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At least 19 records

Is selfing a reproductive assurance promoting polyploid establishment? Reduced fitness, leaky self‐incompatibility and lower inbreeding depression in neotetraploids

Premise Newly formed polyploids face significant obstacles to persistence and population establishment because of fitness costs of intercytotype mating. Selfing provides the opportunity to escape mate limitation, enabling production of new individuals and increasing the likelihood of fixation of new polyploid lineages. Still, association between self‐compatibility and polyploidy is not always clear. We compared self‐incompatibility and inbreeding depression in neotetraploids and their diploid progenitor to explore the direct effects of whole genome duplications on self‐incompatibility and the implications of ploidy‐driven changes for polyploid establishment. Methods Outcross and self‐pollinations were performed in diploids and synthetic neotetraploids of Jasione maritima var. maritima , and reproductive success was measured through fruit and seed production and seed germination. Self‐ and outcross offspring were grown under controlled conditions, and plant performance was measured through several fitness parameters. Results Neotetraploids showed an overall lower performance than diploids. Reproductive success was negatively affected by selfing in both cytotypes. However, greater variation in the expression of self‐incompatibility was observed in neotetraploids; additionally, developmental and physiological parameters were not affected by selfing on neotetraploids, with an overall similar fitness of outcrossed and selfed individuals, resulting in lower inbreeding depression indexes. Conclusions Neotetraploids might have benefited from selfing at initial stages after their formation. Genome duplications resulted in leaky self‐incompatibility, enabling the production of offspring under minority cytotype disadvantage with similar fitness as outcrossed offspring. Our results support theoretical assumptions that selfing might be important for neopolyploid establishment, although changes in self‐incompatibility might not be abrupt.

Siopa, Catarina↗

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗

Expanding the breeder’s toolbox for perennial grasses

With the increase in world energy demand and the environmental impacts associated with continued fossil fuel use, there is a great need for the development of alternative and sustainable fuel sources. Switchgrass ( Panicum virgatum L. ), a perennial grass native to North America, is poised to become one of the first dedicated biomass crops deployed on a large scale in the United States in large part due to its inherent high yield, adaptability and perennial nature. Current ‘cultivars’ of switchgrass are essentially undomesticated wild selections from natural populations. Thus, there is considerable potential for improvement of this emerging energy crop. Traditional breeding approaches in switchgrass have been hampered by its self-incompatibility and sensitivity to inbreeding, therefore there is a significant need to develop new tools for improved switchgrass breeding. The proposed research uses a systems biology approach to accelerate switchgrass breeding, to develop its biotechnological improvement through the generation of stress-tolerant varieties, and to establish ways to minimize the potential impact of transgenes on ecosystems. In this proposal, we will develop new breeding tools for perennial grasses and apply these tools toward improving switchgrass. Specifically, we will employ two complementary approaches to overcome the difficulty of breeding a large, polyploid, self-incompatible plant. The first approach will accelerate conventional breeding by developing a method to rapidly create doubled haploid (homozygous) lines for breeding. This approach is based on altering CENH3, a centromere-specific histone, leading to the production of haploid offspring when the centromere mutant is crossed to wild type plants. Subsequent genome doubling results in fully homozygous individuals and overcomes one of the major limitations in breeding self-incompatibile crops. These homozygous lines would allow switchgrass breeders to apply a variety of breeding approaches that have been previously impossible. The second approach is to develop tools and reagents to accelerate the biotechnological improvement of switchgrass including: modules for improved stress tolerance, a test bed to evaluate transgenes in a perennial model grass and a robust gene containment system. In order to maintain a favorable energy balance and avoid competition with food crops, dedicated biomass crops must be grown with minimal inputs (fertilizer and water) on marginal lands that are unsuited to the traditional high input agriculture necessary to produce food. Thus, abiotic stress tolerance and efficient water and nutrient use are of paramount importance. Considerable basic research has been directed at these areas and this knowledge has been used to develop transgenic approaches to greatly improve water and nutrient use efficiency. By applying these approaches to switchgrass we will rapidly increase drought tolerance and nutrient use efficiency. This approach can rapidly introduce these traits in different cultivars allowing breeders to add these traits to their elite germplasm. Since biotechnologically improved switchgrass must ultimately be grown in open fields, they must be designed to minimize the potential impact of the transgenes on non-target ecosystems. The best way to do this is to minimize gene flow from the transgenic plants. Thus, we will develop technology to introduce sterility into the transgenic plants. We will then combine this technology with the stress resistance modules to create switchgrass lines with enhanced resistance to abiotic stresses.

09 BIOMASS FUELS↗

Expanding the Breeder’s Toolbox for Perennial Grasses

With the increase in world energy demand and the environmental impacts associated with continued fossil fuel use, there is a great need for the development of alternative and sustainable fuel sources. Switchgrass (Panicum virgatum L.), a perennial grass native to North America, is poised to become one of the first dedicated biomass crops deployed on a large scale in the United States in large part due to its inherent high yield, adaptability and perennial nature. Current ‘cultivars’ of switchgrass are essentially undomesticated wild selections from natural populations. Thus, there is considerable potential for improvement of this emerging energy crop. Traditional breeding approaches in switchgrass have been hampered by its self-incompatibility and sensitivity to inbreeding, therefore there is a significant need to develop new tools for improved switchgrass breeding. The proposed research uses a systems biology approach to accelerate switchgrass breeding, to develop its biotechnological improvement through the generation of stress-tolerant varieties, and to establish ways to minimize the potential impact of transgenes on ecosystems. In this proposal, we will develop new breeding tools for perennial grasses and apply these tools toward improving switchgrass. Specifically, we will employ two complementary approaches to overcome the difficulty of breeding a large, polyploid, self-incompatible plant. The first approach will accelerate conventional breeding by developing a method to rapidly create doubled haploid (homozygous) lines for breeding. This approach is based on altering CENH3, a centromere-specific histone, leading to the production of haploid offspring when the centromere mutant is crossed to wild type plants. Subsequent genome doubling results in fully homozygous individuals and overcomes one of the major limitations in breeding self-incompatibile crops. These homozygous lines would allow switchgrass breeders to apply a variety of breeding approaches that have been previously impossible. The second approach is to develop tools and reagents to accelerate the biotechnological improvement of switchgrass including: modules for improved stress tolerance, a test bed to evaluate transgenes in a perennial model grass and a robust gene containment system. In order to maintain a favorable energy balance and avoid competition with food crops, dedicated biomass crops must be grown with minimal inputs (fertilizer and water) on marginal lands that are unsuited to the traditional high input agriculture necessary to produce food. Thus, abiotic stress tolerance and efficient water and nutrient use are of paramount importance. Considerable basic research has been directed at these areas and this knowledge has been used to develop transgenic approaches to greatly improve water and nutrient use efficiency. By applying these approaches to switchgrass we will rapidly increase drought tolerance and nutrient use efficiency. This approach can rapidly introduce these traits in different cultivars allowing breeders to add these traits to their elite germplasm. Since biotechnologically improved switchgrass must ultimately be grown in open fields, they must be designed to minimize the potential impact of the transgenes on non-target ecosystems. The best way to do this is to minimize gene flow from the transgenic plants. Thus, we will develop technology to introduce sterility into the transgenic plants. We will then combine this technology with the stress resistance modules to create switchgrass lines with enhanced resistance to abiotic stresses.

09 BIOMASS FUELS↗

Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores

Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.

59 BASIC BIOLOGICAL SCIENCES↗

Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass ( Thinopyrum intermedium )

Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. Finally, these findings elucidate pathways and possible hurdles in the domestication of IWG.

59 BASIC BIOLOGICAL SCIENCES↗

Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass

Abstract A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum ( Paspalum vaginatum ) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum . Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation.

59 BASIC BIOLOGICAL SCIENCES↗

Wormholes without averaging

After averaging over fermion couplings, SYK has a collective field description that sometimes has “wormhole” solutions. We study the fate of these wormholes when the couplings are fixed. Working mainly in a simple model, we find that the wormhole saddles persist, but that new saddles also appear elsewhere in the integration space — “half-wormholes.” The wormhole contributions depend only weakly on the specific choice of couplings, while the half-wormhole contributions are strongly sensitive. The half-wormholes are crucial for factorization of decoupled systems with fixed couplings, but they vanish after averaging, leaving the non-factorizing wormhole behind.

1/N Expansion↗

Temperature-Agnostic Pt/Au Ohmic Contacts on n -Type Gallium Nitride for Self-Aligned MOSFETs

Five alternative metals are investigated as ohmic contacts to n-GaN including Cr/Au, Mo/Au, Pt/Au, Pd/Au, and Ge/Au. Ti-based contacts are traditionally used for ohmic contacts on n-GaN. However, conventional Ti/Al/Ni/Au metallization is found to be incompatible with a self-aligned process for GaN trench MOSFETs due to wet etch restrictions. Therefore, an alternative metallization is needed that is unreactive to the etch chemistry used in the self-aligned process. Additionally, the contact should remain ohmic following anneal at 900 °C so that contact formation can precede the anneal required for p-dopant activation. Here, in the present work, an n-GaN bilayer, consisting of a thin heavily doped contact layer (n 0 = 1 × 10 20 cm −3 ) atop a thick lesser doped layer, is used to demonstrate ohmic contacts of alternative metals with low specific contact resistance and extended thermal budget. Cr/Au ohmic contacts are demonstrated up to anneal temperatures of 800 °C, an increase of 200 °C compared to the highest known reports for Cr/Au contacts on n-GaN. Pt/Au metallization is demonstrated as an ohmic contact to n-GaN for the first time and exhibits true temperature-agnostic behavior up to anneal temperatures of 900 °C with specific contact resistance that is near parity with Ti/Al/Ni/Au. The temperature-agnostic behavior of Pt/Au ohmic contacts on the n-GaN bilayer, in addition to chemical compatibility with the self-aligned process, positions Pt/Au contacts as a key enabling element for self-aligned trench MOSFETs on GaN.

Reilly, Kevin James [Sandia National Laboratories ↗

On the Nature of Valence Charge and Spin Excitations via Multi-Orbital Hubbard Models for Infinite-Layer Nickelates

Building upon the recent progress on the intriguing underlying physics for the newly discovered infinite-layer nickelates, in this article we review an examination of valence charge and spin excitations via multi-orbital Hubbard models as way to determine the fundamental building blocks for Hamiltonians that can describe the low energy properties of infinite-layer nickelates. We summarize key results from density-functional approaches, and apply them to the study of x-ray absorption to determine the valence ground states of infinite-layer nickelates in their parent form, and show that a fundamental d 9 configuration as in the cuprates is incompatible with a self-doped ground state having holes in both d x 2 - y 2 and a rare-earth-derived axial orbital. When doped, we determine that the rare-earth-derived orbitals empty and additional holes form low spin (S = 0) d 8 Ni states, which can be well-described as a doped single-band Hubbard model. Using exact diagonalization for a 2-orbital model involving Ni and rare-earth orbitals, we find clear magnons at 1/2 filling that persist when doped, albeit with larger damping, and with a dependence on the precise orbital energy separation between the Ni- and rare-earth-derived orbitals. Taken together, a full two-band model for infinite-layer nickelates can well describe the valence charge and spin excitations observed experimentally.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Self-Assembly of Flexible Linear–Semiflexible Bottlebrush–Flexible Linear Triblock Copolymers

Block copolymer (BCP) self-assembly is a fundamental process in which incompatible blocks spontaneously form organized microstructures with broad practical applications. Classical understanding is that the domain spacing is limited by the contour length of the polymer backbone. Here, using a combination of molecular design, chemical synthesis, small-/wide-angle X-ray scattering, transmission electron microscopy, and electron tomography, we discover that this molecular picture does not hold for architecturally semiflexible BCPs. For strongly segregated linear–semiflexible bottlebrush–linear triblock copolymers, the size of the bottlebrush domain can be twice the bottlebrush backbone contour length. The mechanism of such anomalous self-assembly is likely that the interfacial repulsion between the incompatible blocks is large enough to pull a part of the linear end blocks into the bottlebrush domain. This effectively increases the bottlebrush domain size. Moreover, the semiflexible bottlebrush widens the regime for the cylinder morphology that is associated with the volume fraction of the end blocks fC SFB ∈ (0.10, >0.41). This window is much wider than that for flexible linear BCPs, fC F ∈ (0.14, 0.35), and that predicted by the recent self-consistent field theory for linear-bottlebrush BCPs of the same chemistry and molecular architecture. Finally, our experimental findings reveal previously unrecognized mechanisms for the self-assembly of architecturally complex BCPs.

36 MATERIALS SCIENCE↗

Spontaneous assembly of hierarchical phases

We report the grand promise of self-assembly is the creation of target nanostructures through spontaneous molecular organization, a process that is — in principle — simpler and more scalable than laborious top-down nanofabrication methods. Yet self-assembly faces a fundamental challenge: the structures that form thermodynamically tend to minimize surface area and maximize symmetry; the most readily-accessible structures are thus quite simple. Block copolymer (BCP) self-assembly, for example, takes advantage of the chemical incompatibility along a polymer backbone to drive local phase separation; frustrated assembly leads to a nanoscale morphology whose unit cell is dictated by chain architecture. Canonical BCPs (linear chains with two blocks) form alternating lamellae and hexagonally-packed cylinders in a straightforward manner; but more exotic phases require additional control, for example directing the assembly using external forces, such as shear or chemical templates. An elegant alternative is to use synthetic methods to design more sophisticated chain architectures, which may give rise to new morphologies. An outstanding challenge is to achieve morphological control without undue synthetic burden. Sun et al. now report in Nature Nanotechnology the design and synthesis of novel triblock copolymers that give rise to structural order at multiple length scales, thereby forming complex and hierarchical nanoscale phases.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Lines of Bound States in the Continuum in Monodisperse Microsphere Structures

Incorporating epitaxially grown active semiconductor media into self-assembled microsphere crystals has remained a major challenge as the curved geometry of the spheres is incompatible with conventional planar growth and patterning techniques. As a result, active photonic devices based on such self-assembled structures, which have other desirable properties such as enabling the rapid assembly of large area systems, have been elusive. Here, we numerically demonstrate an alternative route to creating high-Q resonances in microsphere-based nanophotonic assemblies compatible with standard optical gain materials. We show that close-packed layers of monodisperse microspheres can exhibit symmetry bandgaps, regardless of their layer stacking order. Thus, this microsphere environment can be used to create lines of bound states in the continuum (BICs) of an embedded slab made of active material. Using a realistic ZnS@SiO 2 (core-shell) architecture and sphere diameters compatible with scalable colloidal assembly, we predict sharp spectral features in angle-resolved transmission that trace these lines of BICs and persist in the presence of some fabrication disorder. Altogether, in enabling the integration of unpatterned epitaxial gain slabs with large-area colloidal microsphere assemblies, this approach opens a practical path toward active, dynamically reconfigurable photonic devices that leverage BIC physics for narrow-linewidth lasing and enhanced light–matter interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Nanotubes Growth by Self-Assembly of DNA Strands at Room Temperature

Artificial biomolecular nanotubes are a promising approach to building materials mimicking the capacity of the cellular cytoskeleton to grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated a variety of self-assembling nanotubes with programmable, robust features and morphological similarities to actual cytoskeleton components. However, their production typically requires thermal annealing, which not only poses a general constraint on their potential applications but is also incompatible with physiological conditions. Here, we demonstrate that DNA nanotubes can self-assemble from a simple mixture of five short DNA strands at constant room temperature, growing for extended periods of time in bulk conditions as well as under confinement. Assembly is achieved using a monovalent salt buffer, which ensures a faithful nanoscale arrangement and avoids nanotube aggregation. We observe the formation of individual nanotubes up to 20 days with a diameter of 22 ± 4 nm and length of several tens of micrometers. We finally encapsulate the strands in microsized compartments, such as water-in-oil microdroplets and giant unilamellar vesicles serving as simple cell models. Notably, nanotubes not only isothermally self-assemble directly inside the microcompartments but also self-organize into dynamic higher-order structures resembling rings and dynamic networks. Our study provides an advantageous method for in situ assembly of programmable biomolecular scaffolds and materials using synthetic DNA strands without requirements of thermal treatment.

Chemistry↗

3D-printable engineered cementitious composites (3DP-ECC): Fresh and hardened properties

3D printing (3DP) is an emerging digital construction method for concrete materials. A major impediment to efficient 3D concrete printing (3DCP) is the need for steel reinforcement, the placement of which is incompatible with the 3DP process. Unlike plain concrete, ductile self-reinforced engineered cementitious composite (ECC) holds promise to remove the dependence on steel reinforcement. The objective of this research is to develop a 3D-printable ECC (3DP-ECC). The fresh rheological and hardened mechanical properties of 3DP-ECC are investigated. The robotically printed tensile specimens demonstrated the familiar multiple microcracking and strain-hardening behavior of conventionally cast ECC. Significant orthotropy is revealed in the compressive properties. The interface between printed layers is found to be toughened by a printed groove-tongue joint. The developed 3DP-ECC was used to print a twisted column with 150 layers, reaching a height of 1.5 m. This research lays the groundwork for efficient robotically 3D-printed structures of complex shapes.

36 MATERIALS SCIENCE↗

Photothermally Directed Assembly of Block Copolymers

Block copolymers self-assemble into nanoscale morphologies, spontaneously ordering under thermal annealing conditions owing to the chemical incompatibility between the blocks. Although the morphologies that form can be rationalized based on equilibrium arguments, the structures seen experimentally are strongly influenced by kinetic effects including process history. Recently, a variety of photothermal processing techniques have been used to control block copolymer ordering. Photothermal methods provide access to extreme conditions, including high temperatures, large heating rates, and sharp thermal gradients. Furthermore, this can be used to greatly accelerate block copolymer ordering kinetics, to pattern material order, or to probe fundamental aspects of self-assembly by exploring process histories.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Excitation and Excavation of the Claws of the Southern Crab

We show that the Southern Crab (aka Hen2–104) presents an auspicious opportunity to study the form and speed of the invisible winds that excavate and shock the lobes of various types of bipolar nebulae associated with close and highly evolved binary stars. A deep three-color image overlay of Hen2–104 reveals that the ionization state of its lobe edges, or “claws,” increases steadily from singly to doubly ionized values with increasing wall latitude. This “reverse” ionization pattern is unique among planetary nebulae (and similar objects) and incompatible with UV photoionization from a central source. We show that the most self-consistent explanation for the ionization pattern is shock ionization by a fast (~600 km s -1 ) “tapered” stellar wind in which the speed and momentum flux of the wind increase with equatorial latitude. We present a hydrodynamic simulation that places the latitude-dependent form, the knotty walls, and the reverse ionization of the outer lobes of Hen2–104 into a unified context.

79 ASTRONOMY AND ASTROPHYSICS↗