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At least 145 records · Page 8

Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence–absence variation on a local scale. This diversity is invisible to classical reference-based strategies and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.

Thlaspi arvense

The magnetic evolution of the activity complex AR 7260: A roadmap

The active region NOAA 7260 rotated onto the north solar hemisphere as a mature bipole: a dominant negative-polarity sunspot with trailing plage and scattered small spots in attendance. The dominant p spot itself had strong magnetic fields and covered almost 400 x 10(exp -6) of a solar hemisphere. For a period of seven days beginning 14 August, 1992 this active region displayed rapid and drastic evolution: no fewer than 50 magnetic bipoles emerged in the area trailing the large sunspot, increasing the region's magnetic flux by more than 10(exp 22) Mx. This new group of sunspots formed a complex Beta gamma delta configuration with two delta spots and a high degree of magnetic shear. This region was very well observed by Yohkoh and various ground-based instruments. It presented opportunities to study new emerging flux, flares, and also the decay of a large sunspot. For the benefit of later studies we present a description of the global characteristics of this active region, a detailed 'roadmap' of its evolution during disk passage including the development of the two delta regions. We compare proper motion trends and flaring activity to observations of other delta-spots reported in the literature. We also comment on the observed outflow of magnetic elements from the decaying p spot.

Leka, K. D.

NEUTRINO EMISSION PROCESSES, STELLAR EVOLUTION AND SUPERNOVA. PART II.

When the internal temperature of a star exceeds 1 BK (109 °K) the evolution is very rapid. The time scale is around 3000 years. Energy dissipated by emission of neutrinos is several orders of magnitude higher than that by optical radiation. Neutrinos have exceedingly long mean free path (∼10(exp 20) gram/cm(exp 2)) and they will escape as soon as they are produced. The star will contract to release gravitational energy to make up the energy lost to neutrinos and the internal temperature will rise to comply with the virial theorem. It is possible in this fast evolutionary phase, to neglect optical radiations all together as compared with the neutrino radiation. A set of structural equations is thus obtained. The envelope is replaced by boundary conditions. A simple model is constructed to illustrate our approach.

Star

Probing the limits of genetic recoding using multi-omics-guided evolution

Engineering the genetic code—by reassigning multiple of the 64 natural codons—enables making organisms resistant to all viruses, preventing genetic information exchange, and allowing the biosynthesis of genetically encoded unnatural polymers. However, synonymous codon replacement—recoding—is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using genome synthesis, directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple synthetic Escherichia coli genomes. We construct six partially recoded E. coli strains bearing up to 45.8% of a synthetic genome with a deleterious 57-codon genetic code. As our analyses revealed widespread defects—including unassigned codons in Syn61 and Syn57—we apply multi-omics to revise our genome design and mitigate defects. Using multi-omics, we show that recoding induces transcriptional and translational changes leading to fitness defects under hundreds of conditions. Finally, we develop a multi-omics-guided evolution strategy that rapidly restores fitness, enabling genome synthesis with radical changes.

Nyerges, Akos [Harvard Medical School, Boston, MA

Binary vector copy number engineering improves Agrobacterium -mediated transformation

The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that influence copy number and screen for mutants that improve Agrobacterium-mediated transformation (AMT) efficiency. By introducing these mutations into binary vectors within the plasmid backbone used for AMT, we observe improved transient transformation of Nicotiana benthamiana in four diverse tested origins (pVS1, RK2, pSa and BBR1). For the best-performing origin, pVS1, we isolate higher-copy-number variants that increase stable transformation efficiencies by 60–100% in Arabidopsis thaliana and 390% in the oleaginous yeast Rhodosporidium toruloides. Our work provides an easily deployable framework to generate plasmid copy number variants that will enable greater precision in prokaryotic genetic engineering, in addition to improving AMT efficiency.

59 BASIC BIOLOGICAL SCIENCES

Hydraulic jumps in 'viscous' accretion disks

It is proposed that the dissipative process necessary for rapid accretion disk evolution is driven by hydraulic jump waves on the surface of the disk. These waves are excited by the asymmetric nature of the central rotator (e.g., neutron star magnetosphere) and spiral out into the disk to form a pattern corotating with the central object. Disk matter in turn is slowed slightly at each encounter with the jump and spirals inward. In this process, the disk is heated by true turbulence produced in the jumps. Additional effects, such as a systematic misalignment of the magnetic moment of the neutron star until it is nearly orthogonal, and systematic distortion of the magnetosphere in such a way as to form an even more asymmetric central 'paddle wheel', may enhance the interaction with inflowing matter. The application to X-ray sources corresponds to the 'slow' solutions of Ghosh and Lamb, and therefore to rms magnetic fields of about 4 x 10 to the 10th gauss. Analogous phenomena have been proposed to act in the formation of galactic spiral structure.

Michel, F. C.

Photometry of variable AFGL sources

Results of infrared photometric observations of 63 AFGL sources over the past 9 years are presented. Using these data together with previous measurements of these stars, pulsation periods and mean photometric characteristics are determined. These stars are found to lie midway between optically identified Mira variables and the radio-luminous OH/IR stars in their period distribution and photometric properties. For the sample as a whole, there is no evidence for sudden or transient behavior such as a switch in pulsation mode. Rather, these stars suggest rapid, but continuous, evolution from shorter period Miras with weak mass loss to longer periods and larger mass-loss rates. The carbon-rich stars in the sample have the same period distribution as the oxygen-rich stars. None of the carbon stars have periods as long as those of the very long period radio-luminous OH/IR stars.

Jones, Terry Jay

Radiative properties of a plasma moving across a magnetic field. I - Theoretical analysis. II - Numerical results

The early-time evolution of plasmas moving across a background magnetic field is addressed with a 2D model in which a plasma cloud is assumed to have formed instantaneously with a velocity across a uniform background magnetic field and with a Gaussian density profile in the two dimensions perpendicular to the direction of motion. This model treats both the dynamics associated with the formation of a polarization field and the generation and propagation of electromagnetic waves. In general, the results indicate that, to zeroth order, the plasma cloud behaves like a large dipole antenna oriented in the direction of the polarization field which oscillates at frequencies defined by the normal mode of the system. Radiation damping is shown to play an important role in defining the plasma cloud evolution, causing a rapid decay of the polarizaiton field and a loss of plasma kinetic energy and momentum on time scales comprable to several ion gyroperiods. Scaling laws are derived for the plasma momentum and energy loss rates, and predictions for the braking time, the amplitude and spectrum of the radiation field, and the total radiated power are presented for conditions relevant to the recent Combined Release and Radiation Effects Satellite experiments.

Roussel-Dupre, Robert

A proposed research program in information processing

The goal of the Formalized Software Development (FSD) project was to demonstrate improvements productivity of software development and maintenance through the use of a new software lifecycle paradigm. The paradigm calls for the mechanical, but human-guided, derivation of software implementations from formal specifications of the desired software behavior. It relies on altering a system's specification and rederiving its implementation as the standard technology for software maintenance. A system definition for this paradigm is composed of a behavioral specification together with a body of annotations that control the derivation of executable code from the specification. Annotations generally achieve the selection of certain data representations and/or algorithms that are consistent with, but not mandated by, the behavioral specification. In doing this, they may yield systems which exhibit only certain behaviors among multiple alternatives permitted by the behavioral specification. The FSD project proposed to construct a testbed in which to explore the realization of this new paradigm. The testbed was to provide operational support environment for software design, implementation, and maintenance. The testbed was proposed to provide highly automated support for individual programmers ('programming in the small'), but not to address the additional needs of programming teams ('programming in the large'). The testbed proposed to focus on supporting rapid construction and evolution of useful prototypes of software systems, as opposed to focusing on the problems of achieving production quality performance of systems.

Schorr, Herbert

The solar minimum X2.6/1B flare and CME of 9 July 1996: Solar data - Pt. 1

The solar observations from GOES-8, the Solar and Heliospheric Observatory (SOHO), and the Yohkoh satellite concerning the events of the X-class flare are discussed. The Michelson Doppler imager (MDI) magnetometer shows a new region of magnetic activity in AR 7978. The rapid development and evolution of this region is shown by the MDI and the extreme-ultraviolet Doppler telescope (EDT) data. The coronal mass ejections (CMEs) observed using coronagraphs are presented. The possible association between the CME and the X-flare is considered.

Andrews, M. D.

Multiple Nebular Gas Reservoirs Recorded by Oxygen Isotope Variation in a Spinel-rich CAI in CO3 MIL 090019

We conducted NanoSIMS O-isotopic imaging of a primitive spinel-rich CAI spherule (27-2) from the MIL 090019 CO3 chondrite. Inclusions such as 27-2 are proposed to record inner nebula processes during an epoch of rapid solar nebula evolution. Mineralogical and textural analyses suggest that this CAI formed by high temperature reactions, partial melting, and condensation. This CAI exhibits radial O-isotopic heterogeneity among multiple occurrences of the same mineral, reflecting interactions with distinct nebular O-isotopic reservoirs.

Simon, J. I.

Along-Orbit Analysis of GRACE Follow-On Inter-Satellite Laser Ranging Measurements for Sub-Monthly Surface Mass Variations

We examined the sensitivity of GRACE Follow-On (GRACE-FO) laser ranging interferometer (LRI) measurements to sub-monthly time-variable gravity (TVG) signals caused by transient, high-frequency mass changes in the Earth system. GRACE-FO LRI provides complementary inter-satellite ranging measurements with higher precision over a wider range of frequencies than the baseline K-band microwave ranging system. The common approach for studying mass variation relies on the inverted TVG or mascon solutions over a period of, for example, one month or 10 days which are adversely affected by temporal aliasing and/or smoothing. In this article, we present the alternative along-orbit analysis methodology in terms of line-of-sight gravity difference (LGD) to fully exploit the higher precision LRI measurements for examination of sub-monthly mass changes. The discrepancy between “instantaneous” LGD LRI observations and monthly mean LGD (from Level-2 data) at satellite altitude indicates the sub-monthly gravitational variability not captured by monthly-mean solutions. In conjunction with the satellite ocean altimetry observations, high frequency non-tidal atmosphere and ocean models, and hydrology models, we show that the LGD LRI observations detect the high-frequency oceanic mass variability in the Argentine Basin and the Gulf of Carpentaria, and sub-monthly variations in surface (river) water in the Amazon Basin. We demonstrate the benefits gained from repeat ground track analysis of GRACE-FO LRI data in the case of the Amazon surface water flow. The along-orbit analysis methodology based on LGD LRI time series presented here is especially suitable for quantifying temporal and spatial evolution of extreme, rapidly changing mass variations.

Khosro Ghobadi-Far

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES

Stellar models and the brightening of P Cygni

P Cygni is currently in the transition phase between core hydrogen and helium burning. The behavior of the stellar envelope in this phase is strongly affected by the intermittant dominance of hydrogen shell burning. We perform detailed stellar evolution calculations of this rapid transition phase using the most recent Livermore opacities. We find that observations and stellar evolution models agree very well if the initial main-sequence mass of P Cygni was about 60 +/- 5 solar masses. Depending on the mass-loss rate, P Cygni's current mass could be as low as 50 solar masses, which is still about a factor of 2 higher than that predicted by the radiation driven wind theory. Our calculations seem to favor the Schwarzschild criterion for convection over the Ledoux criterion in conjunction with semiconvection.

El Eid, Mounib F.

AT2025ulz and S250818k: Zooming in with the Hubble Space Telescope

AT2025ulz is an optical/near-infrared transient discovered during follow-up of the candidate gravitational wave (GW) event S250818k. Its young age (≲1 day), rapid decline, and strong color evolution over the first 48 hr classify it as a potential kilonova candidate. In this work, we present the results of our observing campaign, carried out with the Gran Telescopio Canarias and the Hubble Space Telescope (HST). Although the early time evolution of AT2025ulz resembles some aspects of a kilonova, its rapid onset (∼3 hr after the GW trigger) and luminosity (a factor of ∼5 brighter than AT2017gfo in g band) are difficult to reproduce. Only a small subset of our kilonova models matches its multicolor light curve, and the inferred ejecta mass is uncomfortably large given the low chirp mass (≲0.87 M ⊙ ) of the GW candidate. HST observations place the transient within a nearby (z = 0.08489) spiral galaxy with ongoing star formation and measure a color (F336W − F160W ≈ 1.4 mag) that is too blue to match with a kilonova. Our data support the classification of AT2025ulz as a supernova, initially undergoing a shock-cooling phase and later entering its photospheric phase and spectroscopically identified via its broad absorption features.

79 ASTRONOMY AND ASTROPHYSICS

Supervised Autonomous Assembly to Create and Evolve Persistent Assets

Supervised autonomous assembly (SAA) will create a paradigm shift in the planning and design of future persistent assets (PAs), both in near zero-g environments and on planetary surfaces. SAA refers to an autonomy approach that has the benefits of autonomous assembly as well as the benefits provided by a supervisor (operator) who is available to resolve unexpected situations. SAA provides both increased design freedom as well as reduced programmatic risk. SAA enables evolution of future PAs over decades as in-space operations transition from single purpose missions to creation of PAs, such as laboratories and experimental stations which more closely resembling terrestrial laboratories that can easily adapt and evolve to new missions leveraging repeated visits to the PA. The ability to evolve enables PAs to rapidly respond to changing objectives resulting from new questions as our understanding improves. A recently initiated National Aeronautics and Space Administration (NASA) project in the Space Technology Mission Directorate (STMD) Game Changing Development (GCD) Program called the Precision Assembled Space Structure (PASS), leverages the advantages of SAA to develop technologies that enable efficient creation and evolution of hexagonal topologies; both planar (example: fuel depots) and curved (examples: telescopes and shelters). PASS will be used to provide context for the philosophy and concepts discussed as well as the decision and selections made. PASS objectives are: a) Develop confidence in SAA and on-orbit servicing, assembly and manufacturing (OSAM) technologies by executing a test campaign that uses a path-to-flight autonomous precision assembly process directly applicable to future space telescopes. b) Test autonomous technologies including automated path planning and error recovery, to emphasize a robust approach that relies on generic robots and special purpose tools. c) Validate critical component models using a digital twin that includes the assembled primary mirror support structure and assembly process. A digital twin is a high-fidelity simulation of the asset capable of predicting the on-orbit performance. The paper concludes after identifying the critical need for a modest assembly flight experiment to validate and develop confidence in the SAA paradigm, thus accelerating adoption of the benefits described. SAA is a game changing paradigm that enhances the ability of an organization to infuse new technology through rapid evolution of PAs while leveraging OSAM technologies.

Structural Modeling

Long-term orbital evolution of short-period comets found in Project Cosmo-DICE

Orbital evolutions of about 160 short-period (SP) comets are numerically integrated for 4400 years in the framework of a realistic dynamical model. By the round-trip error in closure test, a reliable time space of the integrated orbits is estimated for each comet. Majority of the SP comets with their Tisserand's constant(J) between 2.8 and 3.1 are found to evolve within the past 1000-2000 years from the orbits whose perihelia are near the Jovian orbit to the orbits with perihelia of 1-2 AU. This evolution is much more rapid than that expected from Monte Carlo simulations based on symmetric distribution of planetary perturbations, thus suggesting that asymmetry of perturbation distribution play an important role in cometary evolution. Several comets are shown to evolve from the near-Saturn orbits and then to be handed over under the control of Jupiter. We also find that a few comets were captured from long-period orbits (a = 75-125 AU) via only a few close encounters with Jupiter. It is confirmed that the captured SP comets of low-inclination with 2.7 less than J less than 3.1 show more or less strong chaotic behavior. On the other hand, comets with longer orbital period and/or of high inclination reveal slow or quasi-periodic orbital evolution.

Nakamura, Tsuko

A proposed production model of rapid subauroral ion drifts and their relationship to substorm evolution

The temporal relationship between subauroral ion drifts (SAIDs) and the phases of an auroral substorm is examined on the basis of multisatellite data. The time of expansive phase onset is identified and the time at which recovery begins is estimated. SAIDs are found to typically occur well after substorm onset (more than 30 min), during the substorm recovery phase. Substantial westward ion drifts and field-aligned currents are observed well equatorward of the auroral oval during the expansion phase of a substorm, but the drifts lack the narrow spike signature associated with SAIDs. A phenomenological model of SAID production that qualitatively agrees with the observed ionospheric signatures and substorm temporal relationship is proposed.

Anderson, P. C.