Data From EMSL Project 51710: Opportunities linking omics and structural biology at PNNL: Excelling at Cryo-EM
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Evans, James↗
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Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon
Genome-resolved metagenomics was applied to recover soil archaeal and bacterial metagenome-assembled genomes (MAGs) from three forests and three pastures of the Brazilian Eastern Amazon.
Venturini, Andressa [(1) Former: Cell and Molecula↗
Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes
Motivation: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As `omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results: We propose a workflow (`Omics to Reactive Transport – ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBASE and PFLOTRAN. Live, interactive models, which incorporate the results from this narrative into a PFLOTRAN simulation, are available (without login) at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/.
Rubinstein, Rebecca L↗
Comparison of copper and aluminum as the thermal link material for conduction-cooled accelerator cavities
Cryocooler conduction-cooling has recently emerged as a new frontier for cryogenic cooling for superconducting radiofrequency (SRF) cavities. In this scheme, an SRF cavity is mechanically coupled to a closed-cycle cryocooler using linkages made of high thermal conductivity metals. In this note, we compare the thermal transport properties of high purity aluminum and high purity copper as applied to SRF cavity conduction cooling. We show that copper can enable faster cooldown than aluminum from room temperature to the base temperature near 4 K and behave equally well or better during steady state cavity operation near the base temperature.
36 MATERIALS SCIENCE↗
The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential
Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.
59 BASIC BIOLOGICAL SCIENCES↗
Proteomics reveals pathways linked to septoria canker resistance and susceptibility in Populus trichocarpa
A major threat to forest ecosystems and plantation forestry is the introduction of a non-native pathogen. Among non-domesticated populations with relatively high levels of genetic diversity, a measurable range of susceptibility to resistance can be expected. Identifying genetic determinants of resistant and susceptible individuals can inform the development of new strategies to engineer disease resistance. Here we describe pathogen-induced changes in the proteome of Populus trichocarpa stem tissue in response to Sphaerulia musiva (Septoria canker). This hemibiotrophic fungal pathogen causes stem canker disease in susceptible poplar genotypes. Proteomics analyses were performed on stem tissue harvested across 0-, 12-, 24- and 48-h post-inoculation with Septoria from three genotypes including one resistant (BESC-22) and two susceptible [BESC-801; Nisqually-1 (NQ-1)]. In total, 11,897 Populus proteins at FDR <0.01 were identified across all time points and genotypes. Analysis of protein abundances between genotypes revealed that the resistant poplar genotype (BESC-22) mounts a rapid and sustained defense response involving pattern recognition receptors, calcium signaling proteins, SAR inducers, transcriptional regulators, resistance proteins, and proteins involved with the hypersensitive response. One susceptible genotype (BESC-801) had a downregulated and delayed defense response whereas the second susceptible genotype (NQ-1) lacked a distinct pattern. Overall, the proteome-wide and protein-specific trends suggest that responses to the Septoria canker infection are genotype-specific for the naïve host, Populus trichocarpa .
59 BASIC BIOLOGICAL SCIENCES↗
Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome
Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama ( Bouteloua gracilis ), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota , Thermoproteota (formerly Thaumarchaeota ), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.
Goemann, Hannah M.↗
Linking Hydrobiogeochemical Processes and Management Techniques to Close Nutrient Loops in an Arid River
In this study, we explore opportunities to optimize food-energy-water (FEW) resources by closing nutrient loops in arid-land rivers. Specifically, we evaluate source and sink behavior of nitrogen as nitrate (NO 3 -N) in three characteristic channels in the Middle Rio Grande Basin (Delivery and Drain channels associated with agriculture and the main channel of the Rio Grande). All three channels are located downstream of a large wastewater treatment plant that is the main contributor of nutrients to this reach of the Rio Grande. We used a mass balance approach paired with stable isotope analysis to determine sources and processing of NO 3 -N within the channels over time (a year) and through space (along ~15 to 50 km reaches). Results indicated the growing season was an important period of sink behavior for the Delivery channel and the Rio Grande, but the Drain channel was a year-round source. Stable isotope analysis of 15 N and 18 O found a distinct nitrate signature in the Drain associated with biological processing, as well as Rio Grande sites impacted by agricultural outflow, but no equivalent signature was present in the Delivery channel. Based on our findings, we provide recommendations to help close nutrient loops in the study system and analogous aridland irrigation networks by 1) minimizing loss during the transfer of nutrients from wastewater facilities to agricultural areas, and 2) minimizing enrichment to downstream aquatic ecosystems by sequestering nutrients that escape the nutrient loop.
54 ENVIRONMENTAL SCIENCES↗
Editorial: Linking Hydrological and Biogeochemical Processes in Riparian Corridors
The riparian corridor is a key component of the critical zone and an essential component of watershed systems. According to Merriam-Webster Dictionary, the word riparian is derived from the Latin word riparius, meaning “existing alongside a river.” Riparian corridors typically extend from a few meters to hundreds of meters adjacent to a river and are marked by rich biodiversity, vegetation, and intense biogeochemical activity. They act as integrators of watershed processes and constitute the primary pathways for the subsurface geochemical exports from the watershed. Although riparian corridors comprise only 2–10% of a watershed's area, as much as 90–98% of biogeochemical processing in watersheds occurs in this region, thereby affecting the subsurface geochemical exports and downstream river water quality. Indeed, the riparian corridor is a good example of the Pareto principle. This outsized contribution occurs at the interface between aquatic (river) and terrestrial (land) environments, where interactions between hydrologic and biogeochemical processes are intensified. Variations in the river corridor over time can thus also have outsize impacts. Therefore, it is important to understand the hydrological and biogeochemical linkages in riparian corridors to determine water availability and quality for sustainable management.
54 ENVIRONMENTAL SCIENCES↗
Diverse PFAS produce unique transcriptomic changes linked to developmental toxicity in zebrafish
Per- and polyfluoroalkyl substances (PFAS) are a widespread and persistent class of contaminants posing significant environmental and human health concerns. Comprehensive understanding of the modes of action underlying toxicity among structurally diverse PFAS is mostly lacking. To address this need, we recently reported on our application of developing zebrafish to evaluate a large library of PFAS for developmental toxicity. In the present study, we prioritized 15 bioactive PFAS that induced significant morphological effects and performed RNA-sequencing to characterize early transcriptional responses at a single timepoint (48 h post fertilization) after early developmental exposures (8 h post fertilization). Internal concentrations of 5 of the 15 PFAS were measured from pooled whole fish samples across multiple timepoints between 24–120 h post fertilization, and additional temporal transcriptomics at several timepoints (48–96 h post fertilization) were conducted for Nafion byproduct 2. A broad range of differentially expressed gene counts were identified across the PFAS exposures. Most PFAS that elicited robust transcriptomic changes affected biological processes of the brain and nervous system development. While PFAS disrupted unique processes, we also found that similarities in some functional head groups of PFAS were associated with the disruption in expression of similar gene sets. Body burdens after early developmental exposures to select sulfonic acid PFAS, including Nafion byproduct 2, increased from the 24–96 h post fertilization sampling timepoints and were greater than those of sulfonamide PFAS of similar chain lengths. In parallel, the Nafion byproduct 2-induced transcriptional responses increased between 48 and 96 h post fertilization. PFAS characteristics based on toxicity, transcriptomic effects, and modes of action will contribute to further prioritization of PFAS structures for testing and informed hazard assessment.
59 BASIC BIOLOGICAL SCIENCES↗
Whole Genome Sequencing Links Mycobacterium bovis From Cattle, Cheese and Humans in Baja California, Mexico
Mycobacterium bovis causes tuberculosis (TB) in cattle, which in turn can transmit the pathogen to humans. Tuberculosis in dairy cattle is of particular concern where the consumption of raw milk and dairy products is customary. Baja California (BCA), Mexico, presents high prevalence of TB in both cattle and humans, making it important to investigate the molecular epidemiology of the disease in the region. A long-term study was undertaken to fully characterize the diversity of M. bovis genotypes circulating in dairy cattle, cheese and humans in BCA by whole-genome sequencing (WGS). During a 2-year period, 412 granulomatous tissue samples were collected from local abattoirs and 314 cheese samples were purchased from local stores and vendors in BCA and sent to the laboratory for mycobacterial culture, histology, direct PCR and WGS. For tissue samples M. bovis was recovered from 86.8%, direct PCR detected 90% and histology confirmed 85.9% as mycobacteriosis-compatible. For cheese, M. bovis was recovered from 2.5% and direct PCR detected 6% of the samples. There was good agreement between diagnostic tests. Subsequently, a total of 345 whole-genome SNP sequences were obtained. Phylogenetic analysis grouped these isolates into 10 major clades. SNP analysis revealed putative transmission clusters where the pairwise SNP distance between isolates from different dairies was ≤3 SNP. Also, human and/or cheese isolates were within 8.45 (range 0–17) and 5.8 SNP (range 0–15), respectively, from cattle isolates. Finally, a comparison between the genotypes obtained in this study and those reported previously suggests that the genetic diversity of M. bovis in BCA is well-characterized, and can be used to determine if BCA is the likely source of M. bovis in humans and cattle in routine epidemiologic investigations and future studies. In conclusion, WGS provided evidence of ongoing local transmission of M. bovis among the dairies in this high-TB burden region of BCA, as well as show close relationships between isolates recovered from humans, cheese, and cattle. This confirms the need for a coordinated One Health approach in addressing the elimination of TB in animals and humans. Overall, the study contributes to the knowledge of the molecular epidemiology of M. bovis in BCA, providing insight into the pathogen's dynamics in a high prevalence setting.
59 BASIC BIOLOGICAL SCIENCES↗
Simulated Microgravity Alters Gene Regulation Linked to Immunity and Cardiovascular Disease
Microgravity exposure induces a cephalad fluid shift and an overall reduction in physical activity levels which can lead to cardiovascular deconditioning in the absence of countermeasures. Future spaceflight missions will expose crew to extended periods of microgravity among other stressors, the effects of which on cardiovascular health are not fully known. In this study, we determined cardiac responses to extended microgravity exposure using the rat hindlimb unloading (HU) model. We hypothesized that exposure to prolonged simulated microgravity and subsequent recovery would lead to increased oxidative damage and altered expression of genes involved in the oxidative response. To test this hypothesis, we examined hearts of male (three and nine months of age) and female (3 months of age) Long–Evans rats that underwent HU for various durations up to 90 days and reambulated up to 90 days post-HU. Results indicate sex-dependent changes in oxidative damage marker 8-hydroxydeoxyguanosine (8-OHdG) and antioxidant gene expression in left ventricular tissue. Three-month-old females displayed elevated 8-OHdG levels after 14 days of HU while age-matched males did not. In nine-month-old males, there were no differences in 8-OHdG levels between HU and normally loaded control males at any of the timepoints tested following HU. RNAseq analysis of left ventricular tissue from nine-month-old males after 14 days of HU revealed upregulation of pathways involved in pro-inflammatory signaling, immune cell activation and differential expression of genes associated with cardiovascular disease progression. Taken together, these findings provide a rationale for targeting antioxidant and immune pathways and that sex differences should be taken into account in the development of countermeasures to maintain cardiovascular health in space.
Genetics & Heredity↗
De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus Vetrix are interesting for comparative studies of sex determination systems, yet genomic resources for these species are still quite limited. Only a few annotated reference genome assemblies are available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of 11 shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism, and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance.
59 BASIC BIOLOGICAL SCIENCES↗
The Messy Alkaline Formose Reaction and Its Link to Metabolism
Sugars are essential for the formation of genetic elements such as RNA and as an energy/food source. Thus, the formose reaction, which autocatalytically generates a multitude of sugars from formaldehyde, has been viewed as a potentially important prebiotic source of biomolecules at the origins of life. When analyzing our formose solutions we find that many of the chemical species are simple carboxylic acids, including α-hydroxy acids, associated with metabolism. In this work we posit that the study of the formose reaction, under alkaline conditions and moderate hydrothermal temperatures, should not be solely focused on sugars for genetic materials, but should focus on the origins of metabolism (via metabolic molecules) as well.
59 BASIC BIOLOGICAL SCIENCES↗
Linking Pharmacogenomic Information on Drug Safety and Efficacy with Ethnic Minority Populations
Numerous prescription drugs’ labeling contains pharmacogenomic (PGx) information to aid health providers and patients in the safe and effective use of drugs. However, clinical studies for such PGx biomarkers and related drug doses are generally not conducted in diverse ethnic populations. Thus, it is urgently important to incorporate PGx information with genetic characteristics of racial and ethnic minority populations and utilize it to promote minority health. In this project a bioinformatics approach was developed to enhance the collection of PGx information related to ethnic minorities to pave the way toward understanding the population-wide utility of PGx information. To address this challenge, we first gathered PGx information from drug labels. Second, we extracted data on the allele frequency information of genetic variants in ethnic minority groups from public resources. Then, we collected published research articles on PGx biomarkers and related drugs for reference. Finally, the data were integrated and formatted to build a new PGx database containing information on known drugs and biomarkers for ethnic minority groups. This database provides scientific information needed to evaluate available PGx information to enhance drug dose selection and drug safety for ethnic minority populations.
60 APPLIED LIFE SCIENCES↗
Quasars with Proper Motions and the Link to Double and Multiple AGNs
Gaia used a large sample of photometrically selected active galactic nuclei (AGNs) and quasars to remove the residual spin of its global proper motion system in order to achieve a maximally inertial reference frame. A small fraction of these reference objects have statistically significant astrometric proper motions in Gaia EDR3. We compile a source sample of 105,593 high-fidelity AGNs with accurate spectroscopically determined redshifts above 0.5 from the SDSS and normalized proper motions below 4. The rate of genuinely perturbed proper motions is at least 0.17%. A smaller high completeness sample of 152 quasars with excess proper motions at a confidence level of 0.9995 is examined in detail. Pan-STARRS images and Gaia-resolved pairs reveal that 29% of the sample are either double sources or gravitationally lensed quasars. An Anderson–Darling test on parameters of a smaller high-reliability sample and their statistical controls reveals 17 significant factors that favor multiplicity and multi-source structure as the main cause of perturbed astrometry. Using a nearest-neighbor distance statistical analysis and counts of close companions in Gaia on a much larger initial sample of AGNs, an excess of closely separated sources in Gaia is detected. At least 0.33% of all optical quasars are genuinely double or multiply imaged. We provide a list of 44 candidate double or multiple AGNs and four previously known gravitational lenses. Many proper motion quasars may be more closely separated, unresolved doubles exhibiting the variability imposed motion effect, and a smaller fraction may be chance alignments with foreground stars causing weak gravitational lensing.
Astrometric microlensing effect↗
Warped Disk Galaxies. I. Linking U-type Warps in Groups/Clusters to Jellyfish Galaxies
Warped disk galaxies are classified into two morphologies: S and U types. Conventional theories routinely attribute both types to galactic tidal interaction and/or gas accretion, but reproducing U types in simulations is extremely challenging. Here we investigate whether both types are governed by the same mechanisms using the most extensive sample of ~8000 nearby (0.02 < z < 0.06) massive (M*/M ⊙ > 10 9 ) edge-on disks from the Sloan Digital Sky Survey. We find that U types show on average bluer optical colors and a higher specific star formation rate (sSFR) than S types, with more strongly warped U types having a higher sSFR. We also find that while the S-type warp properties correlate with the tidal force by the nearest neighbor regardless of the environment, there is no such correlation for U types in groups/clusters, suggesting a nontidal mechanism could be at play for U types, such as ram pressure stripping (RPS). Indeed, U types are more common in groups/clusters than in fields and they have stellar mass, gas fraction, sSFR enhancement, and phase-space distribution closely analogous to RPS-induced jellyfish galaxies in clusters. We furthermore show that the stellar disks of most RPS galaxies in the IllustrisTNG simulation are warped in a U shape and bent in the opposite direction of stripped gas tails, satisfying theoretical expectations for stellar warps embedded in jellyfishes. We therefore suggest that despite the majority of U types that live in fields being still less explained, RPS can be an alternative origin for those in groups/clusters.
79 ASTRONOMY AND ASTROPHYSICS↗
DESI Emission-line Galaxies: Unveiling the Diversity of [O II ] Profiles and Its Links to Star Formation and Morphology
We study the [O II ] profiles of emission-line galaxies (ELGs) from the Early Data Release of the Dark Energy Spectroscopic Instrument (DESI). To this end, we decompose and classify the shape of [O II ] profiles with the first two eigenspectra derived from principal component analysis. Our results show that DESI ELGs have diverse line profiles, which can be categorized into three main types: (1) narrow lines with a median width of ∼50 km s −1 , (2) broad lines with a median width of ∼80 km s −1 , and (3) two redshift systems with a median velocity separation of ∼150 km s −1 , i.e., double-peak galaxies. To investigate the connections between the line profiles and galaxy properties, we utilize the information from the COSMOS data set and compare the properties of ELGs, including star formation rate (SFR) and galaxy morphology, with the average properties of reference star-forming galaxies with similar stellar mass, sizes, and redshifts. Our findings show that, on average, DESI ELGs have a higher SFR and more asymmetrical/disturbed morphology than the reference galaxies. Moreover, we uncover a relationship between the line profiles, the excess SFR, and the excess asymmetry parameter, showing that DESI ELGs with broader [O II ] line profiles have more disturbed morphology and higher SFR than the reference star-forming galaxies. Finally, we discuss possible physical mechanisms giving rise to the observed relationship and the implications of our findings on the galaxy clustering measurements, including the halo occupation distribution modeling of DESI ELGs and the observed excess velocity dispersion of the satellite ELGs.
79 ASTRONOMY AND ASTROPHYSICS↗