Prospects for Improving Alfalfa Yield Using Genomic- and Phenomic-Based Breeding

Alfalfa (Medicago sativa L.) is a perennial outcrossing legume that is cultivated as an important forage crop in many parts of the world. Yield is the most important trait for profitable alfalfa production, yet over the last 30 years yield improvement in California has stagnated. Current breeding methods focus on recurrent phenotypic selection; however, alternatives incorporating genomic- and phenomic-based information may enhance genetic gain and help to address the lack of yield improvement. Here we attempt to increase the yield potential of alfalfa using genomic selection (GS) in combination with high throughput phenotyping (HTP). A total of 193 families from two closely related elite populations were sown in the greenhouse and transplanted into mini sward plots at two locations near Davis, CA in May 2020. The trial was managed as a high-input system under full irrigation. Families were genotyped and phenotyped for biomass yield by mechanical harvest and a combination of drone and tower-based remote sensors across 12 harvests, 3 in the establishment year (2020), 7 in the first full year of production (2021) and 2 in 2022. Alfalfa yields ranged from 13-27 tonnes DM/hectare/year with a number of half-sib families outperforming popular cultivars in the first 2 years of production. Biomass volume predicted from the drone-based cameras had a moderate prediction accuracy with an overall R2 of 0.55. Some individual harvests reached accuracies as high as 0.85. Genotyping resulted in a dataset with 6,838 SNPs. Allele frequencies were used to generate a relationship matrix for GS. Narrow-sense heritability for dry matter yield was 0.31 and the predictive ability of the GS model was 0.15

Solution of gauge theories induced by fundamental representation scalars

Gauge theories induced by scalars in the fundamental representation of the $U(N_c)_{gauge}\times U(N_f)_{global}$ group are investigated in the large $N_c$ and $N_f$ limit. A master field is defined from bilinears of the scalar field following an Eguchi-Kawai type reduction of spacetime. The density function for the master field satisfies an integral equation that can be solved exactly in two dimensions (D=2) and in a convergent series of approximations at $D>2$. While at D=2 the system is in the same phase at all $\epsilon=N_c/N_f$, it undergoes a phase transition at a critical value, $\epsilon_c(D)$, for $D>2$.Comment: 12 pages, LaTe

How does a cadaver model work for testing ultrasound diagnostic capability for rheumatic-like tendon damage?

To establish whether a cadaver model can serve as an effective surrogate for the detection of tendon damage characteristic of rheumatoid arthritis (RA). In addition, we evaluated intraobserver and interobserver agreement in the grading of RA-like tendon tears shown by US, as well as the concordance between the US findings and the surgically induced lesions in the cadaver model. RA-like tendon damage was surgically induced in the tibialis anterior tendon (TAT) and tibialis posterior tendon (TPT) of ten ankle/foot fresh-frozen cadaveric specimens. Of the 20 tendons examined, six were randomly assigned a surgically induced partial tear; six a complete tear; and eight left undamaged. Three rheumatologists, experts in musculoskeletal US, assessed from 1 to 5 the quality of US imaging of the cadaveric models on a Likert scale. Tendons were then categorized as having either no damage, (0); partial tear, (1); or complete tear (2). All 20 tendons were blindly and independently evaluated twice, over two rounds, by each of the three observers. Overall, technical performance was satisfactory for all items in the two rounds (all values over 2.9 in a Likert scale 1-5). Intraobserver and interobserver agreement for US grading of tendon damage was good (mean κ values 0.62 and 0.71, respectively), with greater reliability found in the TAT than the TPT. Concordance between US findings and experimental tendon lesions was acceptable (70-100 %), again greater for the TAT than for the TPT. A cadaver model with surgically created tendon damage can be useful in evaluating US metric properties of RA tendon lesions

Measurements of polarized photo-pion production on longitudinally polarized HD and Implications for Convergence of the GDH Integral

We report new measurements of inclusive pion production from frozen-spin HD for polarized photon beams covering the Delta(1232) resonance. These provide data simultaneously on both H and D with nearly complete angular distributions of the spin-difference cross sections entering the Gerasimov-Drell-Hearn (GDH) sum rule. Recent results from Mainz and Bonn exceed the GDH prediction for the proton by 22 microbarns, suggesting as yet unmeasured high-energy components. Our pi0 data reveal a different angular dependence than assumed in Mainz analyses and integrate to a value that is 18 microbarns lower, suggesting a more rapid convergence. Our results for deuterium are somewhat lower than published data, considerably more precise and generally lower than available calculations.Comment: 4 pages, 4 figures. Submitted for publication in Physical Review Letter

Construction of Capacities from Overlap Indexes

In many problems, it is crucial to find a relation between groups of data. Such relation can be expressed, for instance, in terms of an appropriate fuzzy measure or capacity([10, 21]) which reflects the way the different data are connected to each other [20]. In this chapter, taking into account this fact and following the developments in [8],we introduce a method to build capacities ([20, 21]) directly from the data (inputs) of a given problem. In order to do so, we make use of the notions of overlap function and overlap index ([5, 12, 13, 7, 4, 14, 16]) for constructing capacities which reflect how different data are related to each other. This paper is organized as follows: after providing some preliminaries, we analyse, in Section 3, some properties of overlap functions and indexes. In Sections 4 we discuss a method for constructing capacities from overlap functions and overlap indexes. Finally, we present some conclusions and references

The inhibitor of differentiation-2 promotes synovial fibroblast-dependent osteoclastogenesis in rheumatoid arthritis

Objectives: Despite indirect evidence suggesting that low oxygen levels might occur in the rheumatoid arthritis (RA) synovium, direct proof of the presence of hypoxia in the arthritic synovium as well as the relevance of low oxygen levels for joint destruction is lacking. The aim of this study was to analyse the distribution of hypoxia in arthritic joints and to evaluate the molecular effects of the hypoxic environment on the phenotype of RA synovial fibroblasts (SF).<p></p> Methods: The hypoxia marker EF-5 was applied in mice with the collagen-induced arthritis (CIA). Expression profile analysis with hypoxic and normoxic SF was performed using subtractive hybridization and microarray. The expression of the inhibitor of differentiation-2 (Id-2), CD68 (macrophage marker) and prolyl hydroxylase (fibroblast marker) was evaluated by immunohistochemistry on synovial tissues from RA, osteoarthritis patients and CIA mice. To evaluate the function of Id-2 in SF, cells were transfected with the pcDNA3.1 containing cDNA for Id-2 or Id-2-specific siRNA or mock controls. The expression of Id-2 and genes regulated by Id-2 in transfected SF was evaluated by SYBR Green real-time PCR and western blot. SF stably transfected with Id-2 were cocultured with bone marrow cells in a transwell system. The expression of the receptor activator of NF-κB ligand (RANKL) and osteoprotegerin were measured by real-time PCR. The development of osteoclasts was evaluated by visualization of the activity of tartrate-resistant acid phosphatase.<p></p> Results: Using the hypoxia marker EF-5 we found that in mice with CIA, synovial cells invading bone and cartilage are exposed to reduced oxygen levels. Expression profile studies identified Id-2 as being upregulated under low oxygen conditions. In addition, IL-1beta stimulation increased the expression of Id-2 in these cells. Histological studies of RA synovium and CIA synovium showed strong expression of Id-2 in SF at sites of synovial invasion into bone. Overproduction of Id-2 in SF by stable transfection triggered the expression of several genes promoting osteoclastogenesis, including BMP-2, PTHrP, Wnt5a and vascular endothelial growth factor. Conversely, the suppression of endogenous Id-2 led to the downregulation of the expression of these molecules. Consistent with these findings coculture of Id-2 transfected SF with bone marrow cells increased the expression of the osteoclast differentiation factor RANKL, and decreased the expression of the osteoclast inhibitory factor osteoprotegerin in bone marrow stromal cells, which was followed by an increase in the number of osteoclasts.<p></p> Conclusion: Taken together, our data provide evidence that hypoxia is present at sites of synovial invasion in RA and that Id-2 induced by hypoxia contributes at these sites to joint destruction by promoting SF-dependent osteoclastogenesis

Associations involving delays (particularly long delays) between certain weather parameters and geomagnetic activity

Four sunspot-minimum periods (1963-1966, 1971-1977, 1983-1987 and 1992-1997) have been examined for the results which are presented. Using several different weather parameters, tropospheric gravity waves, enhanced cold fronts and two rainfall data sets in Eastern Australia, associations at reasonably high levels of significance have been found with enhanced geomagnetic activity (EGA). Statistically this EGA involved either short delays of several days or long delays of about 20 days. The geomagnetic parameters used were (a) the AE index (b) the hourly H component for a number of stations and (c) the daily K-P-sum value. The K-P-sum analyses have shown that the EGA associated with the delays form part of four or five cycles of recurrent geomagnetic activity for 27-day periodicities. Furthermore statistically two recurrent cycles are found to exist concurrently, one apparently related to the short delays and the other to the long delays. Periodicities of 13.5 days are created because the two sets are displaced from each other by approximately this interval. A brief reference is made to the 13.5 periodicity known to exist for geomagnetic activity and the evidence in the literature for active regions on the sun to be displaced by 180 degrees of solar longitude

Evolutionary Games with Affine Fitness Functions: Applications to Cancer

We analyze the dynamics of evolutionary games in which fitness is defined as an affine function of the expected payoff and a constant contribution. The resulting inhomogeneous replicator equation has an homogeneous equivalent with modified payoffs. The affine terms also influence the stochastic dynamics of a two-strategy Moran model of a finite population. We then apply the affine fitness function in a model for tumor-normal cell interactions to determine which are the most successful tumor strategies. In order to analyze the dynamics of concurrent strategies within a tumor population, we extend the model to a three-strategy game involving distinct tumor cell types as well as normal cells. In this model, interaction with normal cells, in combination with an increased constant fitness, is the most effective way of establishing a population of tumor cells in normal tissue.Comment: The final publication is available at http://www.springerlink.com, http://dx.doi.org/10.1007/s13235-011-0029-