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Facile Labeling of Sieve Element Phloem-Protein Bodies Using the Reciprocal Oligosaccharide Probe OGA488
Sieve elements of many angiosperms contain structural phloem proteins (P-proteins) that can interact to create large P-protein bodies. P-protein bodies can occlude sieve plates upon injury but the range of functional and physiological roles of P-proteins remains uncertain, in part because of challenges in labeling and visualization methods. Here, we show that a reciprocal oligosaccharide probe, OGA 488 , can be used in rapid and sensitive labeling of P-protein bodies in Arabidopsis, poplar, snap bean and cucumber in histological sections. OGA 488 labeling of knockouts of the two Arabidopsis P-protein-encoding genes, AtSEOR1 and AtSEOR2 , indicated that labeling is specific to AtSEOR2. That protein bodies were labeled and visible in Atseor1 knockouts indicates that heterodimerization of AtSEOR1 and AtSEOR2 may not be necessary for P-protein body formation. Double labeling with a previously characterized stain for P-proteins, sulphorhodamine 101, confirmed P-protein labeling and also higher specificity of OGA 488 for P-proteins. OGA 488 is thus robust and easily used to label P-proteins in histological sections of multiple angiosperm species.
Binding of Formic Acid on Anatase TiO2(101)
The adsorption of formic acid (FA) and the formation of formate species on metal oxide surfaces are of great interest in catalysis. Formic acid is used to probe the adsorption properties of surface sites and formates are common intermediates in many catalytic reactions. Here we focus on the interaction of FA with a prototypical anatase TiO2(101) surface by using a combination of scanning tunneling microscopy (STM), infrared reflection absorption spectroscopy (IRAS), electron stimulated desorption (ESD), and density functional theory (DFT) to assess the coverage dependent evolution of different FA-derived surface species at low temperatures (80–240 K). We find that isolated FA adsorbs at 80 K in both monodentate (MD) and bidentate (BD) configurations on top of undercoordinated Ti sites (Ti5c). The MD form is likely deprotonated and readily converts upon annealing to bridging BD on two neighboring Ti5c sites. DFT calculations show that molecularly-bound MD FA is metastable and readily converts into a deprotonated state in the proximity of subsurface oxygen vacancy. The stability of the MD species increases as the availability of the paired Ti5c sites for BD formation diminishes at high coverages. Upon surface saturation, a mixed configuration of alternating bidentate and monodentate species with coverage of 2/3 FA/Ti5c represents the most favorable configuration. This is in contrast with the adsorption of FA on rutile TiO2(110) and many other oxides, where bidentate formate species dominate. Y.W., A.D., G.A.K., R.R., N.G.P., and Z.D. were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences (CSGB) under FWP 47319. B.W. and A.S. acknowledge the support of DOE BES, CSGB Division under Award DESC0007347. The experimental studies were performed in EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated for DOE by Battelle. The authors also acknowledge computational resources from the TIGRESS high-performance computer center at Princeton University.
PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction
Abstract Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute ( Pf Ago)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology.
Observation of molecular hydrogen produced from bridging hydroxyls on anatase TiO2(101)
Anatase TiO2 is used extensively in a wide range of catalytic and photocatalytic processes and is a promising catalyst for hydrogen production. Here, we show that molecular hydrogen was produced from bridging hydroxyls, HOb, on the (101) surface of single crystal anatase (a-TiO2(101)). Electron bombardment at 30 K produced bridging oxygen vacancies in the surface. Deuterated bridging hydroxyls, DOb, were subsequently formed via dissociation of adsorbed D2O and confirmed by infrared reflection-absorption spectroscopy. During temperature programmed desorption (TPD) spectroscopy, D2 desorption was observed at 520 K. Density functional theory calculations show that both H2 and H2O production from HOb are endothermic at 0 K on a-TiO2(101), but H2 (H2O) desorption is entropically driven above 230 K (800 K). The calculated activation barrier for H2 desorption is 1.40 eV, which is similar to the desorption energy obtained from analysis of the D2 TPD spectra. The H2 desorption likely proceeds in two steps: H atom diffusion on the surface and then recombination. The calculations indicate that diffusion of the hydrogen atoms into the subsurface could also be an important process. We thank Drs. Z. Dohnalek and R. Rousseau for stimulating discussions. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, & Biosciences and performed in EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated for DOE by Battelle. We also acknowledge the WPI computational facilities for providing resources to perform the DFT studies.
De novo design of protein homodimers containing tunable symmetric protein pockets
Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.
Little prairie under the panel: testing native pollinator habitat seed mix establishment at three utility-scale solar sites in Minnesota
Abstract As more land is being utilized for large-scale solar energy projects, there are increasing discussions from stakeholders on how to utilize land under solar panels to promote biodiversity. One path is to plant habitat beneficial to pollinators and other insects, but there have been few long-term studies that examine how different vegetation and seed mixes establish underneath solar panels. This study addresses a scientific gap to determine whether native pollinator seed mixes successfully establish over time under solar arrays using a systematic assessment of eight seed mixes planted at three utility-scale solar sites in Minnesota. We assess establishment with a percent native coverage metric, which is an assessment of native species observations compared to total observations during percent cover analyses in our vegetative test plots. The percent native coverage metric allows for a measurement of how the seed mix established and how the seed mix persists over time. The percent native coverage under and in between the solar photovoltaic (PV) arrays rose from 10% after one year of planting to 58% after three years across all sites, while the native coverage of the full sun control area rose from 9.6% to 70% under the same period, showing that native prairie and pollinator plants successfully established under the array, although to a lesser extent than in full sun conditions. Percent native coverage under the PV arrays rose 5- to 8-fold for each of the three sites from over the course of the study, while the coverage of weeds decreased for all three sites over the same period. Percent native coverage varied by seed mix over the project years, but every seed mix experienced a higher percent native coverage year after year under the PV arrays. Our results did not indicate a difference in establishment across placement within the array; the center, west, and east portions of the areas in between panels had similar establishment rates at two out of three sites, indicating that the same seed mix can be applied throughout the array. Out of 101 plant species seeded, we observed the establishment of 68 species in our vegetative test plots, and we detailed the top 20 observed species to inform future seed mix development. Based on these findings, native pollinator vegetation can establish over time at solar arrays, and it can be suitable for creating habitat at utility-scale solar sites.
The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species
This study investigated the diversity of yeast species associated with rotting wood in Brazilian Amazonian rainforests. Herein, a total of 569 yeast strains were isolated from rotting wood samples collected in three Amazonian areas (Universidade Federal do Amazonas-Universidade Federal do Amazonas [UFAM], Piquiá, and Carú) in the municipality of Itacoatiara, Amazon state. The samples were cultured in yeast nitrogen base (YNB)-d-xylose, YNB-xylan, and sugarcane bagasse and corncob hemicellulosic hydrolysates (undiluted and diluted 1:2 and 1:5). Sugiyamaella was the most prevalent genus identified in this work, followed by Kazachstania. The most frequently isolated yeast species were Schwanniomyces polymorphus, Scheffersomyces amazonensis, and Wickerhamomyces sp., respectively. The alpha diversity analyses showed that the dryland forest of UFAM was the most diverse area, while the floodplain forest of Carú was the least. Additionally, the difference in diversity between UFAM and Carú was the highest among the comparisons. Thirty candidates for new yeast species were obtained, representing 36% of the species identified and totaling 101 isolates. Among them were species belonging to the clades Spathaspora, Scheffersomyces, and Sugiyamaella, which are recognized as genera with natural xylose-fermenting yeasts that are often studied for biotechnological and ecological purposes. The results of this work showed that rotting wood collected from the Amazonian rainforest is a tremendous source of diverse yeasts, including candidates for new species.
101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens
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Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti.
The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers. Citation: Nybo JL, Vesth TC, Theobald S, Frisvad JC, Larsen TO, Kjaerboelling I, Rothschild-Mancinelli K, Lyhne EK, Barry K, Clum A, Yoshinaga Y, Ledsgaard L, Daum C, Lipzen A, Kuo A, Riley R, Mondo S, LaButti K, Haridas S, Pangalinan J, Salamov AA, Simmons BA, Magnuson JK, Chen J, Drula E, Henrissat B, Wiebenga A, Lubbers RJM, Müller A, dos Santos Gomes AC, Mäkelä MR, Stajich JE, Grigoriev IV, Mortensen UH, de Vries RP, Baker SE, Andersen MR (2025). Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti. Studies in Mycology 111: 101-114. doi: 10.3114/sim.2025.111.03.
A subdermal tagging technique for juvenile sturgeon using a new self-powered acoustic tag
Abstract Background A new technology for a self-powered acoustic tag (SPT) was developed for active tracking of juvenile fish, intended to avoid the typical battery life constraints associated with active telemetry technology. We performed a laboratory study to evaluate a subdermal tagging technique for the SPT and effects of the tag on survival, tag retention, and growth in juvenile white sturgeon ( Acipenser transmontanus ). Results Survival was associated with tag retention. White sturgeon implanted with the SPT ( n = 30) had 93% survival and tag retention by day 28, 67% by day 101, and 38% by day 595 post-tagging. Sturgeon implanted with a passive integrated transponder (PIT) tag only (control group) had 96% survival and tag retention by day 28, and through day 101 post-tagging. Fish in the PIT group were repurposed after day 101, so no comparisons with this group were made at day 595 post-tagging. Specific growth rate (SGR) for fork length was a median of 0.25% day −1 by day 28 for the SPT group, which was significantly lower than the PIT group (median: 0.42% day −1 ; n = 27). The SPT and PIT groups had similar SGR fork length by day 101 post-tagging (0.22 and 0.25% day −1 , respectively). SGR weight was also lower for the SPT group compared to the PIT group on day 28 (1.39 and 2.11% day −1 , respectively), but the difference again dissipated by day 101 (0.79 and 0.88% day −1 , respectively). Conclusion The tagging technique and placement of the SPT allowed the tag to remain upright along the flank of the sturgeon to ensure maximum battery output of the SPT; however, retention rates of the SPT were not ideal. We provided suggestions to improve the tagging technique. Suggestions included tagging fish that are > 400 mm FL, moving the incision location to extend the cavity and create a pocket for the placement of the SPT, and performing a quantitative wound-healing evaluation. Future studies are therefore recommended to evaluate these suggestions.
Effects of photon irradiation in the presence and absence of hindlimb unloading on the behavioral performance and metabolic pathways in the plasma of Fischer rats
The space environment astronauts experience during space missions consists of multiple environmental challenges, including microgravity. In this study, we assessed the behavioral and cognitive performances of male Fisher rats 2 months after sham irradiation or total body irradiation with photons in the absence or presence of simulated microgravity. We analyzed the plasma collected 9 months after sham irradiation or total body irradiation for distinct alterations in metabolic pathways and to determine whether changes to metabolic measures were associated with specific behavioral and cognitive measures. A total of 344 male Fischer rats were irradiated with photons (6 MeV; 3, 8, or 10 Gy) in the absence or presence of simulated weightlessness achieved using hindlimb unloading (HU). To identify potential plasma biomarkers of photon radiation exposure or the HU condition for behavioral or cognitive performance, we performed regression analyses. The behavioral effects of HU on activity levels in an open field, measures of anxiety in an elevated plus maze, and anhedonia in the M&M consumption test were more pronounced than those of photon irradiation. Phenylalanine, tyrosine, and tryptophan metabolism, and phenylalanine metabolism and biosynthesis showed very strong pathway changes, following photon irradiation and HU in animals irradiated with 3 Gy. Here, 29 out of 101 plasma metabolites were associated with 1 out of 13 behavioral measures. In the absence of HU, 22 metabolites were related to behavioral and cognitive measures. In HU animals that were sham-irradiated or irradiated with 8 Gy, one metabolite was related to behavioral and cognitive measures. In HU animals irradiated with 3 Gy, six metabolites were related to behavioral and cognitive measures. These data suggest that it will be possible to develop stable plasma biomarkers of behavioral and cognitive performance, following environmental challenges like HU and radiation exposure.
Genomes OnLine Database (GOLD) v.8: overview and updates
The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world. The current version of the database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) and Analysis Projects (283 481). These four levels contain over 600 metadata fields, which includes 76 controlled vocabulary (CV) tables containing 3873 terms. GOLD provides an interactive web user interface for browsing and searching by a wide range of project and metadata fields. Users can enter details about their own projects in GOLD, which acts as a gatekeeper to ensure that metadata is accurately documented before submitting sequence information to the Integrated Microbial Genomes (IMG) system for analysis. In order to maintain a reference dataset for use by members of the scientific community, GOLD also imports projects from public repositories such as GenBank and SRA. Here, the current status of the database, along with recent updates and improvements are described in this manuscript.
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi
Abstract Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.
DISCOVR strain pipeline screening – Part I: Maximum specific growth rate as a function of temperature and salinity for 38 candidate microalgae for biofuels production
Here, to identify high productivity strains for microalgal biofuels generation, the maximum specific growth rate of 38 strains was measured as a function of salinity (i.e., 5, 15, and 35 PSU) and temperature (i.e., at 8 temperatures along a linear gradient from ca. 5 to 45°C) to determine the most suitable growth medium salinity and best growing season, respectively, for outdoor raceway pond cultivation. The following strains were evaluated: Agmenellum quadruplicatum UTEX 2268, Anabaena sp. ATCC 33081, Arthrospira fusiformis UTEX 2721, Arthrospira platensis UTEX 3086, Chlorella vulgaris NREL 4-C12, Chlorella autotrophica CCMP 243, Chlorella sorokiniana DOE1044, Chlorella sorokiniana DOE 1116, Chlorella sorokiniana DOE 1412 (UTEXB3016), Chlorella vulgaris LRB AZ-1201, Chlorococcum littorale UTEX 117, Chlorococcum sp. UTEX-B P7, Chloromonas reticulata CCALA 870, Coelastrella sp. DOE 0202, Cyanobacterium sp. AB1, Micractinium reisseri NREL 14-F2, Microchloropsis gaditana CCMP1894, Microchloropsis salina CCMP 1776, Monoraphidium sp. MONOR1, Monoraphidium minutum 26B-AM, Nannochloropsis oceanica CCAP 849/10, Oscillatoria cf. priestleyi CCMEE 5020.1-1, Picochlorum celeri TG2-WT-CSM/EMRE, Picochlorum oklahomensis CCMP 2329, Picochlorum renovo NREL 39-A8, Picochlorum soloecismus DOE 101, Porphyridium cruentum CCMP 675, Scenedesmus acutus LRB-AP-0401, Scenedesmus obliquus DOE 0152.z, Scenedesmus obliquus UTEX393,Scenedesmus rubescens NREL 46B-D3, Scenedesmus sp. IITRIND2, Stichococcus minor CCMP 819, Stichococcus minutus CCALA 727, Synechococcus elongatus UTEX2973.1, Tetraselmis striata LANL 1001, Tisochrysis lutea CCMP 1324, and Tribonema minus UTEXB3156. For each strain, the identity and the presence of bacterial cohorts was determined using 18S and 16S rDNA sequencing, respectively. The maximum specific growth rate versus temperature data were also used to determine the activation energies (Arrhenius equation) for most strains. For all strains, the measured salinity and temperature tolerance data were compared to those reported in the literature. The fastest growing strains were down-selected for subsequent biomass productivity measurements in climate-simulation photobioreactors, as reported in the next paper in the issue.
Unveiling the transferability of PLSR models for leaf trait estimation: lessons from a comprehensive analysis with a novel global dataset
Leaf traits are essential for understanding many physiological and ecological processes. Partial least squares regression (PLSR) models with leaf spectroscopy are widely applied for trait estimation, but their transferability across space, time, and plant functional types (PFTs) remains unclear. We compiled a novel dataset of paired leaf traits and spectra, with 47 393 records for >700 species and eight PFTs at 101 globally distributed locations across multiple seasons. Using this dataset, we conducted an unprecedented comprehensive analysis to assess the transferability of PLSR models in estimating leaf traits. While PLSR models demonstrate commendable performance in predicting chlorophyll content, carotenoid, leaf water, and leaf mass per area prediction within their training data space, their efficacy diminishes when extrapolating to new contexts. Specifically, extrapolating to locations, seasons, and PFTs beyond the training data leads to reduced R 2 (0.12–0.49, 0.15–0.42, and 0.25–0.56) and increased NRMSE (3.58–18.24%, 6.27–11.55%, and 7.0–33.12%) compared with nonspatial random cross-validation. The results underscore the importance of incorporating greater spectral diversity in model training to boost its transferability. These findings highlight potential errors in estimating leaf traits across large spatial domains, diverse PFTs, and time due to biased validation schemes, and provide guidance for future field sampling strategies and remote sensing applications.
Isolation of phosphorus-hyperaccumulating microalgae from revolving algal biofilm (RAB) wastewater treatment systems
Excess phosphorus (P) in wastewater effluent poses a serious threat to aquatic ecosystems and can spur harmful algal blooms. Revolving algal biofilm (RAB) systems are an emerging technology to recover P from wastewater before discharge into aquatic ecosystems. In RAB systems, a community of microalgae take up and store wastewater P as polyphosphate as they grow in a partially submerged revolving biofilm, which may then be harvested and dried for use as fertilizer in lieu of mined phosphate rock. In this work, we isolated and characterized a total of 101 microalgae strains from active RAB systems across the US Midwest, including 82 green algae, 9 diatoms, and 10 cyanobacteria. Strains were identified by microscopy and 16S/18S ribosomal DNA sequencing, cryopreserved, and screened for elevated P content (as polyphosphate). Seven isolated strains possessed at least 50% more polyphosphate by cell dry weight than a microalgae consortium from a RAB system, with the top strain accumulating nearly threefold more polyphosphate. These top P-hyperaccumulating strains include the green alga Chlamydomonas pulvinata TCF-48 g and the diatoms Eolimna minima TCF-3d and Craticula molestiformis TCF-8d, possessing 11.4, 12.7, and 14.0% polyphosphate by cell dry weight, respectively. As a preliminary test of strain application for recovering P, Chlamydomonas pulvinata TCF-48 g was reinoculated into a bench-scale RAB system containing Bold basal medium. The strain successfully recolonized the system and recovered twofold more P from the medium than a microalgae consortium from a RAB system treating municipal wastewater. These isolated P-hyperaccumulating microalgae may have broad applications in resource recovery from various waste streams, including improving P removal from wastewater.