Mutation scanning of peach floral genes

<p>Abstract</p> <p>Background</p> <p>Mutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM) analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, <it>Prunus persica</it>. The targeted genes were the putative floral regulators <it>PpAGAMOUS </it>and <it>PpTERMINAL FLOWER I</it>.</p> <p>Results</p> <p>HRM analysis of <it>PpAG </it>and <it>PpTFL1 </it>coding regions in 36 peach cultivars found one polymorphic site in each gene. <it>PpTFL1 </it>and <it>PpAG </it>SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA.</p> <p>Conclusions</p> <p>Natural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.</p

Atomic insights into mechanisms of carbon coating on titania nanoparticle during flame synthesis

Carbon-metal oxide (CMO) nanocomposites have seen increasing research due to their extraordinary properties for energy storage materials and photocatalysts. Flame aerosol synthesis provides a promising route for producing CMO nanocomposites. Various CMO nanocomposites have been successfully synthesized through flame aerosol techniques in laboratories. However, a detailed understanding of the formation and growth mechanisms of such materials is lacking. Therefore, in this study, the reactive force-field molecular dynamics (ReaxFF MD) was deployed to gain atomic insights into the initial stage of carbon coating on the titania nanoparticle. We performed a large number of simulations of carbon coating with 18 typical hydrocarbon species in flames including aliphatics of C1-C4 species and polycyclic aromatic hydrocarbons (PAHs) at temperatures ranging from 400 K to 2500 K. We found that the titania nanoparticle can not only serve as a nucleus for physical adsorption of the surrounding hydrocarbons, but also can form Csingle bondTi/O bonds with them, and abstract H atoms from the surrounding hydrocarbons. The optimal temperature range for carbon coating is , because Csingle bondTi/O bonds are unstable at higher temperatures. At , hydrocarbons tend to gather to form larger carbonaceous species instead of coating onto the particle surface, as the formation of C-C bonds is promoted at high temperatures. Small aliphatics are favored to be chemically coated on the particle, while PAH molecules tend to be physically absorbed on the nanoparticle surface due to their stable electronic structure and large size. Coating tendencies of aliphatics are closely related to the number of C-C triple bonds

Near-Real Time Data for Space Weather Analyses: Present Status and Future

Assessments of the present state and future evolution of the space environment heavily relies on timely access to appropriate environmental measurements. These, near real-time (nrt), measurements provide a direct assessment of local or remote space environment conditions, they contribute to a more global description of Space Weather parameters through assimilative models, and they provide essential input into forecasting models. Unlike meteorology, however, the provision of these data is not a mainstream activity in the sense that critical space environment data are often derived from research rather than operational sensors. In addition, space research is a relatively immature field, where SUbstantial gaps in our knowledge impede our ability to optimally use available data streams. In this presentation, we provide examples of presently employed nrt data streams and their utility. We further discuss challenges and opportunities associated with the present approach to space weather forecasting. Finally, an outlook toward the future will be presented

Dynamics and kinetics of reversible homo-molecular dimerization of polycyclic aromatic hydrocarbons

Physical dimerization of polycyclic aromatic hydrocarbons (PAHs) has been investigated via molecular dynamics (MD) simulation with the ReaxFF reactive force field that is developed to bridge the gap between the quantum mechanism and classical MD. Dynamics and kinetics of homo-molecular PAH collision under different temperatures, impact parameters, and orientations are studied at an atomic level, which is of great value to understand and model the PAH dimerization. In the collision process, the enhancement factors of homo-molecular dimerizations are quantified and found to be larger at lower temperatures or with smaller PAH instead of size independent. Within the capture radius, the lifetime of the formed PAH dimer decreases as the impact parameter increases. Temperature and PAH characteristic dependent forward and reverse rate constants of homo-molecular PAH dimerization are derived from MD simulations, on the basis of which a reversible model is developed. This model can predict the tendency of PAH dimerization as validated by pyrene dimerization experiments [H. Sabbah et al., J. Phys. Chem. Lett. 1(19), 2962 (2010)]. Results from this study indicate that the physical dimerization cannot be an important source under the typical flame temperatures and PAH concentrations, which implies a more significant role played by the chemical route

Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful computational method for fundamental research in science branches such as biology, chemistry, biomedicine and physics over the past 60 years. Powered by rapidly advanced supercomputing technologies in recent decades, MD has entered the engineering domain as a first-principle predictive method for material properties, physicochemical processes, and even as a design tool. Such developments have far-reaching consequences, and are covered for the first time in the present paper, with a focus on MD for combustion and energy systems encompassing topics like gas/liquid/solid fuel oxidation, pyrolysis, catalytic combustion, heterogeneous combustion, electrochemistry, nanoparticle synthesis, heat transfer, phase change, and fluid mechanics. First, the theoretical framework of the MD methodology is described systemically, covering both classical and reactive MD. The emphasis is on the development of the reactive force field (ReaxFF) MD, which enables chemical reactions to be simulated within the MD framework, utilizing quantum chemistry calculations and/or experimental data for the force field training. Second, details of the numerical methods, boundary conditions, post-processing and computational costs of MD simulations are provided. This is followed by a critical review of selected applications of classical and reactive MD methods in combustion and energy systems. It is demonstrated that the ReaxFF MD has been successfully deployed to gain fundamental insights into pyrolysis and/or oxidation of gas/liquid/solid fuels, revealing detailed energy changes and chemical pathways. Moreover, the complex physico-chemical dynamic processes in catalytic reactions, soot formation, and flame synthesis of nanoparticles are made plainly visible from an atomistic perspective. Flow, heat transfer and phase change phenomena are also scrutinized by MD simulations. Unprecedented details of nanoscale processes such as droplet collision, fuel droplet evaporation, and CO2 capture and storage under subcritical and supercritical conditions are examined at the atomic level. Finally, the outlook for atomistic simulations of combustion and energy systems is discussed in the context of emerging computing platforms, machine learning and multiscale modelling

Deep Historical Borrowing Framework to Prospectively and Simultaneously Synthesize Control Information in Confirmatory Clinical Trials with Multiple Endpoints

In current clinical trial development, historical information is receiving more attention as providing value beyond sample size calculation. Meta-analytic-predictive (MAP) priors and robust MAP priors have been proposed for prospectively borrowing historical data on a single endpoint. To simultaneously synthesize control information from multiple endpoints in confirmatory clinical trials, we propose to approximate posterior probabilities from a Bayesian hierarchical model and estimate critical values by deep learning to construct pre-specified decision functions before the trial conduct. Simulation studies and a case study demonstrate that our method additionally preserves power, and has a satisfactory performance under prior-data conflict

Van Allen Probes observations linking radiation belt electrons to chorus waves during 2014 multiple storms

Abstract During 18 February to 2 March 2014, the Van Allen Probes encountered multiple geomagnetic storms and simultaneously observed intensified chorus and hiss waves. During this period, there were substantial enhancements in fluxes of energetic (53.8–108.3 keV) and relativistic (2–3.6 MeV) electrons. Chorus waves were excited at locations L = 4–6.2 after the fluxes of energetic were greatly enhanced, with a lower frequency band and wave amplitudes ∼20–100 pT. Strong hiss waves occurred primarily in the main phases or below the location L = 4 in the recovery phases. Relativistic electron fluxes decreased in the main phases due to the adiabatic (e.g., the magnetopause shadowing) or nonadiabatic (hiss-induced scattering) processes. In the recovery phases, relativistic electron fluxes either increased in the presence of enhanced chorus or remained unchanged in the absence of strong chorus or hiss. The observed relativistic electron phase space density peaked around L∗ = 4.5, characteristic of local acceleration. This multiple-storm period reveals a typical picture that chorus waves are excited by the energetic electrons at first and then produce efficient acceleration of relativistic electrons. This further demonstrates that the interplay between both competing mechanisms of chorus-driven acceleration and hiss-driven scattering often occurs in the outer radiation belts

Association of 6-Minute Walk Performance and Physical Activity With Incident Ischemic Heart Disease Events and Stroke in Peripheral Artery Disease.

BackgroundWe determined whether poorer 6-minute walk performance and lower physical activity levels are associated with higher rates of ischemic heart disease (IHD) events in people with lower extremity peripheral artery disease (PAD).Methods and resultsFive hundred ten PAD participants were identified from Chicago-area medical centers and followed prospectively for 19.0±9.5 months. At baseline, participants completed the 6-minute walk and reported number of blocks walked during the past week (physical activity). IHD events were systematically adjudicated and consisted of new myocardial infarction, unstable angina, and cardiac death. For 6-minute walk, IHD event rates were 25/170 (14.7%) for the third (poorest) tertile, 10/171 (5.8%%) for the second tertile, and 6/169 (3.5%) for the first (best) tertile (P=0.003). For physical activity, IHD event rates were 21/154 (13.6%) for the third (poorest) tertile, 15/174 (8.6%) for the second tertile, and 5/182 (2.7%) for the first (best) tertile (P=0.001). Adjusting for age, sex, race, smoking, body mass index, comorbidities, and physical activity, participants in the poorest 6-minute walk tertile had a 3.28-fold (95% CI 1.17 to 9.17, P=0.024) higher hazard for IHD events, compared with those in the best tertile. Adjusting for confounders including 6-minute walk, participants in the poorest physical activity tertile had a 3.72-fold (95% CI 1.24 to 11.19, P=0.019) higher hazard for IHD events, compared with the highest tertile.ConclusionsSix-minute walk and physical activity predict IHD event rates in PAD. Further study is needed to determine whether interventions that improve 6-minute walk, physical activity, or both can reduce IHD events in PAD