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At least 775 records · Page 43

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H 2 O 2 -producing enzymes with H 2 O 2 -consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.

59 BASIC BIOLOGICAL SCIENCES↗

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

59 BASIC BIOLOGICAL SCIENCES↗

Deducing the N- and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2

The current emergence of the novel coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands the development of new therapeutic strategies to prevent rapid progress of mortalities. The coronavirus spike (S) protein, which facilitates viral attachment, entry and membrane fusion is heavily glycosylated and plays a critical role in the elicitation of the host immune response. The spike protein is comprised of two protein subunits (S1 and S2), which together possess 22 potential N-glycosylation sites. Herein, we report the glycosylation mapping on spike protein subunits S1 and S2 expressed on human cells through high-resolution mass spectrometry. We have characterized the quantitative N-glycosylation profile on spike protein and interestingly, observed unexpected O-glycosylation modifications on the receptor-binding domain of spike protein subunit S1. Even though O-glycosylation has been predicted on the spike protein of SARS-CoV-2, this is the first report of experimental data for both the site of O-glycosylation and identity of the O-glycans attached on the subunit S1. Our data on the N- and O-glycosylation are strengthened by extensive manual interpretation of each glycopeptide spectra in addition to using bioinformatics tools to confirm the complexity of glycosylation in the spike protein. Here, the elucidation of the glycan repertoire on the spike protein provides insights into the viral binding studies and more importantly, propels research toward the development of a suitable vaccine candidate.

59 BASIC BIOLOGICAL SCIENCES↗

Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2

The emergence of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created the need for development of new therapeutic strategies. Understanding the mode of viral attachment, entry and replication has become a key aspect of such interventions. The coronavirus surface features a trimeric spike (S) protein that is essential for viral attachment, entry and membrane fusion. The S protein of SARS-CoV-2 binds to human angiotensin converting enzyme 2 (hACE2) for entry. Herein, we describe glycomic and glycoproteomic analysis of hACE2 expressed in HEK293 cells. We observed high glycan occupancy (73.2 to 100%) at all seven possible N-glycosylation sites and surprisingly detected one novel O-glycosylation site. To deduce the detailed structure of glycan epitopes on hACE2 that may be involved in viral binding, we have characterized the terminal sialic acid linkages, the presence of bisecting GlcNAc and the pattern of N-glycan fucosylation. We have conducted extensive manual interpretation of each glycopeptide and glycan spectrum, in addition to using bioinformatics tools to validate the hACE2 glycosylation. Our elucidation of the site-specific glycosylation and its terminal orientations on the hACE2 receptor, along with the modeling of hACE2 glycosylation sites can aid in understanding the intriguing virus-receptor interactions and assist in the development of novel therapeutics to prevent viral entry. Here, the relevance of studying the role of ACE2 is further increased due to some recent reports about the varying ACE2 dependent complications with regard to age, sex, race and pre-existing conditions of COVID-19 patients.

59 BASIC BIOLOGICAL SCIENCES↗

Characteristics of a cost-effective blood test for colorectal cancer screening

Background: Blood-based biomarker tests can potentially change the landscape of colorectal cancer (CRC) screening. We characterize the conditions under which blood test screening would be as effective and cost-effective as annual fecal immunochemical testing or decennial colonoscopy. Methods: We used the 3 Cancer Information and Surveillance Modeling Network–Colon models to compare scenarios of no screening, annual fecal immunochemical testing, decennial colonoscopy, and a blood test meeting Centers for Medicare & Medicaid (CMS) coverage criteria (74% CRC sensitivity and 90% specificity). We varied the sensitivity to detect CRC (74%-92%), advanced adenomas (10%-50%), screening interval (1-3 years), and test cost ($25-$500). Primary outcomes included quality-adjusted life-years (QALY) gained from screening and costs for a US average-risk cohort of individuals aged 45 years. Results: Annual fecal immunochemical testing yielded 125-163 QALY gained per 1000 at a cost of 3811-5384 dollars per person, whereas colonoscopy yielded 132-177 QALY gained at a cost of 5375-7031 dollars per person. A blood test with 92% CRC sensitivity and 50% advanced adenoma sensitivity yielded 117-162 QALY gained if used every 3 years and 133-173 QALY gained if used every year but would not be cost-effective if priced above $$125 per test. If used every 3 years, a $500 blood test only meeting CMS coverage criteria yielded 83-116 QALY gained at a cost of $8559-$9413 per person. Conclusion: Blood tests that only meet CMS coverage requirements should not be recommended to patients who would otherwise undergo screening by colonoscopy or fecal immunochemical testing because of lower benefit. Blood tests need higher advanced adenoma sensitivity (above 40%) and lower costs (below $125) to be cost-effective.

60 APPLIED LIFE SCIENCES↗

Constraining primordial non-Gaussianity from the large scale structure two-point and three-point correlation functions

Surveys of cosmological large-scale structure (LSS) are sensitive to the presence of local primordial non-Gaussianity (PNG), and may be used to constrain models of inflation. Local PNG, characterized by f NL ⁠, the amplitude of the quadratic correction to the potential of a Gaussian random field, is traditionally measured from LSS two-point and three-point clustering via the power spectrum and bi-spectrum. We propose a framework to measure f NL using the configuration space two-point correlation function (2pcf) monopole and three-point correlation function (3pcf) monopole of survey tracers. Our model estimates the effect of the scale-dependent bias induced by the presence of PNG on the 2pcf and 3pcf from the clustering of simulated dark matter haloes. We describe how this effect may be scaled to an arbitrary tracer of the cosmological matter density. The 2pcf and 3pcf of this tracer are measured to constrain the value of f NL ⁠. In LSS surveys, the effect of imaging systematics on two-point statistics is often degenerate with the PNG signal. Our proposed model employs three-point statistics primarily to break this degeneracy. Using simulations of luminous red galaxies observed by the Dark Energy Spectroscopic Instrument (DESI), we demonstrate the accuracy and constraining power of our method. Our forecast indicates the ability to constrain f NL to a precision of σf NL ≈ 22 with one year of DESI survey data, as well as the ability to constrain the imaging systematic weights in situ.

early Universe↗

Dark Energy Survey Year 6 results: cell-based coadds and METADETECTION weak lensing shape catalogue

We present the metadetection weak lensing galaxy shape catalogue from the 6-yr Dark Energy Survey (DES Y6) imaging data. This data set is the final release from DES, spanning 4422 deg 2 of the southern sky. We describe how the catalogue was constructed, including the two new major processing steps, cell-based image coaddition, and shear measurements with metadetection. The DES Y6 M etadetection weak lensing shape catalogue consists of 151 922 791 galaxies detected over riz bands, with an effective number density of n eff = 8.22 galaxies per arcmin 2 and shape noise of σ e = 0.29. We carry out a suite of validation tests on the catalogue, including testing for point spread function (PSF) leakage, testing for the impact of PSF modelling errors, and testing the correlation of the shear measurements with galaxy, PSF, and survey properties. In addition to demonstrating that our catalogue is robust for weak lensing science, we use the DES Y6 image simulation suite to estimate the overall multiplicative shear bias of our shear measurement pipeline. We find no detectable multiplicative bias at the roughly half-per cent level, with m = (3.4 ± 6.1) x 10 –3 , at 3σ uncertainty. This is the first time both cell-based coaddition and Metadetection algorithms are applied to observational data, paving the way to the Stage-IV weak lensing surveys.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Galaxy-multiplet clustering from DESI DR2

We present an efficient estimator for higher-order galaxy clustering using small groups of nearby galaxies, or multiplets. Using the Luminous Red Galaxy (LRG) sample from the Dark Energy Spectroscopic Instrument (DESI) Data Release 2, we identify galaxy multiplets as discrete objects and measure their cross-correlations with the general galaxy field. Our results show that the multiplets exhibit stronger clustering bias as they trace more massive dark matter halos than individual galaxies. When comparing the observed clustering statistics with the mock catalogs generated from the N-body simulation AbacusSummit, we find that the mocks underpredict multiplet clustering despite reproducing the galaxy two-point auto-correlation reasonably well. This discrepancy indicates that the standard Halo Occupation Distribution (HOD) model is insufficient to describe the properties of galaxy multiplets, revealing the greater constraining power of this higher-order statistic on galaxy-halo connection and the possibility that multiplets are specific to additional assembly bias. We demonstrate that incorporating secondary biases into the HOD model improves agreement with the observed multiplet statistics, specifically by allowing galaxies to preferentially occupy halos in denser environments. Our results highlight the potential of utilizing multiplet clustering, beyond traditional two-point correlation measurements, to break degeneracies in models describing the galaxy-dark matter connection.

cosmology↗

Calibrating the absolute magnitude of type Ia supernovae in nearby galaxies using [O II ] and implications for H 0

The present state of cosmology is facing a crisis where there is a fundamental disagreement in measurements of the Hubble constant ($H_{0}$), with significant tension between the early and late Universe methods. Type Ia supernovae (SNe Ia) are important to measuring $H_{0}$ through the astronomical distance ladder. However, there remains potential to better standardize SN Ia light curves by using known dependencies on host galaxy properties after the standard light curve width and colour corrections have been applied to the peak SN Ia luminosities. To explore this, we use the 5-yr photometrically identified SNe Ia sample obtained by the Dark Energy Survey, along with host galaxy spectra obtained by the Australian Dark Energy Survey. Using host galaxy spectroscopy, we find a significant trend with the equivalent width (EW) of the [O II ] $\lambda \lambda$ 3727, 29 doublet, a proxy for specific star formation rate, and Hubble residuals. We find that the correlation with [O II ] EW is a powerful alternative to the commonly used mass step after initial light-curve corrections. Applying this [O II ] EW correction to 20 SNe Ia in calibrator galaxies observed with WiFeS, we examined the impact on SN Ia absolute magnitudes and $H_{0}$. Our [O II ] EW corrections result in $H_{0}$ values ranging between 73.04 and 73.51 $km$ $s^{-1} \, Mpc^{-1}$, with a combined statistical and systematic uncertainty of $\sim 1.31$ $km$ $s^{-1} \, Mpc^{-1}$. However, even with this additional correction, the impact of host galaxy properties in standardizing SNe Ia appears limited in reducing the current tension ($\sim 5\sigma$) with the cosmic microwave background result for $H_{0}$.

79 ASTRONOMY AND ASTROPHYSICS↗

It is not σ 8 : constraining the non-linear matter power spectrum with the Dark Energy Survey Year-5 supernova sample

The weak gravitational lensing magnification of Type Ia supernovae (SNe Ia) is sensitive to the matter power spectrum on scales $k\gt 1 h$ Mpc$^{-1}$, making it unwise to interpret SNe Ia lensing in terms of power on linear scales. We compute the probability density function of SNe Ia magnification as a function of standard cosmological parameters, plus an empirical parameter $A_{\rm mod}$ which describes the suppression or enhancement of matter power on non-linear scales compared to a cold dark matter only model. While baryons are expected to enhance power on the scales relevant to SN Ia lensing, other physics such as neutrino masses or non-standard dark matter may suppress power. Using the Dark Energy Survey Year-5 sample, we find $A_{\rm mod} = 0.77^{+0.69}_{-0.40}$ (68 per cent credible interval around the median). Although the median is consistent with unity there are hints of power suppression, with $A_{\rm mod} \lt 1.09$ at 68 per cent credibility.

79 ASTRONOMY AND ASTROPHYSICS↗

Unraveling emission line galaxy conformity at z ∼ 1 with DESI early data

Emission line galaxies (ELGs) are now the preeminent tracers of large-scale structure at z > 0.8 due to their high density and strong emission lines, which enable accurate redshift measurements. However, relatively little is known about ELG evolution and the ELG–halo connection, exposing us to potential modelling systematics in cosmology inference using these sources. In this paper, we use a variety of observations and simulated galaxy models to propose a physical picture of ELGs and improve ELG–halo connection modelling in a halo occupation distribution framework. We investigate Dark Energy Spectroscopic Instrument (DESI)-selected ELGs in COSMOS data, and infer that ELGs are rapidly star-forming galaxies with a large fraction exhibiting disturbed morphology, implying that many of them are likely to be merger-driven starbursts. We further postulate that the tidal interactions from mergers lead to correlated star formation in central–satellite ELG pairs, a phenomenon dubbed ‘conformity’. We argue for the need to include conformity in the ELG–halo connection using galaxy models such as IllustrisTNG, and by combining observations such as the DESI ELG autocorrelation, ELG cross-correlation with luminous red galaxies, and ELG–cluster cross-correlation. We also explore the origin of conformity using the UniverseMachine model and elucidate the difference between conformity and the well-known galaxy assembly bias effect.

79 ASTRONOMY AND ASTROPHYSICS↗

Constraining the phase shift of relativistic species in DESI BAOs

In the early Universe, neutrinos decouple quickly from the primordial plasma and propagate without further interactions. The impact of free-streaming neutrinos is to create a temporal shift in the gravitational potential that impacts the acoustic waves known as baryon acoustic oscillations (BAOs), resulting in a non-linear spatial shift in the Fourier-space BAO signal. In this work, we make use of and extend upon an existing methodology to measure the phase shift amplitude $\beta _{\phi }$ and apply it to the Dark Energy Spectroscopic Instrument (DESI) Data Release 1 (DR1) BAOs with an anisotropic BAO fitting pipeline. We validate the fitting methodology by testing the pipeline with two publicly available fitting codes applied to highly precise cubic box simulations and realistic simulations representative of the DESI DR1 data. We find further study towards the methods used in fitting the BAO signal will be necessary to ensure accurate constraints on $\beta _{\phi }$ in future DESI data releases. Using DESI DR1, we present individual measurements of the anisotropic BAO distortion parameters and the $\beta _{\phi }$ for the different tracers, and additionally a combined fit to $\beta _{\phi }$ resulting in $\beta _{\phi } = 2.7 \pm 1.7$. After including a prior on the distortion parameters from constraints using Planck we find $\beta _{\phi } = 2.7^{+0.60}_{-0.67}$ suggesting $\beta _{\phi } > 0$ at 4.3$\sigma$ significance. This result may hint at a phase shift that is not purely sourced from the standard model expectation for $N_{\rm {eff}}$ or could be a upwards statistical fluctuation in the measured $\beta _{\phi }$; this result relaxes in models with additional freedom beyond Lambda-cold dark matter.

79 ASTRONOMY AND ASTROPHYSICS↗

The rate of extreme coronal line emitters in the Baryon Oscillation Spectroscopic Survey LOWZ sample

Extreme coronal line emitters (ECLEs) are a rare class of galaxy that exhibit strong, high-ionization iron coronal emission lines in their spectra. In some cases, these lines are transient and may be the result of tidal disruption event (TDEs). To test this connection, we calculate the rate of variable ECLEs (vECLEs) at redshift $\sim 0.3$. We search for ECLEs in the Baryon Oscillation Spectroscopic Survey (BOSS) LOWZ sample and discover two candidate ECLEs. Using follow-up spectra from the Dark Energy Spectroscopic Instrument and Gemini Multi-Object Spectrograph, and mid-infrared observations from the Wide-field Infrared Survey Explorer, we determine that one of these galaxies is a vECLE. Using this galaxy, we calculate the galaxy-normalized vECLE rate at redshift $\sim 0.3$ to be $R_\mathrm{G}=1.6~^{+3.8}_{-1.4}\times 10^{-6}~\mathrm{galaxy}^{-1}~\mathrm{yr}^{-1}$and the mass-normalized rate to be $R_\mathrm{M}=7~^{+16}_{-6}\times 10^{-18}~\mathrm{M_\odot ^{-1}}~\mathrm{yr}^{-1}$. This is then converted to a volumetric rate of $R_\mathrm{V}=1.8~^{+4.5}_{-1.5}\times 10^{-9}~\mathrm{Mpc}^{-3}~\mathrm{yr}^{-1}$. Formally, the LOWZ vECLE rates are $2 \!-\! 4$ times lower than the rates calculated from the Sloan Digital Sky Survey Legacy sample at redshift $\sim 0.1$. However, given the large uncertainties on both measurements, they are consistent with each other at $1\sigma$. Both the galaxy-normalized and volumetric rates are one to two orders of magnitude lower than TDE rates from the literature, consistent with vECLEs being caused by $5 \!-\! 20$ per cent of all TDEs.

79 ASTRONOMY AND ASTROPHYSICS↗

AT 2018dyk: tidal disruption event or active galactic nucleus? Follow-up observations of an extreme coronal line emitter with the Dark Energy Spectroscopic Instrument

We present fresh insights into the nature of the tidal disruption event (TDE) candidate AT 2018dyk. AT 2018dyk has sparked a debate in the literature around its classification as either a bona-fide TDE or as an active galactic nucleus (AGN) turn-on state change. A new follow-up spectrum taken with the Dark Energy Spectroscopic Instrument, in combination with host-galaxy analysis using archival SDSS–MaNGA data, supports the identification of AT 2018dyk as a TDE. Specifically, we classify this object as a TDE that occurred within a gas-rich environment, which was responsible for both its mid-infrared (MIR) outburst and development of Fe coronal emission lines. Comparison with the known sample of TDE-linked extreme coronal line emitters (TDE-ECLEs) and other TDEs displaying coronal emission lines (CrL-TDEs) reveals similar characteristics and shared properties. For example, the MIR properties of both groups appear to form a continuum with links to the content and density of the material in their local environments. This includes evidence for a MIR colour–luminosity relationship in TDEs occurring within such gas-rich environments, with those with larger MIR outbursts also exhibiting redder peaks.

79 ASTRONOMY AND ASTROPHYSICS↗

Stacked reverberation mapping of high-redshift quasars in DESI. I. Feasibility analysis

The broad-line region of quasars has long been probed by reverberation mapping techniques that measure time lags between continuum and broad emission-line variations. Stacked reverberation mapping has been proposed as a less observationally expensive alternative to traditional methods. This ensemble approach also reduces biases from small-number statistics. The Dark Energy Spectroscopic Instrument (DESI) is conducting the most extensive spectroscopic survey of quasars to date. We create mock light curves emulating expected DESI quasar observations at redshifts $1.48\lt z\lt 5.2$ and luminosities $44.68 \le \log \lambda L_{1350 \mathring{\rm A}{}} / \mathrm{erg\, s^{-1}} \le 45.99$ to test stacked reverberation mapping feasibility using sparse spectroscopic data paired with well-sampled photometric data. The pipeline, using the lag estimation code JAVELIN (Just Another Vehicle for Estimating Lags In Nuclei), successfully recovers the simulated C IV lags within 1σ of the true values using spectroscopic light curves composed of only a few spectral epochs (2–10) with irregular cadences. We investigate how observational factors, including C IV flux error magnitude, number of stacked quasars, and spectral epoch count, affect performance. This work motivates a pathway for future stacked reverberation mapping projects with large-scale spectroscopic surveys of quasars having $\ge 2$ spectroscopic observations. Our results suggest an economical alternative for constraining and extending the radius–luminosity relation to higher redshifts and luminosities. Subsequently, this relation can be employed more reliably in single-epoch black hole mass measurements and quasar cosmology in these distant regimes.

quasars: general, quasars: supermassive black hole↗

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗

X-Ray Imaging and Spectroscopy Mission

The X-Ray Imaging and Spectroscopy Mission (XRISM) is a joint mission between the Japan Aerospace Exploration Agency (JAXA) and the National Aeronautics and Space Administration (NASA) in collaboration with the European Space Agency (ESA). In addition to the three space agencies, universities and research institutes from Japan, North America, and Europe have joined to contribute to developing satellite and onboard instruments, data-processing software, and the scientific observation program. XRISM is the successor to the ASTRO-H (Hitomi) mission, which ended prematurely in 2016. Its primary science goal is to examine astrophysical problems with precise, high-resolution X-ray spectroscopy. XRISM promises to discover new horizons in X-ray astronomy. It carries a 6 × 6 pixelized X-ray microcalorimeter on the focal plane of an X-ray mirror assembly (Resolve) and a co-aligned X-ray CCD camera (Xtend) that covers the same energy band over a large field of view. XRISM utilizes the Hitomi heritage, but all designs were reviewed. The attitude and orbit control system was improved in hardware and software. The spacecraft was launched from the JAXA Tanegashima Space Center on 2023 September 6 (UTC). During the in-orbit commissioning phase, the onboard components were activated. Although the gate valve protecting the Resolve sensor with a thin beryllium X-ray entrance window was not yet opened, scientific observation started in 2024 February with the planned performance verification observation program. The nominal observation program commenced with the following guest observation program beginning in 2024 September.

Astronomy and AstroPhysics↗