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At least 1,297 records · Page 72

Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.

59 BASIC BIOLOGICAL SCIENCES↗

1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae

Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae , encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1.45 Å, including nearly the entire RCL in one of the two molecules in the asymmetric unit. The structure reveals that the SRPN18 RCL is extremely short and constricted, a feature associated with noncanonical inhibitors or non-inhibitory serpin superfamily members. Furthermore, the SRPN18 RCL does not contain a suitable protease target site and contains a large number of prolines. The SRPN18 structure therefore reveals a unique RCL architecture among the highly conserved serpin fold.

36 MATERIALS SCIENCE↗

Xanthos-Lake Model Source Code

This repository contains the source code for Xanthos-Lake, a lake-modeling extension of the Xanthos framework that introduces a coupled lake component comprising the Xanthos-Lake Snow and Ice Model (xLSIM) and the Xanthos-Lake Water Balance Model (xLWBM). xLSIM is a basin-aware machine-learning model for lake snow, ice, and thermal conditions. It predicts monthly lake ice thickness, snow depth, snow-cover fraction, mixing-layer temperature, and lake ice fraction from meteorological forcing and lake surface-area information. It uses sequence-based deep-learning architectures, including Transformer and hybrid Long Short-Term Memory–Transformer (LSTM–Transformer) models, together with seasonal encoding, multi-lake learning, physical masking, and basin-level cryospheric and non-cryospheric classification. The training workflow uses Ray for scalable execution and includes optional Ray Tune hyperparameter optimization. Model predictions, observations, diagnostics, and feature-importance outputs are written in NetCDF. xLWBM is the water-balance component of the new lake framework. It simulates monthly lake storage, surface area, evaporation, inflow, outflow, and lake–groundwater exchange. It combines physical water-balance equations with calibrated bathymetric relationships, weir-based outlet flow, modified Penman open-water evaporation, groundwater head relaxation, Penman–Monteith snow and ice sublimation, and snow, ice, and thermal conditions supplied by xLSIM. The model calibrates lake parameters against satellite-derived surface-area data, using evaporation-based calibration where surface-area data are unavailable, and supports small, medium, and large lake classes. For large lakes, xLWBM is integrated with the managed-routing workflow so that lake storage and outflow interact directly with downstream river routing and reservoir operations. Together, xLSIM and xLWBM provide Xanthos with a coupled lake-modeling capability. xLSIM supplies the snow, ice, and thermal conditions that affect lake evaporation and snow- and ice-related water exchanges, while xLWBM translates those conditions into dynamic lake storage, surface area, evaporation, and discharge. In return, xLWBM supplies evolving lake surface area to xLSIM. This coupling enables Xanthos to represent lakes as active hydrologic components within basin-scale water-availability and routing simulations.

Machine Learning↗

The location of the site of energy release in a solar X-ray subflare

A rapid sequence of high-resolution X-ray photographs was obtained by the S-054 X-ray Telescope Experiment on Skylab on 1973 September 1. During the course of this observation, photographs were obtained of a flarelike brightening in a simple, bipolar active region. Analysis reveals the following facts. The event had the form of a small, elongated bright feature whose narrowest dimension was less than seconds of arc. The brightness peak of the flarelike brightening was located within seconds of arc of the center of brightness of a preexisting loop structure that crossed the magnetic neutral line. This loop was observed to brighten gradually beginning approximately 10 minutes prior to the flarelike event. During the rise of the event, the 2-17 A X-ray brightness of the center of the subflare core rose by over a factor of 10 in a time period of 196 seconds or less.

Petrasso, R. D.↗

Spectrophotometry of Wolf-Rayet stars. I - Continuum energy distributions

All available low-resolution IUE spectra are assembled for Galactic, LMC, and SMC W-R stars and are merged with ground-based optical and NIR spectra in order to collate in a systematic fashion the shapes of these energy distributions over the wavelength range 0.1-1 micron. They can be consistently fitted by a power law of the form F(lambda) is approximately equal to lambda exp -alpha over the range 1500-9000 A to derive color excesses E(B-V) and spectral indices by removing the 2175-A interstellar absorption feature. The WN star color excesses derived are found to be in good agreement with those of Schmutz and Vacca (1991) and Koesterke et al. (1991). Significant heterogeneity in spectral index values was generally seen with any given subtype, but the groups consisting of the combined set of Galactic and LMC W-R stars, the separate WN and WC sequences, and the Galactic and LMC W-R stars all showed a striking and consistent Gaussian-like frequency distribution of values.

Morris, Patrick W.↗

Ultra-Compact Motor Controller

This invention is an electronically commutated brushless motor controller that incorporates Hall-array sensing in a small, 42-gram package that provides 4096 absolute counts per motor revolution position sensing. The unit is the size of a miniature hockey puck, and is a 44-pin male connector that provides many I/O channels, including CANbus, RS-232 communications, general-purpose analog and digital I/O (GPIO), analog and digital Hall inputs, DC power input (18-90 VDC, 0-l0 A), three-phase motor outputs, and a strain gauge amplifier. This controller replaces air cooling with conduction cooling via a high-thermal-conductivity epoxy casting. A secondary advantage of the relatively good heat conductivity that comes with ultra-small size is that temperature differences within the controller become smaller, so that it is easier to measure the hottest temperature in the controller with fewer temperature sensors, or even one temperature sensor. Another size-sensitive design feature is in the approach to electrical noise immunity. At a very small size, where conduction paths are much shorter than in conventional designs, the ground becomes essentially isopotential, and so certain (space-consuming) electrical noise control components become unnecessary, which helps make small size possible. One winding-current sensor, applied to all of the windings in fast sequence, is smaller and wastes less power than the two or more sensors conventionally used to sense and control winding currents. An unexpected benefit of using only one current sensor is that it actually improves the precision of current control by using the "same" sensors to read each of the three phases. Folding the encoder directly into the controller electronics eliminates a great deal of redundant electronics, packaging, connectors, and hook-up wiring. The reduction of wires and connectors subtracts substantial bulk and eliminates their role in behaving as EMI (electro-magnetic interference) antennas. A shared knowledge by each motor controller of the state of all the motors in the system at 500 Hz also allows parallel processing of higher-level kinematic matrix calculations.

Townsend, William T.↗

Features of the Emission Spectra of Ni-Like Ions. Application to Calculating the Wavelengths of Self-Photo-Pumped X-Ray Lasers

The energy levels and probabilities of radiative transitions to the ground state of Ni-like ions with Z = 36–51 are calculated. The energies of the upper working level 3d{sub 3/2}4f{sub 5/2} [J = 1] and the lower working level 3d{sub 3/2}4d{sub 3/2} [J = 1] of self-photo-pumped X-ray lasers along the sequence of Ni-like ions are studied. It is shown that, at the points of intersection of levels of the same parity, a strong interaction of these levels takes place, which leads to a redistribution of the oscillator strengths of the radiative transitions from these levels. Near the intersection points, the emission spectra change abruptly with variation in the nuclear charge Z.

74 ATOMIC AND MOLECULAR PHYSICS↗

Shared Features of Cryptic Plasmids from Environmental and Pathogenic Francisella Species

The Francisella genus includes several recognized species, additional potential species, and other representatives that inhabit a range of incredibly diverse ecological niches, but are not closely related to the named species. Francisella species have been obtained from a wide variety of clinical and environmental sources; documented species include highly virulent human and animal pathogens, fish pathogens, opportunistic human pathogens, tick endosymbionts, and free-living isolates inhabiting brackish water. While more than 120 Francisella genomes have been sequenced to date, only a few contain plasmids, and most of these appear to be cryptic, with unknown benefit to the host cell. We have identified several putative cryptic plasmids in the sequenced genomes of three Francisella novicida and F. novicida-like strains (TX07-6608, AZ06-7470, DPG_3A-IS) and two new Francisella species (F. frigiditurris CA97-1460 and F. opportunistica MA06-7296). These plasmids were compared to each other and to previously identified plasmids from other Francisella species. Some of the plasmids encoded functions potentially involved in replication, conjugal transfer and partitioning, environmental survival (transcriptional regulation, signaling, metabolism), and hypothetical proteins with no assignable functions. In conclusion, genomic and phylogenetic comparisons of these new plasmids to the other known Francisella plasmids revealed some similarities that add to our understanding of the evolutionary relationships among the diverse Francisella species.

59 BASIC BIOLOGICAL SCIENCES↗

Toward initial conditions of conserved charges. Part I. Spatial correlations of quarks and antiquarks

In this work, we study the spatial correlations among quarks and antiquarks produced at mid-rapidity by gluon pair production in the color glass condensate framework. This paper is the first part of a series in which we calculate a complete set of quark/quark, quark/antiquark, and antiquark/antiquark spatial correlation functions in heavy-light ion collisions, with the goal of incorporating their conserved charges into the initial conditions of hydrodynamics. The physical mechanisms captured in this calculation include geometric, entanglement, and interaction-mediated correlations. In this first paper, we construct the building blocks for the correlations arising from single- and double-pair production, studying in detail the single-pair case and the general features of the double-pair case. We find a rich correlation structure in transverse coordinate space, with different mechanisms dominating over different length scales, and we present explicit results for the quark-antiquark correlations in the single-pair production regime. We reserve a detailed discussion of the double-pair production regime for the next paper in this sequence.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments

Abstract Bacillus cereus strain CPT56D‐587‐MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF‐matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%–40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species—largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.

59 BASIC BIOLOGICAL SCIENCES↗

Two novel Patescibacteria: Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov., both associated with microalgae optimized for carbon dioxide sequestration from flue gas

The functional roles of bacterial symbionts associated with microalgae remain understudied despite the importance of microalgae in biotechnology and environmental microbiology. 16S rRNA gene sequencing was conducted to analyze bacterial communities associated with two microalgae optimized for growth with flue gas containing 5%–10% CO 2 . Two dominant bacteria with no taxonomic classification beyond the class level (Paceibacteria) were discovered repeatedly in the most productive algal cultures. Long-read metagenomic sequencing was conducted to yield high-quality metagenomes, from which two novel species were discovered under the Seqcode (seqco.de/r:ywe1blo2), Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov. The genus Phycocordibacter gen. nov. was proposed as the nomenclatural type of the family Phycocordibacteraceae fam. nov. and the order Phycocordibacterales ord. nov. Both bacteria possessed features typical of Patescibacteria such as reduced genomes (<800 kbp), lack of complete glycolysis and tricarboxylic acid (TCA) cycle pathways, and inability to synthesize amino acids. Instead, they rely on the reductive pentose phosphate pathway (Calvin cycle) for essential biosynthesis and redox balance. P. aenigmaticus may also rely on elemental sulfur oxidation (sdo), partial nitrite reduction (nirK), and sulfur-related amino acid metabolism (SAMe → SAH). Both bacteria were found in high relative abundance in cultures of Tetradesmus obliquus HTB1 (freshwater) and Nannochloropsis oceanica IMET1 (marine), suggesting a tight association with microalgae in various environments. The absence of full metabolic pathways for energy production suggests extreme metabolic limitations and obligate symbiosis, most likely with other bacteria associated with the microalgae.

54 ENVIRONMENTAL SCIENCES↗

Development of a pattern recognition algorithm for reconstructing multi-particle events in the Mu2e detector

Mu2e is an upcoming experiment at Fermilab and its main goal is to search for the Charged Lepton Flavor Violation (CLFV) in the coherent transition of a muon into an electron on an Al target. In Mu2e, multi-particle events can occur simultaneously within the same time region and it is crucial to accurately identify each particle track, including signals, to improve the robustness of track finding methods and enhance reconstruction efficiency. ¯p annihilation is one of the background events and produces multiple particles that can mimic signal events. Additionally, photons from radiative pion captures can produce a γ → $e+e−$ pair, which can be used to calibrate the Mu2e momentum scale and the resolution. The Mu2e track reconstruction sequence begins by grouping hits produced in the tracker based on time and z coordinate information, called TimeCluster, and selected hits are processed to reconstruct helices and determine their momentum. The current pattern recognition algorithms identify a single helix per TimeCluster for single track events. A new pattern recognition algorithm is being developed to reconstruct multi-particle events and its features for finding multiple tracks and the current evaluation results are reported.

Kitagawa, H. [Pisa U.]↗

Interstellar Gas-phase Element Depletions in the Small Magellanic Cloud: A Guide to Correcting for Dust in QSO Absorption Line Systems

We present data on the gas-phase abundances for 9 different elements in the interstellar medium of the Small Magellanic Cloud (SMC), based on the strengths of ultraviolet absorption features over relevant velocities in the spectra of 18 stars within the SMC. From this information and the total abundances defined by the element fractions in young stars in the SMC, we construct a general interpretation on how these elements condense into solid form onto dust grains. As a group, the elements Si, S, Cr, Fe, Ni, and Zn exhibit depletion sequences similar to those in the local part of our Galaxy defined by Jenkins. The elements Mg and Ti deplete less rapidly in the SMC than in the Milky Way, and Mn depletes more rapidly. We speculate that these differences might be explained by the different chemical affinities to different existing grain substrates. For instance, there is evidence that the mass fractions of polycyclic aromatic hydrocarbons in the SMC are significantly lower than those in the Milky Way. We propose that the depletion sequences that we observed for the SMC may provide a better model for interpreting the element abundances in low-metallicity Damped Lyman Alpha (DLA) and sub-DLA absorption systems that are recorded in the spectra of distant quasars and gamma-ray burst afterglows.

79 ASTRONOMY AND ASTROPHYSICS↗

A Titan gravity-assist technique for ballistic tours skimming over the rings of Saturn

A novel type of Titan-flyby orbits featuring passes of the Saturn rings at close range has been recently discovered. The purpose of this study is to explore the trajectory design space and assess the applicability of such orbits to the design of a Saturn Ring Tour mission concept. A set of initial conditions required to start a tour of the rings is first determined and a flyby sequence to maximize the science observation time over desired ring regions in terms of range distance, relative velocity and duration is then selected. To demonstrate the potential of this technique, a sample high-fidelity ballistic ring tour is detailed.

Tiscareno, Matthew↗

The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen

Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay.

59 BASIC BIOLOGICAL SCIENCES↗

CHARACTERIZING THE POPULATION OF BRIGHT INFRARED SOURCES IN THE SMALL MAGELLANIC CLOUD

We have used the Infrared Spectrograph (IRS) on the Spitzer Space Telescope to observe stars in the Small Magellanic Cloud (SMC) selected from the Point Source Catalog of the Midcourse Space Experiment (MSX). We concentrate on the dust properties of the oxygen-rich evolved stars. The dust composition has smaller contributions from alumina compared to the Galaxy. This difference may arise from the lower metallicity in the SMC, but it could be a selection effect, as the SMC sample includes more stars that are brighter and thus more massive. The distribution of the SMC stars along the silicate sequence looks more like the Galactic sample of red supergiants than asymptotic giant branch stars (AGBs). While many of the SMC stars are definitively on the AGB, several also show evidence of hot bottom burning. Three of the supergiants show PAH emission at 11.3 μ m. Two other sources show mixed chemistry, with both carbon-rich and oxygen-rich spectral features. One, MSX SMC 134, may be the first confirmed silicate/carbon star in the SMC. The other, MSX SMC 049, is a candidate post-AGB star. MSX SMC 145, previously considered a candidate OH/IR star, is actually an AGB star with a background galaxy at z = 0.16 along the same line of sight. We consider the overall characteristics of all the MSX sources, the most infrared-bright objects in the SMC, in light of the higher sensitivity and resolution of Spitzer , and compare them with the object types expected from the original selection criteria. This population represents what will be seen in more distant galaxies by the upcoming James Webb Space Telescope ( JWST ). Color–color diagrams generated from the IRS spectra and the mid-infrared filters on JWST show how one can separate evolved stars from young stellar objects (YSOs) and distinguish among different classes of YSOs.

79 ASTRONOMY AND ASTROPHYSICS↗

A survey of mass-loss effects in early-type stars

Intermediate-resolution data obtained with the Copernicus satellite are surveyed in order to define the region in the H-R diagram where mass loss occurs. The survey includes 40 stars, providing good coverage of supergiants from O4 to A2 and main-sequence stars from O4 to B7 as well as spotty coverage of late O giants and intermediate to late B stars. The spectral transitions examined are primarily resonance lines of ions of abundant elements plus some lines arising from excited states (e.g., C III at 1175.7 A and Si IV at 1122.5 A). Observed P Cygni profiles are discussed along with interesting features of some individual profiles. The data are shown to indicate that mass-loss effects occur over a wide portion of the H-R diagram, that mass ejection generally occurs when the holometric magnitude is greater than -6.0, and that the mass-ejection rate is usually high enough to produce P Cygni profile whenever the N V feature at 1240 A is present in a spectrum.

Snow, T. P., Jr.↗

Gaseous Etching for Characterization of Structural Defects in Silicon Carbide Single Crystals

Single crystal SiC substrates were subjected to high-temperature H2/C3H8 gaseous etches. The etches resulted in a variety of surface features on 4H-SiC substrates that included elongated hillocks from 10 to more than 100 microns in length by a few microns in width. In some 4H- and 6H-SiC substrates, the etches resulted in a continuous coverage of macrosteps. We conclude that the morphology observed after the etching process is influenced by the local Si-C bilayer stacking sequence on the surface of off-(0001)oriented substrates. A model is presented for the formation of the hillocks, based on localized transformations of the 4H substrates during the high temperature etch process.

Powell, J. A.↗