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At least 1,369 records · Page 76
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. Furthermore, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway

Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicum Strain L-1. The genome consists of a primary chromosome that encodes most of the genes for core processes, a secondary chromosome that encodes primarily genes that appear to be involved in environmental adaptation, and a small plasmid. The genes responsible for degradation of PCP are found on chromosome 2. We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane. Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.

3-DIOXYGENASE↗
DOE OSTI2012

Genome Sequence of the Mesophilic Thermotogales Bacterium Mesotoga prima MesG1.Ag.4.2 Reveals the Largest Thermotogales Genome To Date

Here we describe the genome of Mesotoga prima MesG1.Ag4.2, the first genome of a mesophilic Thermotogales bacterium. Mesotoga prima was isolated from a polychlorinated biphenyl (PCB)-dechlorinating enrichment culture from Baltimore Harbor sediments. Its 2.97 Mb genome is considerably larger than any previously sequenced Thermotogales genomes, which range between 1.86 and 2.30 Mb. This larger size is due to both higher numbers of protein-coding genes and larger intergenic regions. In particular, the M. prima genome contains more genes for proteins involved in regulatory functions, for instance those involved in regulation of transcription. Together with its closest relative, Kosmotoga olearia, it also encodes different types of proteins involved in environmental and cell-cell interactions as compared with other Thermotogales bacteria. Amino acid composition analysis of M. prima proteins implies that this lineage has inhabited low-temperature environments for a long time. A large fraction of the M. prima genome has been acquired by lateral gene transfer (LGT): a DarkHorse analysis suggests that 766 (32%) of predicted protein-coding genes have been involved in LGT after Mesotoga diverged from the other Thermotogales lineages. A notable example of a lineage-specific LGT event is a reductive dehalogenase gene - a key enzyme in dehalorespiration, indicating M. prima may have a more active role in PCB dechlorination than was previously assumed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbiome Comparison and Pathogen Identification for Three Migrating Passerines Captured During Spring Season in Jordan Using 16S rRNA Sequencing

Jordan is located on an important spot along the Mediterranean and Black Sea Flyway. Hundreds of migratory bird species have been identified stopping over in Jordan during spring and autumn migratory seasons. Compared to mammals and economically important birds, the microbiomes of wild bird species are severely understudied. Gut microbial composition is a valuable source of information that reflects food preferences, foraging behavior, and the risk of pathogen transmission to humans and other animals. In this study, we assessed the microbiome composition of three species of migrating passerines (willow warblers, lesser whitethroats, and common reed warblers) captured during the spring migration stopover in Jordan in 2023. A total of 59 fecal samples were selected evenly from the three species and subjected to 16S sequencing and microbiome analysis. Our objectives were to determine the diversity of bacteria in these three species, assess the amount of intra- and inter-specific variation, and detect pathogenic genera and species that could pose health risks to humans, domestic animals, and wildlife. Bacteria mainly belonged to the phyla Proteobacteria (62%), Actinobacteriota (18%), Firmicutes (13%), Cyanobacteria (5%), and Bacteroidota (1%). The results reveal that lesser whitethroats had the greatest variation in bacterial genus richness, Shannon diversity, and microbial composition compared to willow warblers and common reed warblers. The three bird species harbored several pathogenic genera and species, including Campylobacter, Enterococcus, Escherichia-Shigella, Mycoplasma, Rickettsia, Clostridium perfringens, and Vibrio cholerae. We suggest further investigation to understand the relationship between migratory behavior and their gut microbiome. We advocate for the use of advanced molecular techniques to characterize the pathogens found in migratory birds that might have public and environmental health impacts in addition to economic loss.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PLATO hare-and-hounds exercise: asteroseismic model fitting of main-sequence solar-like pulsators

ABSTRACT Asteroseismology is a powerful tool to infer fundamental stellar properties. The use of these asteroseismic-inferred properties in a growing number of astrophysical contexts makes it vital to understand their accuracy. Consequently, we performed a hare-and-hounds exercise where the hares simulated data for six artificial main-sequence stars and the hounds inferred their properties based on different inference procedures. To mimic a pipeline such as that planned for the PLATO mission, all hounds used the same model grid. Some stars were simulated using the physics adopted in the grid, others a different one. The maximum relative differences found (in absolute value) between the inferred and true values of the mass, radius, and age were 4.32, 1.33, and 11.25 per cent, respectively. The largest systematic differences in radius and age were found for a star simulated assuming gravitational settling, not accounted for in the model grid, with biases of −0.88 per cent (radius) and 8.66 per cent (age). For the mass, the most significant bias (−3.16 per cent) was found for a star with a helium enrichment ratio outside the grid range. Moreover, an ∼7 per cent dispersion in age was found when adopting different prescriptions for the surface corrections or shifting the classical observations by ±1σ. The choice of the relative weight given to the classical and seismic constraints also impacted significantly the accuracy and precision of the results. Interestingly, only a few frequencies were required to achieve accurate results on the mass and radius. For the age the same was true when at least one l = 2 mode was considered.

Cunha, M. S. (ORCID:0000000182377343)↗
DOE OSTI2021

Stars in the local galactic thick disc and halo in Gaia EDR3: a catalogue of half a million local main-sequence stars with photometric metallicities

We present a catalogue of 551 214 main-sequence stars in the local (d < 2 kpc) Galactic thick disc and halo, based on a search of stars with large proper motions ($\mu _{\rm tot} \gt 40.0~\rm mas\, yr^{-1}$) in the Gaia Early Data Release 3. We derive photometric metallicity calibrated from the colour–luminosity–metallicity distribution of 20 047 stars with spectroscopic metallicities, collected from various spectroscopic surveys, including SDSS SEGUE/APOGEE, GALAH DR3, and LAMOST DR6. We combine these results to construct an empirical colour–magnitude–metallicity grid, which can be used to estimate photometric metallicities for low-mass metal-poor stars of K and M subtypes from their absolute G magnitude and colour values. We find that low-mass, high-velocity stars in our catalogue share similar kinematics as reported in recent studies of more luminous Galactic halo stars. The pseudo-kinematic analysis of our sample recovers the main local halo structures, including the Gaia–Enceladus Stream and the Helmi stream; aside from these, the local halo stars appear to show a remarkably smooth distribution in velocity space. Since the future Gaia data release will provide radial velocity measurements for only a small number of our sample, our catalogue provides targets of high interest for the future spectroscopic observation programs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Jets from main sequence and white dwarf companions during common envelope evolution

ABSTRACT It has long been speculated that jet feedback from accretion on to the companion during a common envelope (CE) event could affect the orbital evolution and envelope unbinding process. We present global 3D hydrodynamical simulations of CE evolution (CEE) that include a jet subgrid model and compare them with an otherwise identical model without a jet. Our binary consists of a 2-M⊙ red giant branch primary and a 1- or 0.5-M⊙ main sequence (MS) or white dwarf (WD) secondary companion modelled as a point particle. We run the simulations for 10 orbits (40 d). Our jet model adds mass at a constant rate $\dot{M}_\mathrm{j}$ of the order of the Eddington rate, with maximum velocity vj of the order of the escape speed, to two spherical sectors with the jet axis perpendicular to the orbital plane. We explore the influence of the jet on orbital evolution, envelope morphology and envelope unbinding, and assess the dependence of the results on the jet mass-loss rate, launch speed, companion mass, opening angle, and accretion rate. In line with our theoretical estimates, jets are choked around the time of first periastron passage and remain choked thereafter. Subsequent to choking, but not before, jets efficiently transfer energy to bound envelope material. This leads to increases in unbound mass of up to $\sim 10{{\ \rm per\ cent}}$, as compared to the simulations without jets. We also estimate the cumulative effects of jets over a full CE phase, finding that jets launched by MS and WD companions are unlikely to dominate envelope unbinding.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Clash of Titans: the impact of cluster mergers in the galaxy cluster red sequence

ABSTRACT Merging of galaxy clusters are some of the most energetic events in the Universe, and they provide a unique environment to study galaxy evolution. We use a sample of 84 merging and relaxed SPT galaxy clusters candidates, observed with the Dark Energy Camera in the 0.11 < z < 0.88 redshift range, to build colour–magnitude diagrams to characterize the impact of cluster mergers on the galaxy population. We divided the sample between relaxed and disturbed, and in two redshifts bin at z = 0.55. When comparing the high-z to low-z clusters we find the high-z sample is richer in blue galaxies, independently of the cluster dynamical state. In the high-z bin, we find that disturbed clusters exhibit a larger scatter in the red sequence, with wider distribution and an excess of bluer galaxies compared to relaxed clusters, while in the low-z bin we find a complete agreement between the relaxed and disturbed clusters. Our results support the scenario in which massive cluster halos at z < 0.55 galaxies are quenched as satellites of another structure, i.e. outside the cluster, while at z ≥ 0.55 the quenching is dominated by in situ processes.

Aldás, Franklin (ORCID:0000000290215114)↗
DOE OSTI2017

Galaxy populations in massive galaxy clusters to $z$ = 1.1: Color distribution, concentration, halo occupation number and red sequence fraction

We study the galaxy populations in 74 Sunyaev–Zeldovich effect selected clusters from the South Pole Telescope survey, which have been imaged in the science verification phase of the Dark Energy Survey. The sample extends up to z ~ 1.1 with 4 × 10 14 M⊙ ≤ M200 ≤ 3 × 10 15 M⊙. Using the band containing the 4000 Å break and its redward neighbour, we study the colour–magnitude distributions of cluster galaxies to ~m* + 2, finding that: (1)The intrinsic rest frame g – r colour width of the red sequence (RS) population is ~0.03 out to z ~ 0.85 with a preference for an increase to ~0.07 at z = 1, and (2) the prominence of the RS declines beyond z ~ 0.6. The spatial distribution of cluster galaxies is well described by the NFW profile out to 4R200 with a concentration of c g = 3.59$+0.20\atop{–0.18}$, 5.37$+0.27\atop{-0.24}$ and 1.38$+0.21\atop{-0.19}$ for the full, the RS and the blue non-RS populations, respectively, but with ~40 per cent to 55 per cent cluster to cluster variation and no statistically significant redshift or mass trends. The number of galaxies within the virial region N200 exhibits a mass trend indicating that the number of galaxies per unit total mass is lower in the most massive clusters, and shows no significant redshift trend. The RS fraction within R200 is (68 ± 3) per cent at z = 0.46, varies from ~55 per cent at z = 1 to ~80 per cent at z = 0.1 and exhibits intrinsic variation among clusters of ~14 per cent. Finally, we discuss a model that suggests that the observed redshift trend in RS fraction favours a transformation time-scale for infalling field galaxies to become RS galaxies of 2–3 Gyr.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Galaxies in X-ray selected clusters and groups in Dark Energy Survey data – II. Hierarchical Bayesian modelling of the red-sequence galaxy luminosity function

Using ~100 X-ray selected clusters in the Dark Energy Survey Science Verification data, in this work we constrain the luminosity function (LF) of cluster red-sequence galaxies as a function of redshift. This is the first homogeneous optical/X-ray sample large enough to constrain the evolution of the LF simultaneously in redshift (0.1 < z < 1.05) and cluster mass ($13.5 \le \rm {log_{10}}(M_{200crit}) \sim \lt 15.0$). We pay particular attention to completeness issues and the detection limit of the galaxy sample. We then apply a hierarchical Bayesian model to fit the cluster galaxy LFs via a Schechter function, including its characteristic break (m*) to a faint end power-law slope (α). Our approach allows us to avoid known issues in similar analyses based on stacking or binning the clusters. We find weak and statistically insignificant (~1.9σ) evolution in the faint end slope α versus redshift. We also find no dependence in α or m* with the X-ray inferred cluster masses. Yet, the amplitude of the LF as a function of cluster mass is constrained to ${\sim } 20{{\ \rm per\ cent}}$ precision. As a by-product of our algorithm, we utilize the correlation between the LF and cluster mass to provide an improved estimate of the individual cluster masses as well as the scatter in true mass given the X-ray inferred masses. This technique can be applied to a larger sample of X-ray or optically selected clusters from the Dark Energy Survey, greatly improving the sensitivity of the analysis.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Dissecting the main sequence: AGN activity and bulge growth in the local Universe

ABSTRACT Local galaxies from the Sloan Digital Sky Survey (SDSS) are used to provide additional support for an evolutionary pathway in which active galactic nucleus activity is associated with star formation quenching. Composite, Seyfert 2, and LINER galaxies account for ∼60 per cent of all star formation in massive galaxies (M⋆ > 1010.5 M⊙). Inclusion of these galaxies results in a ‘turnover’ in the star formation rate and stellar mass (SFR−M⋆) relation for massive galaxies. Our analysis shows that bulge growth has already occurred in the most massive galaxies (M⋆ > 1010.5 M⊙), and bulges continue to grow as galaxies quench and redden, (g − r) = 0.5 → 0.75. Significant bulge growth is also occurring in low mass starburst galaxies (M⋆ < 1010.5 M⊙) at 0.5 dex above the ‘main sequence’ (MS), where we find an increase in B/T from 0.1 → 0.3 and bluer colours, (g − r) < 0.25 compared to low-mass galaxies on the MS.

McPartland, C. (ORCID:000000030639025X)↗
DOE OSTI2021

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome

The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns

The discovery and engineering of new enzymes is important across the bioeconomy, with diverse applications from foods to pharmaceuticals, sensors to agriculture. However, enzyme engineering, in particular machine learning-guided engineering, is hampered by a lack of data. Currently there exists no database designed to capture and interpret datasets created in this domain, nor are there easy analysis and visualisation tools. We developed the Enzyme Engineering Database to provide a centralized resource and an online analysis tool to consolidate sequence-function data from enzyme engineering campaigns, thereby making three contributions: (i) a database into which researchers can deposit public data, (ii) visualisation and analysis tools for protein engineers to analyse their own data or compare enzyme variants to other engineering campaigns, and (iii) a gold-standard dataset for benchmarking automated extraction along with the first large language model extraction pipeline specific for enzyme engineering campaigns. The Enzyme Engineering Database is accessible at http://enzengdb.org/.

Long, Yueming [California Institute of Technology ↗
DOE OSTI2015

Microbial species delineation using whole genome sequences

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase

The photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of its ease of culture in the laboratory. Genomic and systems biology approaches have previously described transcriptome responses to environmental changes using bulk data, thus representing the average behavior from pools of cells. Here, we apply single-cell RNA sequencing (scRNA-seq) to probe the heterogeneity of Chlamydomonas cell populations under three environments and in two genotypes differing by the presence of a cell wall. First, we determined that RNA can be extracted from single algal cells with or without a cell wall, offering the possibility to sample natural algal communities. Second, scRNA-seq successfully separated single cells into nonoverlapping cell clusters according to their growth conditions. Cells exposed to iron or nitrogen deficiency were easily distinguished despite a shared tendency to arrest photosynthesis and cell division to economize resources. Notably, these groups of cells not only recapitulated known patterns observed with bulk RNA-seq but also revealed their inherent heterogeneity. A substantial source of variation between cells originated from their endogenous diurnal phase, although cultures were grown in constant light. We exploited this result to show that circadian iron responses may be conserved from algae to land plants. We document experimentally that bulk RNA-seq data represent an average of typically hidden heterogeneity in the population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Genome Sequence of the Plant Growth Promoting Fungus Serendipita vermifera subsp. bescii : The First Native Strain from North America

Serendipita vermifera (=Sebacina vermifera) has demonstrated plant growth promoting abilities with little or no host specificity. The full genome sequencing of Serendipita vermifera subsp. bescii, the first North American strain, will provide insight into the mechanisms behind mycorrhizal symbiosis and plant enhancement in a variety of agronomically important crops.

59 BASIC BIOLOGICAL SCIENCES↗