Object motion influences feedforward motor responses during mechanical stopping of virtual projectiles: a preliminary study.

An important window into sensorimotor function is how humans interact and stop moving projectiles, such as stopping a door from closing shut or catching a ball. Previous studies have suggested that humans time the initiation and modulate the amplitude of their muscle activity based on the momentum of the approaching object. However, real-world experiments are constrained by laws of mechanics, which cannot be manipulated experimentally to probe the mechanisms of sensorimotor control and learning. An augmented-reality variant of such tasks allows for experimental manipulation of the relationship between motion and force to obtain novel insights into how the nervous system prepares motor responses to interact with moving stimuli. Existing paradigms for studying interactions with moving projectiles use massless objects and are primarily focused on quantifying gaze and hand kinematics. Here, we developed a novel collision paradigm using a robotic manipulandum where participants mechanically stopped a virtual object moving in the horizontal plane. On each block of trials, we varied the virtual object's momentum by increasing either its velocity or mass. Participants stopped the object by applying a force impulse that matched the object momentum. We observed that hand force increased as a function of object momentum linked to changes in virtual mass or velocity, similar to results from studies involving catching free-falling objects. In addition, increasing object velocity resulted in later onset of hand force relative to the impending time-to-contact. These findings show that the present paradigm can be used to determine how humans process projectile motion for hand motor control.

The effect of population density on outcomes of major trauma patients in Ireland.

BACKGROUND: Time-sensitive emergencies in areas of low population density have statistically poorer outcomes. This includes incidents of major trauma. This study assesses the effect that population density at a receiving hospital of a major trauma patient has on survival. METHODS: Patients meeting Trauma Audit Research Network criteria for major trauma from 2016 to 2020 in Ireland were included in this retrospective observational study. Incident data were retrieved from the Major Trauma Audit, while data on population density were calculated from Irish state sources. The primary outcome measure of survival to discharge was compared to population density using logistic regression, adjusted for demographic and incident variables. Records were divided into population density tertiles to assess for between-group differences in potential predictor variables. RESULTS: Population density at a receiving hospital had no impact on mortality in Irish major trauma patients from our logistic regression model (OR = 1.01, 95% CI 0.98-1.05, p = 0.53). Factors that did have an impact were age, Charlson Comorbidity Index, Injury Severity Score, and the presence of an Orthopaedic Surgery service at the receiving hospital (all p < 0.001). Age and Charlson Comorbidity Index differed slightly by population density tertile; both were higher in areas of high population density (all p < 0.001). CONCLUSIONS: Survival to discharge in Irish major trauma patients does not differ substantially based on population density. This is an important finding as Ireland moves to a new trauma system, with features based on population distribution. An Orthopaedic Surgery service is an important feature of a major trauma receiving hospital and its presence improves outcomes.

The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum.

Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.

Study of He*/Ne*+Ar, Kr, N2, H2, D2 Chemi-Ionization Reactions by Electron Velocity-Map Imaging.

The chemi-ionization of Ar, Kr, N2, H2, and D2 by Ne(3P2) and of Ar, Kr, and N2 by He(3S1) was studied by electron velocity map imaging (e-VMI) in a crossed molecular beam experiment. A curved magnetic hexapole was used to state-select the metastable species. Collision energies of 60 meV were obtained by individually controlling the beam velocities of both reactants. The chemi-ionization of atoms and molecules can proceed along different channels, among them Penning ionization and associative ionization. The evolution of the reaction is influenced by the internal redistribution of energy, which happens at the first reaction step that involves the emission of an electron. We designed and built an e-VMI spectrometer in order to investigate the electron kinetic energy distribution, which is related to the internal state distribution of the ionic reaction products. The analysis of the electron kinetic energy distributions allows an estimation of the ratio between the two-reaction channel Penning and associative ionization. In the molecular cases the vibrational or electronic excitation enhanced the conversion of internal energy into the translational energy of the forming ions, thus influencing the reaction outcome.

RDH1 suppresses adiposity by promoting brown adipose adaptation to fasting and re-feeding.

RDH1 is one of the several enzymes that catalyze the first of the two reactions to convert retinol into all-trans-retinoic acid (atRA). Here, we show that Rdh1-null mice fed a low-fat diet gain more weight as adiposity (17% males, 13% females) than wild-type mice by 20 weeks old, despite neither consuming more calories nor decreasing activity. Glucose intolerance and insulin resistance develop following increased adiposity. Despite the increase in white fat pads, epididymal white adipose does not express Rdh1, nor does muscle. Brown adipose tissue (BAT) and liver express Rdh1 at relatively high levels compared to other tissues. Rdh1 ablation lowered body temperatures during ambient conditions. Given the decreased body temperature, we focused on BAT. A lack of differences in BAT adipogenic gene expression between Rdh1-null mice and wild-type mice, including Pparg, Prdm16, Zfp516 and Zfp521, indicated that the phenotype was not driven by brown adipose hyperplasia. Rather, Rdh1 ablation eliminated the increase in BAT atRA that occurs after re-feeding. This disruption of atRA homeostasis increased fatty acid uptake, but attenuated lipolysis in primary brown adipocytes, resulting in increased lipid content and larger lipid droplets. Rdh1 ablation also decreased mitochondrial proteins, including CYCS and UCP1, the mitochondria oxygen consumption rate, and disrupted the mitochondria membrane potential, further reflecting impaired BAT function, resulting in both BAT and white adipose hypertrophy. RNAseq revealed dysregulation of 424 BAT genes in null mice, which segregated predominantly into differences after fasting vs after re-feeding. Exceptions were Rbp4 and Gbp2b, which increased during both dietary conditions. Rbp4 encodes the serum retinol-binding protein-an insulin desensitizer. Gbp2b encodes a GTPase. Because Gbp2b increased several hundred-fold, we overexpressed it in brown adipocytes. This caused a shift to larger lipid droplets, suggesting that GBP2b affects signaling downstream of the ß-adrenergic receptor during basal thermogenesis. Thus, Rdh1-generated atRA in BAT regulates multiple genes that promote BAT adaptation to whole-body energy status, such as fasting and re-feeding. These gene expression changes promote optimum mitochondria function and thermogenesis, limiting adiposity. Attenuation of adiposity and insulin resistance suggests that RDH1 mitigates metabolic syndrome.

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon.

Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide selection scans (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species, and affects different genomic regions across the two populations. Gene ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in B. distachyon. We eventually cross-validated our results with quantitative trait locus data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near base-perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.

PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution.

BACKGROUND: Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences in coarse genome properties like GC content or sequences from related species. Thus, these approaches do not work for subgenomes where gross features are indistinguishable and related genomes are lacking. Here we describe a method that uses rapidly evolving repetitive DNA to circumvent these limitations. RESULTS: By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes from test datasets and subgenomes from two polyploid plants, tobacco and wheat, without any prior knowledge. CONCLUSION: This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

Sub-Kelvin Stereodynamics of the Ne(

We present an experimental study of the low-energy stereodynamics of the Ne(^{3}P_{2})+N_{2} reaction. Supersonic expansions of the two reactants are superposed in a merged beam experiment, where individual velocity control of the two beams allows us to reach average relative velocities of zero, yielding minimum collision energies around 60 mK. We combine the merged beam technique with the orientation of the metastable neon atoms and measure the branching between two reaction channels, Penning ionization and associative ionization, as a function of neon orientation and collision energy, covering the range 0.06-700 K. We find that we lose the ability to orient Ne below ≈100 K due to dynamic reorientation. Associative ionization products Ne-N_{2}^{+} predissociate with a probability of 30%-60% and that associative ionization is entirely due to reactions of the Ω=2 state, where the singly occupied p orbital of the Ne^{*} is oriented along the interatomic axis.

Energy and orientation independence of the channel branching in Ne* + ND3 chemi-ionisation.

Collisions of excited neon atoms with ammonia molecules can lead to two reaction processes, dissociative ionisation and Penning ionisation. Both processes result in the ionisation of the ammonia molecule and redistribution of the electronic energy into the internal ammonia ion rovibrational modes. We performed energy dependent, crossed-beam stereodynamics studies of the branching ratio between the two ionisation processes. It was found that the branching ratio is totally and completely insensitive to both the neon orientation and the collision energy across the range we sampled, 370-520 cm-1. The total lack of stereodynamics can be explained by the structure of the ammonia and that its orientation, which we do not attempt to control, is the critical factor in the reaction outcome.

Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection.

Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T-DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21 078, bringing the overall total to 26 112. Thirty-seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T-DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T-DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/.

Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes.

Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) - Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene (0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+, T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure.

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon.

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.

Stereodynamics of Ne(3P2) reacting with Ar, Kr, Xe, and N2.

Stereodynamics experiments of Ne(3P2) reacting with Ar, Kr, Xe, and N2 leading to Penning and associative ionization have been performed in a crossed molecular beam apparatus. A curved magnetic hexapole was used to state-select and polarize Ne(3P2) atoms which were then oriented in a rotatable magnetic field and crossed with a beam of Ar, Kr, Xe, or N2. The ratio of associative to Penning ionization was recorded as a function of the magnetic field direction for collision energies between 320 cm-1 and 500 cm-1. Reactivities are obtained for individual states that differ only in Ω, the projection of the neon total angular momentum vector on the inter-particle axis. The results are rationalized on the basis of a model involving a long-range and a short-range reaction mechanism. Substantially lower probability for associative ionization was observed for N2, suggesting that predissociation plays a critical role in the overall reaction pathway.

Energy Dependent Stereodynamics of the Ne(

The stereodynamics of the Ne(^{3}P_{2})+Ar Penning and associative ionization reactions have been studied using a crossed molecular beam apparatus. The experiment uses a curved magnetic hexapole to polarize the Ne(^{3}P_{2}), which is then oriented with a shaped magnetic field in the region where it intersects with a beam of Ar(^{1}S). The ratios of Penning to associative ionization were recorded over a range of collision energies from 320 to 500 cm^{-1} and the data were used to obtain Ω state dependent reactivities for the two reaction channels. These reactivities were found to compare favorably to those predicted in the theoretical work of Brumer et al.

Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.

Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.

PIECE: a database for plant gene structure comparison and evolution.

Gene families often show degrees of differences in terms of exon-intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a comparative genomics database named PIECE (http://wheat.pw.usda.gov/piece) for Plant Intron and Exon Comparison and Evolution studies. The database contains all the annotated genes extracted from 25 sequenced plant genomes. These genes were classified based on Pfam motifs. Phylogenetic trees were pre-constructed for each gene category. PIECE provides a user-friendly interface for different types of searches and a graphical viewer for displaying a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. The gene structure evolution of orthologous gene groups was determined using the GLOOME, Exalign and GECA software programs that can be accessed within the database. PIECE also provides a web server version of the software, GSDraw, for drawing schematic diagrams of gene structures. PIECE is a powerful tool for comparing gene sequences and provides valuable insights into the evolution of gene structure in plant genomes.

Cytokinin signaling as a positional cue for patterning the apical-basal axis of the growing Arabidopsis shoot meristem.

The transcription factor WUSCHEL (WUS) acts from a well-defined domain within the Arabidopsis thaliana shoot apical meristem (SAM) to maintain a stem cell niche. A negative-feedback loop involving the CLAVATA (CLV) signaling pathway regulates the number of WUS-expressing cells and provides the current paradigm for the homeostatic maintenance of stem cell numbers. Despite the continual turnover of cells in the SAM during development, the WUS domain remains patterned at a fixed distance below the shoot apex. Recent work has uncovered a positive-feedback loop between WUS function and the plant hormone cytokinin. Furthermore, loss of function of the cytokinin biosynthetic gene, LONELY GUY (LOG), results in a wus-like phenotype in rice. Herein, we find the Arabidopsis LOG4 gene is expressed in the SAM epidermis. We use this to develop a computational model representing a growing SAM to suggest the plausibility that apically derived cytokinin and CLV signaling, together, act as positional cues for patterning the WUS domain within the stem cell niche. Furthermore, model simulations backed by experimental data suggest a previously unknown negative feedback between WUS function and cytokinin biosynthesis in the Arabidopsis SAM epidermis. These results suggest a plausible dynamic feedback principle by which the SAM stem cell niche is patterned.

The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum.

Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.

Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem.

A central unanswered question in stem cell biology, both in plants and in animals, is how the spatial organization of stem cell niches are maintained as cells move through them. We address this question for the shoot apical meristem (SAM) which harbors pluripotent stem cells responsible for growth of above-ground tissues in flowering plants. We find that localized perception of the plant hormone cytokinin establishes a spatial domain in which cell fate is respecified through induction of the master regulator WUSCHEL as cells are displaced during growth. Cytokinin-induced WUSCHEL expression occurs through both CLAVATA-dependent and CLAVATA-independent pathways. Computational analysis shows that feedback between cytokinin response and genetic regulators predicts their relative patterning, which we confirm experimentally. Our results also may explain how increasing cytokinin concentration leads to the first steps in reestablishing the shoot stem cell niche in vitro.