In the name of the rose:a roadmap for rose research in the genome era

The recent completion of the rose genome sequence is not the end of a process,but rather a starting point that opens up a whole set of new and exciting activities.Next to a high-quality genome sequence other genomic tools have also become available for rose,including transcriptomics data,a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids.Rose cultivars are highly heterogeneous and diverse.This vast diversity in cultivated roses can be explained through the genetic potential of the genus,introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders.We can now investigate how this diversity can best be exploited and refined in future breeding work,given the rich molecular toolbox now available to the rose breeding community.This paper presents possible lines of research now that rose has entered the genomics era,and attempts to partially answer the question that arises after the completion of any draft genome sequence:‘Now that we have“the”genome,what’s next?’.Having access to a genome sequence will allow both(fundamental)scientific and(applied)breeding-orientated questions to be addressed.We outline possible approaches for a number of these questions.

Optimization of Maturation of Radio-Cephalic Arteriovenous Fistula Using a Model Relating Energy Loss Rate and Vascular Geometric Parameters

The main reason for the early failure of radio-cephalic arteriovenous fistula (RCAVF) is non-maturity, which means that the blood flow rate in the fistula cannot increase to the expected value for dialysis. From a mechanical perspective, the vascular resistance at the artificially designed anastomosis causes an energy loss that affects blood flow rate growth and leads to early failure. This research studied how to maximize the RCAVF maturity and primary patency by controlling the energy loss rate. We theoretically analyzed and derived a model that evaluates the energy loss rate Eavf in RCAVF as a function of its blood vessel geometric parameters (GPs) for given flow rates. There was an aggregate of five controllable GPs in RCAVF: radial artery diameter (Dra), cephalic vein diameter (Dcv), blood vessel distance between artery and vein (h), anastomotic diameter (Da), and anastomotic angle (θ). Through this analysis, it was found that Eavf was inversely proportional to Dra, Dcv, Da, and θ, whereas proportional to h. Therefore, we recommended surgeons choose the vessels with large diameters, close distance, and increase the diameter and angle of the anastomosis to decrease the early failure of RCAVF. Simultaneously, we could explain the results of many clinical empiricisms with our formula. We found that increasing Dcv and θ was more significant in reducing Eavf than increasing Dra and Da. Based on our model, we could define two critical energy loss rates (CELa, CELb) to help surgeons evaluate the blood vessels and choose the ideal range of θ, and help them design the preoperative RCAVF plan for each patient to increase the maturity and the primary patency of RCAVF.

Lorentz Force Electrical Impedance Detection Using Step Frequency Technique

Lorentz force electrical impedance tomography(LFEIT)inherits the merit of high resolution by ultrasound stimulation and the merit of high contrast through electromagnetic field detection.To reduce the instantaneous peak power of the stimulating signal to the transducer,the sinusoidal pulse and step-frequency technique is investigated in LFEIT.The theory of application of step-frequency technique in LFEIT is formulated with the direct demodulation method and the in-phase quadrature demodulation method.Compared with the in-phase quadrature demodulation method,the direct demodulation method has simple experimental setup but could only detect half of the range.Experiments carried out with copper foils confirmed that LFEIT using the step-frequency technique could detect the electrical conductivity variations precisely,which suggests an alternative method of realization of LFEIT.

Preparation and characterization of octenyl succinic anhydride nano starch from tiger nut meals

Tiger nut(Cyperus esculentus L.)is an ideal raw material for oil extraction,but starch-rich tiger nut meal,a by-product of oil extraction,has not been fully utilized.For this,starch was isolated from tiger nut meal,and then starch nanoparticles were prepared by gelatinization,ultrasonication and nanoprecipitation under different conditions.The preparation parameters were optimized by measuring the particle size with dynamic light scattering,and the physicochemical properties of native starch and nano starch were evaluated.The results showed that,compared to native starch,starch nanoparticle(nano starch)has a higher amylose content(39.05%),solubility(56.13%),and swelling power(58.01%).Furthermore,native starch and nano starch were esterified with octenyl succinic anhydride(OSA),respectively,conferring amphiphilic properties.The effects of OSA modification on the resistant starch content,thermal properties,and microstructure of starches were characterized.The resistant starch content of tiger nut native starch increased by 10.81%after OSA modification,while the resistant starch content of OSA nano starch increased to 37.76%.Compared to native starch,the gelatinization temperature of OSA nano starch decreased by 2.7℃ and nano starch decreased by 5.68℃.OSA modified nano starch showed a unique microstructure,such as a slender fiber structure and a regular oblate structure.The hydrophobic OSA groups aggregated to form hydrophobic cavities with a hydrophilic surface in the aqueous phase.The findings presented in this investigation provide a better understanding of the design and development of OSA nano starch and provide valuable guidance to further enhance the added value of tiger nuts and future applications in the food industry.

Capturing Auxin Response Factors Syntax Using DNA Binding Models

Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/ Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions o1IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation.

An oviraptorid preserved atop an embryo-bearing egg clutch sheds light on the reproductive biology of non-avialan theropod dinosaurs

Recent studies demonstrate that many avialan features evolved incrementally prior to the origin of the group,but the presence of some of these features,such as bird-like brooding behaviours,remains contentious in non-avialan dinosaurs.Here we report the first non-avialan dinosaur fossil known to preserve an adult skeleton atop an egg clutch that contains embryonic remains.The preserved positional relationship of the adult to the clutch,coupled with the advanced growth stages of the embryos and their high estimated incubation temperatures,provides strong support for the brooding hypothesis.Furthermore,embryos in the clutch are at different developmental stages,suggesting the presence of asynchronous hatching—a derived feature even among crown-group birds—in non-avialan theropods.These findings demonstrate that the evolution of reproductive biology along bird-line archosaurs was a complex rather than a linear and incremental process,and suggest that some aspects of non-avialan theropod reproduction were unique to these dinosaurs.

Neutron star cooling and GW170817 constraint within quark-meson coupling models

In the present work,we used five different versions of the quark-meson coupling(QMC)model to compute astrophysical quantities related to the GW170817 event and the neutron star cooling process.Two of the models are based on the original bag potential structure and three versions consider a harmonic oscillator potential to confine quarks.The bag-like models also incorporate the pasta phase used to describe the inner crust of neutron stars.With a simple method studied in the present work,we show that the pasta phase does not play a significant role.Moreover,the QMC model that satisfies the GW170817 constraints with the lowest slope of the symmetry energy exhibits a cooling profile compatible with observational data.