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Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA). Using the recently updated B. napus genome now including pericentromeres, we demonstrated that COs occur in these cold regions in allotriploids, as close as 375 kb from the centromere. Reverse transcription quantitative PCR (RT-qPCR) of various meiotic genes indicated that Class I COs are likely involved in the increased recombination frequency observed in allotriploids. We also demonstrated that this modified recombination landscape can be maintained via successive generations of allotriploidy (odd ploidy level). This deregulated meiotic behavior reverts to strict regulation in allotetraploid (even ploidy level) progeny in the second generation. Overall, we provide an easy way to manipulate tight recombination control in a polyploid crop.

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Nanoparticle manipulation requires careful analysis of the forces at play. Unfortunately, traditional force measurement techniques based on the particle velocity do not provide sufficient resolution, while balancing approaches involving counteracting forces are often cumbersome. Here, we demonstrate that a nanoparticle dielectrophoretic response can be quantitatively studied by a straightforward visual delineation of the dielectrophoretic trapping volume. We reveal this volume by detecting the width of the region depleted of gold nanoparticles by the dielectrophoretic force. Comparison of the measured widths for various nanoparticle sizes with numerical simulations obtained by solving the particle-conservation equation shows excellent agreement, thus providing access to the particle physical properties, such as polarizability and size. These findings can be further extended to investigate various types of nano-objects, including bio- and molecular aggregates, and offer a robust characterization tool that can enhance the control of matter at the nanoscale.

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During the founding of the field of quantitative genetics, Fisher formulated in 1918 his "infinitesimal model" that provided a novel mathematical framework to describe the Mendelian transmission of quantitative traits. If the infinitely many genes in that model are assumed to segregate independently during reproduction, corresponding to having no linkage, directional selection asymptotically leads to a constant genetic gain at each generation. In reality, genes are subject to strong linkage because they lie on chromosomes and thus segregate in a correlated way. Various approximations have been used in the past to study that more realistic case of the infinitesimal model with the expectation that the asymptotic gain per generation is modestly decreased. To treat this system even in the strong linkage limit, we take the genes to lie on continuous chromosomes. Surprisingly, the consequences of genetic linkage are in fact rather singular, changing the nature of the long-term gain per generation: the asymptotic gain vanishes rather than being simply decreased. Nevertheless, the per-generation gain tends to zero sufficiently slowly for the total gain, accumulated over generations, to be unbounded.

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OBJECTIVE: To assess the compliance with French guidelines for the prevention of central venous catheter (CVC)-related infections in two university hospitals. METHODS: An observational audit was conducted in 7 wards using a digital tool. RESULTS: The prerequisite of hand hygiene (HH) were respected by 90% of health-care worker; 86% performed HH prior to equipment preparation and 59% repeated it prior to infusion. Wearing gloves when necessary and rinsing were respected in 46.7% and 75.6% of the observations. CONCLUSION: Findings showed an acceptable level of adherence to recommended practices for CVC management. However, barriers of unrespect evidence-based recommendations need to be investigated in depth.

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Pseudomonas aeruginosa is one of the main causes of healthcare-associated infection in Europe that increases patient morbidity and mortality. Multi-resistant pathogens are a major public health issue in burn centers. Mortality increases when the initial antibiotic treatment is inappropriate, especially if the patient is infected with P. aeruginosa strains that are resistant to many antibiotics. Phage therapy is an emerging option to treat severe P. aeruginosa infections. It involves using natural viruses called bacteriophages, which have the ability to infect, replicate, and, theoretically, destroy the P. aeruginosa population in an infected patient. We report here the case of a severely burned patient who experienced relapsing ventilator-associated pneumonia associated with skin graft infection and bacteremia due to extensively drug-resistant P. aeruginosa. The patient was successfully treated with personalized nebulized and intravenous phage therapy in combination with immunostimulation (interferon-γ) and last-resort antimicrobial therapy (imipenem-relebactam).

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The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens-infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.

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In aging, physiologic networks decline in function at rates that differ between individuals, producing a wide distribution of lifespan. Though 70% of human lifespan variance remains unexplained by heritable factors, little is known about the intrinsic sources of physiologic heterogeneity in aging. To understand how complex physiologic networks generate lifespan variation, new methods are needed. Here, we present Asynch-seq, an approach that uses gene-expression heterogeneity within isogenic populations to study the processes generating lifespan variation. By collecting thousands of single-individual transcriptomes, we capture the Caenorhabditis elegans "pan-transcriptome"-a highly resolved atlas of non-genetic variation. We use our atlas to guide a large-scale perturbation screen that identifies the decoupling of total mRNA content between germline and soma as the largest source of physiologic heterogeneity in aging, driven by pleiotropic genes whose knockdown dramatically reduces lifespan variance. Our work demonstrates how systematic mapping of physiologic heterogeneity can be applied to reduce inter-individual disparities in aging.

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Boolean models of gene regulatory networks (GRNs) have gained widespread traction as they can easily recapitulate cellular phenotypes via their attractor states. Their overall dynamics are embodied in a state transition graph (STG). Indeed, two Boolean networks (BNs) with the same network structure and attractors can have drastically different STGs depending on the type of Boolean functions (BFs) employed. Our objective here is to systematically delineate the effects of different classes of BFs on the structural features of the STG of reconstructed Boolean GRNs while keeping network structure and biological attractors fixed, and explore the characteristics of BFs that drive those features. Using $10$ reconstructed Boolean GRNs, we generate ensembles that differ in BFs and compute from their STGs the dynamics' rate of contraction or 'bushiness' and rate of 'convergence', quantified with measures inspired from cellular automata (CA) that are based on the garden-of-Eden (GoE) states. We find that biologically meaningful BFs lead to higher STG 'bushiness' and 'convergence' than random ones. Obtaining such 'global' measures gets computationally expensive with larger network sizes, stressing the need for feasible proxies. So we adapt Wuensche's $Z$-parameter in CA to BFs in BNs and provide four natural variants, which, along with the average sensitivity of BFs computed at the network level, comprise our descriptors of local dynamics and we find some of them to be good proxies for bushiness. Finally, we provide an excellent proxy for the 'convergence' based on computing transient lengths originating at random states rather than GoE states.

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Lactate dehydrogenase (LDH) from Schistosoma mansoni has peculiar properties for a eukaryotic LDH. Schistosomal LDH (SmLDH) isolated from schistosomes, and the recombinantly expressed protein, are strongly inhibited by ATP, which is neutralized by fructose-1,6-bisphosphate (FBP). In the conserved FBP/anion binding site we identified two residues in SmLDH (Val187 and Tyr190) that differ from the conserved residues in LDHs of other eukaryotes, but are identical to conserved residues in FBP-sensitive prokaryotic LDHs. Three-dimensional (3D) models were generated to compare the structure of SmLDH with other LDHs. These models indicated that residues Val187, and especially Tyr190, play a crucial role in the interaction of FBP with the anion pocket of SmLDH. These 3D models of SmLDH are also consistent with a competitive model of SmLDH inhibition in which ATP (inhibitor) and FBP (activator) compete for binding in a well-defined anion pocket. The model of bound ATP predicts a distortion of the nearby key catalytic residue His195, resulting in enzyme inhibition. To investigate a possible physiological role of this allosteric regulation of LDH in schistosomes we made a kinetic model in which the allosteric regulation of the glycolytic enzymes can be varied. The model showed that inhibition of LDH by ATP prevents fermentation to lactate in the free-living stages in water and ensures complete oxidation via the Krebs cycle of the endogenous glycogen reserves. This mechanism of allosteric inhibition by ATP prevents the untimely depletion of these glycogen reserves, the only fuel of the free-living cercariae. Neutralization by FBP of this ATP inhibition of LDH prevents accumulation of glycolytic intermediates when S. mansoni schistosomula are confronted with the sudden large increase in glucose availability upon penetration of the final host. It appears that the LDH of S. mansoni is special and well suited to deal with the variations in glucose availability the parasite encounters during its life cycle.

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We study theoretically and demonstrate experimentally a 16-band narrow band wavelength selective filter in the near-infrared range. The combination of a pair of distributed Bragg reflectors with a sub-wavelength grating metasurface embedded in the intra-cavity provides a narrow response which can be tuned by adjusting the geometry of the sub-wavelength grating metasurface. The key advantage of this approach is its ease of fabrication, where the spectral response is tuned by merely changing the grating period, resulting in a perfectly planar geometry that can be easily integrated with a broad variety of photodetectors, thus enabling attractive applications such as bio-imaging, time-of-flight sensors and LiDAR. The experimental results are supported by numerical simulations and effective medium theory that unveil the mechanisms that lead to the optical response of the device. It is also shown how the polarization dependence of the structure can be used to determine very accurately the polarization of incoming light.

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Boolean networks (BNs) have been extensively used to model gene regulatory networks (GRNs). The dynamics of BNs depend on the network architecture and regulatory logic rules (Boolean functions (BFs)) associated with nodes. Nested canalyzing functions (NCFs) have been shown to be enriched among the BFs in the large-scale studies of reconstructed Boolean models. The central question we address here is whether that enrichment is due to certain sub-types of NCFs. We build on one sub-type of NCFs, the chain functions (or chain-0 functions) proposed by Gat-Viks and Shamir. First, we propose two other sub-types of NCFs, namely, the class of chain-1 functions and generalized chain functions, the union of the chain-0 and chain-1 types. Next, we find that the fraction of NCFs that are chain-0 (also holds for chain-1) functions decreases exponentially with the number of inputs. We provide analytical treatment for this and other observations on BFs. Then, by analyzing three different datasets of reconstructed Boolean models we find that generalized chain functions are significantly enriched within the NCFs. Lastly we illustrate that upon imposing the constraints of generalized chain functions on three different GRNs we are able to obtain biologically viable Boolean models.

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Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.

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An innovative, concise synthesis of the aminocyclopentenediol fragment of queuosine is reported. The synthesis is based on the stereocontrolled addition of a vinylGrignard·LiCl reagent to a t-butanesulfinyl L-ribofuranosylamine, followed by dehydrodeoxygenation to generate a second vinyl group and ring-closing metathesis to form the five-membered ring scaffold of the natural product. This approach has the potential for the development of a larger scale synthesis.

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It has been observed that achiral nanoparticles, such as flat helices, may be subjected to an optical torque even when illuminated by normally incident linearly polarized light. However, the origin of this fascinating phenomenon has so far remained mostly unexplained. We therefore propose an exhaustive discussion that provides a clear and rigorous explanation for the existence of such a torque. Using multipolar theory and taking into account nonlocal interactions, we find that this torque stems from multipolar pseudochiral responses that generate both spin and orbital angular momenta. We also show that the nature of these peculiar responses makes them particularly dependent on the asymmetry of the particles. By elucidating the origin of this type of torque, this work may prove instrumental for the design of high-performance nano-rotors.

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We derive generalized sheet transition conditions (GSTCs) including dipoles and quadrupoles, using generalized functions (distributions). This derivation verifies that the GSTCs are valid for metasurfaces in non-homogeneous environments, such as for practical metasurfaces fabricated on a substrate. The inclusion of quadrupoles and modeling of spatial dispersion provides additional hyper-susceptibility components which serve as degrees of freedom for wave transformations. We leverage them to demonstrate a generalized Brewster effect with multiple angles of incidence at which reflection is suppressed, along with an "anti-Brewster" effect where transmission is suppressed.

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While interference colors have been known for a long time, conventional color filters have large spatial dimensions and cannot be used to create compact pixelized color pictures. Here we report a simple yet elegant interference-based method of creating microscopic structural color pixels using a single-mask process using standard UV photolithography on an all-dielectric substrate. The technology makes use of the varied aperture-controlled physical deposition rate of low-temperature silicon dioxide inside a hollow cavity to create a thin-film stack with the controlled bottom layer thickness. The stack defines which wavelengths of the reflected light interfere constructively, and thus the cavities act as micrometer-scale pixels of a predefined color. Combinations of such pixels produce vibrant colorful pictures visible to the naked eye. Being fully CMOS-compatible, wafer-scale, and not requiring costly electron-beam lithography, such a method paves the way toward large scale applications of structural colors in commercial products.

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Reflectivity modulation is a critical feature for applications in telecommunications, 3D imaging and printing, advanced laser machining, or portable displays. Tunable metasurfaces have recently emerged as a promising implementation for miniaturized and high-performance tunable optical components. Commonly, metasurface response tuning is achieved by electro-optical effects. In this work, we demonstrate reflectivity modulation based on a nanostructured, mechanically tunable, metasurface, consisting of an amorphous silicon nanopillar array and a suspended amorphous silicon membrane with integrated electrostatic actuators. With a membrane displacement of only 150 nm, we demonstrate reflectivity modulation by Mie resonance enhanced absorption in the pillar array, leading to a reflectivity contrast ratio of 1:3 over the spectral range from 400-530 nm. With fast, low-power electrostatic actuation and a broadband response in the visible spectrum, this mechanically tunable metasurface reflectivity modulator could enable high frame rate dynamic reflective displays.

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Information on honeybee foraging performance and especially bee loss rates at the colony level are crucial for evaluating the magnitude of effects due to pesticide exposure, thereby ensuring that protection goals for honeybee colonies are met (i.e. threshold of acceptable effects). However, current methods for monitoring honeybee foraging activity and mortality are very approximate (visual records) or are time-limited and mostly based on single cohort analysis. We therefore assess the potential of bee counters, that enable a colony-level and continuous monitoring of bee flight activity and mortality, in pesticide risk assessment. After assessing the background activity and bee loss rates, we exposed colonies to two concentrations of sulfoxaflor (a neurotoxic insecticide) in sugar syrup: a concentration that was considered to be field realistic (0.59 µg/ml) and a higher concentration (2.36 µg/ml) representing a worst-case exposure scenario. We did not find any effect of the field-realistic concentration on flight activity and bee loss rates. However, a two-fold decrease in daily flight activity and a 10-fold increase in daily bee losses were detected in colonies exposed to the highest sulfoxaflor concentration as compared to before exposure. When compared to the theoretical trigger values associated with the specific protection goal of 7 % colony-size reduction, the observed fold changes in daily bee losses were often found to be at risk for colonies. In conclusion, the real-time and colony-level monitoring of bee loss rates, combined with threshold values indicating at which levels bee loss rates threaten the colony, have great potential for improving regulatory pesticide risk assessments for honeybees under field conditions.

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Boolean models are a well-established framework to model developmental gene regulatory networks (DGRNs) for acquisition of cellular identities. During the reconstruction of Boolean DGRNs, even if the network structure is given, there is generally a large number of combinations of Boolean functions that will reproduce the different cell fates (biological attractors). Here we leverage the developmental landscape to enable model selection on such ensembles using the relative stability of the attractors. First we show that previously proposed measures of relative stability are strongly correlated and we stress the usefulness of the one that captures best the cell state transitions via the mean first passage time (MFPT) as it also allows the construction of a cellular lineage tree. A property of great computational importance is the insensitivity of the different stability measures to changes in noise intensities. That allows us to use stochastic approaches to estimate the MFPT and thereby scale up the computations to large networks. Given this methodology, we revisit different Boolean models of Arabidopsis thaliana root development, showing that a most recent one does not respect the biologically expected hierarchy of cell states based on relative stabilities. We therefore developed an iterative greedy algorithm that searches for models which satisfy the expected hierarchy of cell states and found that its application to the root development model yields many models that meet this expectation. Our methodology thus provides new tools that can enable reconstruction of more realistic and accurate Boolean models of DGRNs.

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We demonstrate a nonlinear plasmonic metasurface that exhibits strongly asymmetric second-harmonic generation: nonlinear scattering is efficient upon excitation in one direction, and it is substantially suppressed when the excitation direction is reversed, thus enabling a diode-like functionality. A significant (approximately 10 dB) extinction ratio of SHG upon opposite excitations is measured experimentally, and those findings are substantiated with full-wave simulations. This effect is achieved by employing a combination of two commonly used metals─aluminum and silver─producing a material composition asymmetry that results in a bianisotropic response of the system, as confirmed by performing homogenization analysis and extracting an effective susceptibility tensor. Finally, we discuss the implications of our results from the more fundamental perspectives of reciprocity and time-reversal asymmetry.