The genome of Populus alba x Populus tremula var. glandulosa clone 84K

Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Effect of grain and secondary phase morphologies in the mechanical and damping behavior of Al7075 alloys

The present study evaluates the role of the microstructure in the static and dynamic mechanical behavior of as-cast Al7075 alloy promoted by ultrasonic treatment (US) during solidification. The characterization of samples revealed that US treatment promoted grain and intermetallics refinement, changed the shape of the intermetallic phases (equilibrium phases of soluble M and/or T (Al, Cu, Mg, Zn) and their insoluble Al-Cu-Fe compounds) and lead to their uniform distribution along the grain boundaries. Consequently, the mechanical properties and damping capacity above critical strain values were enhanced by comparison with values obtained for castings produced without US vibration. This results suggest that the grain and secondary phases refinement by US can be a promising solution to process materials to obtain high damping and high strength characteristics.This research was supported by FEDER/COMPETE funds and by national funds through FCT - Portuguese Foundation for Science and Technology and was developed on the aim of the research Post-Doctoral grant SFRH/BPD/76680/2011. Also, this work has been supported by the FCT in the scope of the project: UID/EEA/04436/2013.info:eu-repo/semantics/publishedVersio

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science

Self-assembly enables simple structure organic photovoltaics via green-solvent and open-air-printing: Closing the lab-to-fab gap

The ultimate goal of organic solar cells (OSCs) is to deliver cheap, stable, efficient, scalable, and eco-friendly solar-to-power products contributing to the global carbon neutral. However, simultaneously balancing these five critical factors of OSCs toward commercialization is extremely challenging. Herein, a green-solvent-processable and open-air-printable self-assembly strategy is demonstrated to synchronously simplify the device architecture, improve the power conversion efficiency (PCE) and enhance the shelf, thermal as well as light illumination stability of OSCs. The cathode interlayer (CIL)-free self-assembled OSCs exhibit the PCE of 15.5%, higher than that of traditional inverted OSCs of 13.0%, which is among the top values for both CIL-free self-assembled OSCs and open-air blade-coated bulk-heterojunction OSCs. The remarkable enhancements are mainly ascribed to the finely selfassembly, subtly controlled donor/acceptor aggregation rate, and delicately manipulated vertical morphology. Besides, this strategy enables 13.2% efficiency on device area of 0.98 cm(2), implying its potential for scalability. These findings demonstrate that this strategy can close the lab-to-fab gap of OSCs toward commercialized cheap, stable, efficient, scalable, and eco-friendly OSCs

Activated Ribonucleotides Undergo a Sugar Pucker Switch upon Binding to a Single-Stranded RNA Template

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5′-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3′-<i>endo</i> sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2′-<i>endo</i> conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2′-<i>endo</i> and C3′-<i>endo</i> conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5′-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2′-<i>endo</i> in the free state to C3′-<i>endo</i> upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2′-deoxyribonucleotides maintain a C2′-<i>endo</i> sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions

Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Background Nicotiana tabacum is an important economic crop. Topping, a common agricultural practice employed with flue-cured tobacco, is designed to increase leaf nicotine contents by increasing nicotine biosynthesis in roots. Many genes are found to be differentially expressed in response to topping, particularly genes involved in nicotine biosynthesis, but comprehensive analyses of early transcriptional responses induced by topping are not yet available. To develop a detailed understanding of the mechanisms regulating nicotine biosynthesis after topping, we have sequenced the transcriptomes of Nicotiana tabacum roots at seven time points following topping. Results Differential expression analysis revealed that 4830 genes responded to topping across all time points. Amongst these, nine gene families involved in nicotine biosynthesis and two gene families involved in nicotine transport showed significant changes during the immediate 24 h period following topping. No obvious preference to the parental species was detected in the differentially expressed genes (DEGs). Significant changes in transcript levels of nine genes involved in nicotine biosynthesis and phytohormone signal transduction were validated by qRT-PCR assays. 549 genes encoding transcription factors (TFs), found to exhibit significant changes in gene expression after topping, formed 15 clusters based on similarities of their transcript level time-course profiles. 336 DEGs involved in phytohormone signal transduction, including genes functionally related to the phytohormones jasmonic acid, abscisic acid, auxin, ethylene, and gibberellin, were identified at the earliest time point after topping. Conclusions Our research provides the first detailed analysis of the early transcriptional responses to topping in N. tabacum, and identifies excellent candidates for further detailed studies concerning the regulation of nicotine biosynthesis in tobacco roots.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]