An investigation of genotype-phenotype association in a festulolium forage grass population containing genome-spanning <i>Festuca pratensis</i> chromosome segments in a <i>Lolium perenne</i> background

Alien chromosome introgression is used for the transfer of beneficial traits in plant breeding. For temperate forage grasses, much of the work in this context has focused on species within the ryegrasses (Lolium spp.) and the closely related fescues (Festuca spp.) particularly with a view to combining high forage quality with reliability and enhanced environmental services. We have analysed a L. perenne (perennial ryegrass) population containing the majority of a F. pratensis (meadow fescue) genome as introgressed chromosome segments to identify a) marker-trait associations for nutrient use and abiotic stress response across the family, and b) to assess the effects of introgression of F. pratensis genomic regions on phenotype. Using container-based assays and a system of flowing solution culture, we looked at phenotype responses, including root growth, to nitrogen and phosphorus status in the growing medium and abiotic stresses within this festulolium family. A number of significant marker/trait associations were identified across the family for root biomass on chromosomes 2, 3 and 5 and for heading date on chromosome 2. Of particular interest was a region on chromosome 2 associated with increased root biomass in phosphorus-limited conditions derived from one of the L. perenne parents. A genotype containing F. pratensis chromosome 4 as a monosomic introgression showed increased tiller number, shoot and root growth and genotypes with F. pratensis chromosome segment introgressions at different ends of chromosome 4 exhibited differential phenotypes across a variety of test conditions. There was also a general negative correlation between the extent of the F. pratensis genome that had been introgressed and root-related trait performances. We conclude that 1) the identification of alleles affecting root growth has potential application in forage grass breeding and, 2) F. pratensis introgressions can enhance quantitative traits, however, introgression can also have more general negative effects

Soft photon anomaly and gauge/string duality

Motivated by the recent DELPHI report on the anomalous photon production in e^+e^- annihilation, we exactly calculate the inclusive cross section of soft photons in the strong coupling limit of N=4 super Yang-Mills. We find that the energy distribution is that of the Bremsstrahlung, while the angular distribution is spherical. Our result elucidates a new non-perturbative source of soft photons not associated with the final state hadronic Bremsstrahlung.Comment: 22 page

Application of survival analysis and multistate modeling to understand animal behavior: examples from guide dogs

Epidemiology is the study of patterns of health-related states or events in populations. Statistical models developed for epidemiology could be usefully applied to behavioral states or events. The aim of this study is to present the application of epidemiological statistics to understand animal behavior where discrete outcomes are of interest, using data from guide dogs to illustrate. Specifically, survival analysis and multistate modeling are applied to data on guide dogs comparing dogs that completed training and qualified as a guide dog, to those that were withdrawn from the training program. Survival analysis allows the time to (or between) a binary event(s) and the probability of the event occurring at or beyond a specified time point. Survival analysis, using a Cox proportional hazards model, was used to examine the time taken to withdraw a dog from training. Sex, breed, and other factors affected time to withdrawal. Bitches were withdrawn faster than dogs, Labradors were withdrawn faster, and Labrador × Golden Retrievers slower, than Golden Retriever × Labradors; and dogs not bred by Guide Dogs were withdrawn faster than those bred by Guide Dogs. Multistate modeling (MSM) can be used as an extension of survival analysis to incorporate more than two discrete events or states. Multistate models were used to investigate transitions between states of training to qualification as a guide dog or behavioral withdrawal, and from qualification as a guide dog to behavioral withdrawal. Sex, breed (with purebred Labradors and Golden retrievers differing from F1 crosses), and bred by Guide Dogs or not, effected movements between states. We postulate that survival analysis and MSM could be applied to a wide range of behavioral data and key examples are provided

B chromosomes are associated with redistribution of genetic recombination towards lower-recombination chromosomal regions in perennial ryegrass

Supernumerary ‘B’ chromosomes are non-essential components of the genome present in a range of plant and animal species – including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT marker genetic maps for 6 perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progenies and their parents we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared to zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, i.e., pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders

Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN

Neuroimaging research requires sophisticated tools for analyzing complex data, but efficiently leveraging these tools can be a major challenge, especially on large datasets. CBRAIN is a web-based platform designed to simplify the use and accessibility of neuroimaging research tools for large-scale, collaborative studies. In this paper, we describe how CBRAIN’s unique features and infrastructure were leveraged to integrate TAPAS PhysIO, an open-source MATLAB toolbox for physiological noise modeling in fMRI data. This case study highlights three key elements of CBRAIN’s infrastructure that enable streamlined, multimodal tool integration: a user-friendly GUI, a Brain Imaging Data Structure (BIDS) data-entry schema, and convenient in-browser visualization of results. By incorporating PhysIO into CBRAIN, we achieved significant improvements in the speed, ease of use, and scalability of physiological preprocessing. Researchers now have access to a uniform and intuitive interface for analyzing data, which facilitates remote and collaborative evaluation of results. With these improvements, CBRAIN aims to become an essential open-science tool for integrative neuroimaging research, supporting FAIR principles and enabling efficient workflows for complex analysis pipelines

Thermodynamics of the N=2^* strongly coupled plasma

Gauge/string duality is a potentially important framework for addressing the properties of the strongly coupled quark gluon plasma produced at RHIC. However, constructing an actual string theory dual to QCD has so far proven elusive. In this paper, we take a partial step towards exploring the QCD plasma by investigating the thermodynamics of a non-conformal system, namely the N=2^* theory, which is obtained as a mass deformation of the conformal N=4 gauge theory. We find that at temperatures of order the mass scale, the thermodynamics of the mass deformed plasma is surprisingly close to that of the conformal gauge theory plasma. This suggests that many properties of the quark gluon plasma at RHIC may in fact be well described by even relatively simple models such as that of the conformal N=4 plasma.Comment: 41 pages, 22 figure

The complete mitochondrial genome of record-breaking migrant Arctic tern (Sterna paradisaea)

The analysis of mitochondrial DNA (mtDNA) base composition, codon usage, and genome arrangement patterns can provide insight into metabolic pathways and evolutionary history. Here, we report on the complete mitochondrial genome (mitogenome) of Arctic tern (Sterna paradisaea) a species notable for undertaking the longest migrations of any species as well as breeding in sub-polar habitats and capable of enduring extreme altitude. The complete mitogenome was 16,708 bp long and was typical of other avian mitogenomes in size and content. The phylogenetic position of the Arctic tern within Charadriiformes based on the coding region on the mtDNA corresponded closely to that based on nuclear loci. The sequence will provide a useful resource for investigations of metabolic adaptations of this remarkable species

Alpine Corsica Metamorphic Core Complex

International audienceAlpine Corsica is an example where superficial nonmetamorphic allochtonous units rest upon a highly strained metamorphic complex. Early ductile deformation under high pressure-low temperature (HP-LT) conditions is due to the westward thrusting of oceanic material onto a continental basement as shown by previous studies. New thermobarometric estimates yield minimal peak HP-LT metamorphism conditions of 11 kbar at 400°C. The early deformation is overprinted by a ductile deformation with an eastward sense of shear postdating or contemporaneous with mineral recrystallizations in the greenschist facies conditions. Early compressive thrust contacts are reworked as east dipping ductile normal faults and the less competent units display only eastward shear criteria. The upper units are affected by an extensional brittle deformation, and east dipping brittle normal faults bound to the west the early to middle Miocene Saint-Florent half-graben. The greenschist metamorphic event lasted until 33 Ma, which is contemporaneous with the beginning of the extension in the Liguro-Provençal basin. We interpret the second deformation stage as the result of a ductile extension following the overthickening of the crust due to the westward thrusting. Extension reduces the thickness of the crust so that upper units free from early P-T conditions are brought into close contact with a HP-LT metamorphic core complex. The geometry of the late extension is controlled by that of the early compressive thrust

Sum rules, plasma frequencies and Hall phenomenology in holographic plasmas

We study the AC optical and hall conductivities of Dp/Dq-branes intersections in the probe approximation and use sum-rules to study various associated transport coefficients. We determine that the presence of massive fundamental matter, as compared to massless fundamental matter described holographically by a theory with no dimensional defects, reduces the plasma frequency. We further show that this is not the case when the brane intersections include defects. We discuss in detail how to implement correctly the regularization of retarded Green's functions so that the dispersion relations are satisfied and the low energy behaviour of the system is physically realistic.Comment: 25 pages, 5 figures. v2.minor changes, published versio

Multipotent Embryonic Isl1+ Progenitor Cells Lead to Cardiac, Smooth Muscle, and Endothelial Cell Diversification

SummaryCardiogenesis requires the generation of endothelial, cardiac, and smooth muscle cells, thought to arise from distinct embryonic precursors. We use genetic fate-mapping studies to document that isl1+ precursors from the second heart field can generate each of these diverse cardiovascular cell types in vivo. Utilizing embryonic stem (ES) cells, we clonally amplified a cellular hierarchy of isl1+ cardiovascular progenitors, which resemble the developmental precursors in the embryonic heart. The transcriptional signature of isl1+/Nkx2.5+/flk1+ defines a multipotent cardiovascular progenitor, which can give rise to cells of all three lineages. These studies document a developmental paradigm for cardiogenesis, where muscle and endothelial lineage diversification arises from a single cell-level decision of a multipotent isl1+ cardiovascular progenitor cell (MICP). The discovery of ES cell-derived MICPs suggests a strategy for cardiovascular tissue regeneration via their isolation, renewal, and directed differentiation into specific mature cardiac, pacemaker, smooth muscle, and endothelial cell types