence, was more robust when the reaction conditions differed from that of the training data.

Impact of catch shares on diversification of fishers' income and risk.

Many fishers diversify their income by participating in multiple fisheries, which has been shown to significantly reduce year-to-year variation in income. The ability of fishers to diversify has become increasingly constrained in the last few decades, and catch share programs could further reduce diversification as a result of consolidation. This could increase income variation and thus financial risk. However, catch shares can also offer fishers opportunities to enter or increase participation in catch share fisheries by purchasing or leasing quota. Thus, the net effect on diversification is uncertain. We tested whether diversification and variation in fishing revenues changed after implementation of catch shares for 6,782 vessels in 13 US fisheries that account for 20% of US landings revenue. For each of these fisheries, we tested whether diversification levels, trends, and variation in fishing revenues changed after implementation of catch shares, both for fishers that remained in the catch share fishery and for those that exited but remained active in other fisheries. We found that diversification for both groups was nearly always reduced. However, in most cases, we found no significant change in interannual variation of revenues, and, where changes were significant, variation decreased nearly as often as it increased.

Time-domain signal modelling in multidimensional NMR experiments for estimation of relaxation parameters.

We present a model-based method for estimation of relaxation parameters from time-domain NMR data specifically suitable for processing data in popular 2D phase-sensitive experiments. Our model is formulated in terms of commutative bicomplex algebra, which allows us to use the complete information available in an NMR signal acquired with principles of quadrature detection without disregarding any of its dimensions. Compared to the traditional intensity-analysis method, our model-based approach offers an important advantage for the analysis of overlapping peaks and is robust over a wide range of signal-to-noise ratios. We assess its performance with simulated experiments and then apply it for determination of [Formula: see text], [Formula: see text], and [Formula: see text] relaxation rates in datasets of a protein with more than 100 cross peaks.

Three-dimensional imaging of localized surface plasmon resonances of metal nanoparticles.

The remarkable optical properties of metal nanoparticles are governed by the excitation of localized surface plasmon resonances (LSPRs). The sensitivity of each LSPR mode, whose spatial distribution and resonant energy depend on the nanoparticle structure, composition and environment, has given rise to many potential photonic, optoelectronic, catalytic, photovoltaic, and gas- and bio-sensing applications. However, the precise interplay between the three-dimensional (3D) nanoparticle structure and the LSPRs is not always fully understood and a spectrally sensitive 3D imaging technique is needed to visualize the excitation on the nanometre scale. Here we show that 3D images related to LSPRs of an individual silver nanocube can be reconstructed through the application of electron energy-loss spectrum imaging, mapping the excitation across a range of orientations, with a novel combination of non-negative matrix factorization, compressed sensing and electron tomography. Our results extend the idea of substrate-mediated hybridization of dipolar and quadrupolar modes predicted by theory, simulations, and electron and optical spectroscopy, and provide experimental evidence of higher-energy mode hybridization. This work represents an advance both in the understanding of the optical response of noble-metal nanoparticles and in the probing, analysis and visualization of LSPRs.

Multiphoton structured thin-plane imaging with a single optical path.

Optical sectioning has become an indispensable technique for high-speed volumetric imaging in the past decade. Here we present a novel optical-sectioning method that produces a thin plane of illumination by exploiting the spatial and temporal properties of multiphoton excitation. Critically, the illumination and detection share the same optical path, as in a conventional epi-fluorescence microscope configuration. Therefore, the imaged sample can be prepared as for standard fluorescence microscopy. Our method also leads to a laterally structured illumination pattern, and this feature can be utilized in structured illumination microscopy to further enhance the imaging performance. We show an example of such an approach, which achieves axial resolution finer than confocal microscopy. We also demonstrate the potential of the new method for biological applications by performing three-dimensional imaging of living Caenorhabditis elegans.

Income diversification and risk for fishermen.

Catches and prices from many fisheries exhibit high interannual variability, leading to variability in the income derived by fishery participants. The economic risk posed by this may be mitigated in some cases if individuals participate in several different fisheries, particularly if revenues from those fisheries are uncorrelated or vary asynchronously. We construct indices of gross income diversification from fisheries at the level of individual vessels and find that the income of the current fleet of vessels on the US West Coast and in Alaska is less diverse than at any point in the past 30 y. We also find a dome-shaped relationship between the variability of individuals' income and income diversification, which implies that a small amount of diversification does not reduce income risk but that higher levels of diversification can substantially reduce the variability of income from fishing. Moving from a single fishery strategy to a 50-25-25 split in revenues reduces the expected coefficient of variation of gross revenues between 24% and 65% for the vessels included in this study. The increasing access restrictions in many marine fisheries through license reductions and moratoriums have the potential to limit fishermen's ability to diversify their income risk across multiple fisheries. Catch share programs often result in consolidation initially and may reduce diversification. However, catch share programs also make it feasible for fishermen to build a portfolio of harvest privileges and potentially reduce their income risk. Therefore, catch share programs create both threats and opportunities for fishermen wishing to maintain diversified fishing strategies.

Decade-spanning high-precision terahertz frequency comb.

The generation and detection of a decade-spanning terahertz (THz) frequency comb is reported using two Ti:sapphire femtosecond laser oscillators and asynchronous optical sampling THz time-domain spectroscopy. The comb extends from 0.15 to 2.4 THz, with a tooth spacing of 80 MHz, a linewidth of 3.7 kHz, and a fractional precision of 1.8×10^{-9}. With time-domain detection of the comb, we measure three transitions of water vapor at 10 mTorr between 1-2 THz with an average Doppler-limited fractional accuracy of 6.1×10^{-8}. Significant improvements in bandwidth, resolution, and sensitivity are possible with existing technologies.

Less is more: how compressed sensing is transforming metrology in chemistry.

Mathematics has had a profound impact on science, providing a means to understand the world around us in unprecedented ways. With the advent of the digital age, the subject of information theory has grown hugely in importance. In particular, over the last two decades significant advances in our understanding of sampling and function reconstruction have culminated in the development of an idea known as compressed sensing. What seems like an abstract idea is now having a profound impact throughout the scientific world-from enabling high-resolution imaging of pediatric patients in clinical medicine through to advancing 3D electron tomography images of nanoparticle catalysts and NMR spectroscopy studies of proteins. In this Minireview, we summarize these applications and provide an outlook on how the principles of compressed sensing are leading to entirely new approaches to measurement throughout the physical and life sciences.

The wide-field optical sectioning of microlens array and structured illumination-based plane-projection multiphoton microscopy.

We present a theoretical investigation of an optical microscope design that achieves wide-field, multiphoton fluorescence microscopy with finer axial resolution than confocal microscopy. Our technique creates a thin plane of excitation light at the sample using height-staggered microlens arrays (HSMAs), wherein the height staggering of microlenses generate temporal focusing to suppress out-of-focus excitation, and the dense spacing of microlenses enables the implementation of structured illumination technique to eliminate residual out-of-focus signal. We use physical optics-based numerical simulations to demonstrate that our proposed technique can achieve diffraction-limited three-dimensional imaging through a simple optical design.

Identifying ecological and fishing drivers of bycatch in a U.S. groundfish fishery.

Fisheries bycatch is driven by both ecological (e.g., area, season) and social (e.g., fisher behavior) factors that are often difficult to disentangle. We demonstrate a method for comparing fishery-dependent bycatch to fishery-independent catch to delineate the influence of ecological and social factors on bycatch and provide insights for bycatch management. We used data from commercial fishing vessels in the U.S. west coast trawl groundfish fishery (fishery-dependent data collected by fisheries observers) and scientific data from the U.S. west coast bottom trawl groundfish survey (fishery-independent data) to compare the relative effects of season, time of day, target group, depth, and latitude on the expected catch of 12 bycatch species of management interest. This comparison highlights two important relationships that help identify drivers of bycatch. First, when the effect of season, time of day, depth, or latitude on bycatch in both the commercial and scientific data is positive, ecological processes are likely strong drivers of bycatch, suggesting technical approaches (e.g., temporal or spatial closures, gear modifications) might effectively control bycatch. Alternatively, when the effects of season, time of day, depth, latitude, or target group appear only in the commercial data (but not in survey data), fisher behavior is likely the stronger driver of bycatch, suggesting a need to strengthen incentives for fishers to change behavior to avoid bycatch (e.g., regulatory quotas). Two other patterns emerge that suggest that fishery bycatch is not associated with temporal, target, or spatial variables, implying that either current incentives to avoid bycatch are working (i.e., when survey expected catch is positively correlated with variables, but fishery catch is not) or bycatch is a product of unstudied or stochastic processes (i.e., variables are not correlated with expected catch in either data set) and continued monitoring is recommended. Our analysis provides managers and fishers with a basic analytical framework to assess bycatch reduction alternatives and methods useful for researchers interested in comparing bycatch before and after a management shift.

Counselors' Perceptions of Their Preparedness for Telemental Health Services: A Phenomenological Examination.

Background: To examine counselors' perceptions of their formal preparation for engaging in telemental health (TMH) counseling with the intent of gaining an understanding of their lived experiences. Materials and Methods: Semistructured interviews were conducted with seven seasoned counselors who regularly engage in technology-mediated distance counseling. Results: The results highlighted themes within two emerging categories: the counselor and training/education. Themes related to motivation and specific counselor attributes emerged from the first category and themes of availability, inadequacy, and modality emerged from the second category. Discussion: The implications from this study suggest a lack of availability and standardization of effective training on TMH delivery. Conclusion: This study identifies areas of potential future research related to counselors' preparation experiences as well specific areas of need for TMH training in counseling graduate programs and other natural opportunities.

Quantitative examination of the anatomy of the juvenile sugar maple xylem.

New methodologies have enabled viable sap yields from juvenile sugar maple trees. To further improve yields, a better understanding of sap exudation is required. To achieve this, the anatomy of the xylem must first be fully characterised. We examine juvenile maple saplings using light optical microscopy (LOM) and scanning electron microscopy (SEM), looking at sections cut along differing orientations as well as macerations. From this we measure various cell parameters. We find diameter and length of vessel elements to be 28 ± 8 µm and 200 ± 50 µm, for fibre cells 8 ± 3 µm and 400 ± 100 µm, and for ray parenchyma cells 8 ± 2 µm and 50 ± 20 µm. We also examine pitting present on different cell types. On vessel elements we observe elliptical bordered pits connecting to other vessel elements (with major axis of 2.1 ± 0.7 µm and minor 1.3 ± 0.3 µm) and pits connecting to ray parenchyma (with major axis of 4 ± 2 µm and minor 2.0 ± 0.7 µm). We observe two distinct pit sizes on fibres with circular pits 0.7 ± 0.2 µm in diameter and ellipsoidal pits 1.6 ± 0.4 µm by 1.0 ± 0.3 µm. We do not observe distinct pitting patterns on different fibre types. The various cell and pit measurements obtained generally agree with the limited data available for mature trees, with the exception of vessel element and fibre length, both of which were significantly smaller than reported values.