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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake

Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria "MBAE14." While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO 2 -fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation ( amo and hao ) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2010

Permissible Exposure Level for Lunar Dusts: Gaps are Closing

Space faring nations plan to return human explorers to the moon within the next decade. Experience during the Apollo flights suggests that lunar dust will invariably get into the habitat where the finest portion (less than 5 micrometers) could be inhaled by the crew before it is cleared from the atmosphere. NASA is developing a database from which a 6-month, episodic exposure standard for lunar dust can be set. Three kinds of moon dust were prepared from a parent sample of Apollo 14 regolith #14003,96. Our goal was to prepare each type of dust sample with a mean diameter less than 2 m, which is suitable for instillation into the lungs of rats. The three samples were prepared as follows: separation from the parent sample using a fluidized bed, grinding using a jet mill grinder, or grinding with a ball-mill grinder. Grinding simulated restoration of surface activation of dust expected to occur at the surface of the moon on native lunar dust. We used two grinding methods because they seemed to produce different modes of activation. The effects of grinding were preserved by maintaining the dust in ultra-pure nitrogen until immediately before it was placed in suspension for administration to rats. The dust was suspended in physiological saline with 10% Survanta, a lung surfactant. Rats were given intratrachael instillations of the dust suspension at three doses. In addition to the three moon dusts (A, C and E), we instilled the same amount of a negative control (TiO2, B) and a highly-toxic, positive control (quartz, D). These additional mineral dusts were selected because they have well-established and very different permissible exposure levels (PELs). Our goal was to determine where lunar dusts fit between these extremes, and then estimate a PEL for each lunar dust. We evaluated many indices of toxicity to the lung. The figure shows the changes in lactate dehydrogenase (LDH), a marker of cell death, for the five dusts. Benchmark dose software (Version 2.1.2) from the Environmental Protection Agency was used to estimate the 10% effect levels (BMD(sub 10)) using five models. The best-fitting model was used to estimate the optimal BMD(sub 10) (table)

James, John T.↗
DOE OSTI2019

Clinical Significance of {sup 18}F-Fluorodeoxyglucose-Positron Emission Tomography-Positive Lymph Nodes to Outcomes of Trimodal Therapy for Esophageal Squamous Cell Carcinoma

Background: The clinical significance of lymph node (LN) status determined by preoperative {sup 18}F-fluorodeoxyglucose-positron emission tomography (FDG-PET) has not been investigated in patients with locally advanced esophageal squamous cell carcinoma (ESCC) treated with neoadjuvant chemoradiotherapy (NCRT) followed by surgery (trimodal therapy). Methods: This study reviewed 132 consecutive patients with ESCC who had been preoperatively evaluated using FDG-PET before and after NCRT to analyze associations among LN status according to PET findings, pathologic LN metastasis, and prognosis of ESCC after trimodal therapy. Results: Lymph nodes that were PET-positive both before and after NCRT comprised significant predictive markers of pathologic LN metastasis in station-by-station analyses (sensitivity, specificity, and accuracy respectively 41.7%, 95.0%, and 92.7% before, and 12.0%, 99.4%, and 95.6% after NCRT; both p < 0.0001). The numbers of LNs evaluated using PET before and after NCRT were significantly associated with those of pathologic metastatic LNs. Uni- and multivariable analyses selected LN status determined by PET before NCRT as a significant independent predictor of both recurrence-free [LN-negative vs LN-positive: hazard ratio (HR) 1.90; 95% confidence interval (CI) 1.02–3.23; p = 0.045] and overall survival (HR 2.62; 95% CI 1.29–5.30; p = 0.01). Conclusions: The status of LN determined by preoperative FDG-PET is significantly associated with pathologic LN status and the prognosis of ESCC with trimodal therapy. Thus, FDG-PET is a useful diagnostic tool for preoperative prediction of pathologic LN metastasis and survival among patients with ESCC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control

The larvae of click beetles (Coleoptera: Elateridae), known as “wireworms,” are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships of three species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of multiple genetically distinct groups that diverged in the Pleistocene but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. We also found within-species population structure across relatively short geographic distances. Genome scans for selection provided preliminary evidence for signatures of adaptation associated with different pesticide treatments in an agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in developing effective wireworm control strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers

An assessment of genetic diversity of marine populations is critical not only for the understanding and preserving natural biodiversity but also for its commercial potential. As commercial demand rises for marine resources, it is critical to generate baseline information for monitoring wild populations. Furthermore, anthropogenic stressors on the coastal environment, such as warming sea temperatures and overharvesting of wild populations, are leading to the destruction of keystone marine species such as kelps. In this study, we conducted a fine-scale genetic analysis using genome-wide high-density markers on Northwest Atlantic sugar kelp. The population structure for a total of 149 samples from the Gulf of Maine (GOM) and Southern New England (SNE) was investigated using AMOVA, FST, admixture, and PCoA. Genome-wide association analyses were conducted for six morphological traits, and the extended Lewontin and Krakauer (FLK) test was used to detect selection signatures. Our results indicate that the GOM region is more heterogeneous than SNE. These two regions have large genetic difference (between-location FST ranged from 0.21 to 0.32) and were separated by Cape Cod, which is known to be the biogeographic barrier for other taxa. We detected one significant SNP (P = 2.03 × 10 -7 ) associated with stipe length, and 248 SNPs with higher-than-neutral differentiation. The findings of this study provide baseline knowledge on sugar kelp population genetics for future monitoring, managing and potentially restoring wild populations, as well as assisting in selective breeding to improve desirable traits for future commercialization opportunities.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2009

Cytogenetic Response to Ionizing Radiation Exposure in Human Fibroblasts with Suppressed Expression of Non-DSB Repair Genes

Changes of gene expression profile are one of the most important biological responses in living cells after ionizing radiation (IR) exposure. Although some studies have shown that genes up-regulated by IR may play important roles in DNA damage repair, the relationship between the regulation of gene expression by IR, particularly genes not known for their roles in double-strand break (DSB) repair, and its impact on cytogenetic responses has not been well studied. The purpose of this study is to identify new roles of IR inducible genes in radiation-induced chromosome aberrations and micronuclei formation. In the study, the expression of 25 genes selected on the basis of their transcriptional changes in response to IR was individually knocked down by small interfering RNA in human fibroblast cells. Frequencies of micronuclei (MN) formation and chromosome aberrations were measured to determine the efficiency of cytogenetic repair, and the fraction of bi-nucleated cells in the MN analysis was used as a marker for cell cycle progression. In response to gamma radiation, the formation of MN was significantly increased by suppressed expression of five genes: Ku70 (DSB repair pathway), XPA (nucleotide excision repair pathway), RPA1 (mismatch repair pathway), RAD17 and RBBP8 (cell cycle control). Knocked-down expression of four genes (MRE11A, RAD51 in the DSB pathway, SESN1, and SUMO1) significantly inhibited cell cycle progression, possibly because of severe impairment of DNA damage repair. Moreover, decreased XPA, p21, or MLH1 expression resulted in both significantly enhanced cell cycle progression and increased yields of chromosome aberrations, indicating that these gene products modulate both cell cycle control and DNA damage repair. Nine of these eleven genes, whose knock-down expression affected cytogenetic repair, were up-regulated in cells exposed to gamma radiation, suggesting that genes transcriptionally modulated by IR were critical to regulate IR-induced biological consequences. Furthermore, eight non-DBS repair genes showed involvement in regulating DSB repair, indicating that successful DSB repair requires both DSB repair mechanisms and non-DSB repair systems.

Zhang, Ye↗
DOE OSTI2020

Anthropogenic Markers in Alta Irrigation District Water Supply Wells

In July 2016, LLNL produced a report for the Kings River Watershed Coalition Authority (KRWCA) entitled “Groundwater Age and Nitrate Isotopic Composition in Alta Irrigation District Water Supply Wells” (Esser et al., 2016). That report summarized groundwater age and nitrate isotopic composition data produced by LLNL for Alta Irrigation District (AID) groundwater wells sampled by KRWCA in a pilot project to test the utility of advanced isotopic methods for constraining the timing and source of nitrate in groundwater at selected sites in the Kings River service area. One section of that report made recommendations for follow-on study. The first and strongest recommendation was to measure a wider suite of source tracers including co-contaminants such as herbicides, pesticides, pharmaceuticals, personal care products, and food constituents and additives. KRWCA followed up on this recommendation in Phase II of the pilot study by re-sampling the original set of wells and submitting the samples to a commercial laboratory for analysis of a limited range of co-contaminants (including pharmaceuticals, personal care products , and food constituents and additives, but not including herbicides or pesticides). They have asked that LLNL review and interpret these data in the context of previous LLNL analyses and to evaluate the utility of such co-contaminant analyses in providing additional constraints on the source of groundwater nitrate contamination in Alta Irrigation District water supply wells. The goal of the second phase of this pilot project is to evaluate the utility of co-contaminant occurrence for constraining nitrate source in groundwater at selected sites in the Kings River service area, with special reference to the use of such data in conjunction with advanced isotopic methods such as nitrate isotopic composition and groundwater age. Nitrate isotopic composition alone cannot distinguish nitrate derived from animal manure from nitrate derived from human septic waste. The presence or absence of agricultural chemicals (herbicides, pesticides, veterinary pharmaceuticals) or chemicals associated with people (human pharmaceuticals, artificial sweeteners) can help make this distinction. Co-contaminant analyses using multi-analyte LC-MS-MS protocols are now commercially available and reasonably priced. The feasibility and utility of the using co-contaminants for nitrate source attribution can be evaluated by 1) determining the degree to which co-contaminants occur in distinct and easily attributable groupings (e.g. agricultural chemicals vs personal care products and food additives); 2) determining the degree to which co-contaminant occurrence is consistent with nitrate isotopic composition and groundwater age (e.g. no co-contaminant occurrence in very old groundwater; co-contaminants consistent with animal manure or human septic waste occurring in groundwaters having nitrate isotopic composition also consistent with animal manure or human septic waste); and 3) determining the degree to which co-contaminants provide additional constraint on nitrate source over and beyond nitrate isotopic composition and groundwater age (e.g. distinguishing between animal manure and human septic waste).

58 GEOSCIENCES↗
NASA NTRS1999

Effect of optical digitizer selection on the application accuracy of a surgical localization system-a quantitative comparison between the OPTOTRAK and flashpoint tracking systems

Application accuracy is a crucial factor for stereotactic surgical localization systems, in which space digitization camera systems are one of the most critical components. In this study we compared the effect of the OPTOTRAK 3020 space digitization system and the FlashPoint Model 3000 and 5000 3D digitizer systems on the application accuracy for interactive localization of intracranial lesions. A phantom was mounted with several implantable frameless markers which were randomly distributed on its surface. The target point was digitized and the coordinates were recorded and compared with reference points. The differences from the reference points represented the deviation from the "true point." The root mean square (RMS) was calculated to show the differences, and a paired t-test was used to analyze the results. The results with the phantom showed that, for 1-mm sections of CT scans, the RMS was 0.76 +/- 0. 54 mm for the OPTOTRAK system, 1.23 +/- 0.53 mm for the FlashPoint Model 3000 3D digitizer system, and 1.00 +/- 0.42 mm for the FlashPoint Model 5000 system. These preliminary results showed that there is no significant difference between the three tracking systems, and, from the quality point of view, they can all be used for image-guided surgery procedures. Copyright 1999 Wiley-Liss, Inc.

Non-NASA Center↗
DOE OSTI2021

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees. For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR. We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy

In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t 1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4 + T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t 1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ~3 mo, the decay slope changes, and CD4 + T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.

2LTR circles↗
DOE OSTI2021

A synthetic RNA-mediated evolution system in yeast

Laboratory evolution is a powerful approach to search for genetic adaptations to new or improved phenotypes, yet either relies on labour-intensive human-guided iterative rounds of mutagenesis and selection, or prolonged adaptation regimes based on naturally evolving cell populations. Here we present CRISPR- and RNA-assisted in vivo directed evolution (CRAIDE) of genomic loci using evolving chimeric donor gRNAs continuously delivered from an error-prone T7 RNA polymerase, and directly introduced as RNA repair donors into genomic targets under either Cas9 or dCas9 guidance. We validate CRAIDE by evolving novel functional variants of an auxotrophic marker gene, and by conferring resistance to a toxic amino acid analogue in baker's yeast Saccharomyces cerevisiae with a mutation rate >3,000-fold higher compared to spontaneous native rate, thus enabling the first demonstrations of in vivo delivery and information transfer from long evolving RNA donor templates into genomic context without the use of in vitro supplied and pre-programmed repair donors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Machine learning prediction of incidence of Alzheimer’s disease using large-scale administrative health data

Nationwide population-based cohort provides a new opportunity to build an automated risk prediction model based on individuals’ history of health and healthcare beyond existing risk prediction models. We tested the possibility of machine learning models to predict future incidence of Alzheimer’s disease (AD) using large-scale administrative health data. From the Korean National Health Insurance Service database between 2002 and 2010, we obtained de-identified health data in elders above 65 years (N = 40,736) containing 4,894 unique clinical features including ICD-10 codes, medication codes, laboratory values, history of personal and family illness and socio-demographics. To define incident AD we considered two operational definitions: “definite AD” with diagnostic codes and dementia medication (n = 614) and “probable AD” with only diagnosis (n = 2026). We trained and validated random forest, support vector machine and logistic regression to predict incident AD in 1, 2, 3, and 4 subsequent years. For predicting future incidence of AD in balanced samples (bootstrapping), the machine learning models showed reasonable performance in 1-year prediction with AUC of 0.775 and 0.759, based on “definite AD” and “probable AD” outcomes, respectively; in 2-year, 0.730 and 0.693; in 3-year, 0.677 and 0.644; in 4-year, 0.725 and 0.683. The results were similar when the entire (unbalanced) samples were used. Important clinical features selected in logistic regression included hemoglobin level, age and urine protein level. This study may shed a light on the utility of the data-driven machine learning model based on large-scale administrative health data in AD risk prediction, which may enable better selection of individuals at risk for AD in clinical trials or early detection in clinical settings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (~0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Apela Promotes Cardiomyocyte Differentiation from Transgenic Human Embryonic Stem Cell Lines

Although embryonic stem (ES) cells (ESCs) may be a promising donor source for the repair of infarcted or ischemic heart tissues, their successful application in regenerative medicine has been hampered by difficulties in enriching, identifying, and selecting cardiomyocytes from the differentiating cells. We established transgenic human ES cell lines by transcriptional control of the α-cardiac myosin heavy chain (α-MHC) promoter driving green fluorescent protein (GFP) expression. Differentiated GFP-expressing cells display the characteristics of cardiomyocytes (CMs). Apela, a recently identified short peptide, up-regulated the expression of the cardiac-restricted transcription factors Tbx5 and GATA4 as well as differentiated the cardiomyocyte markers α-MHC and β-MHC. Flow cytometric analysis showed that apela increased the percentage of GFP-expressing cells in the beating foci of the embryoid bodies. The percentage of cardiac troponin T (TNT)-positive cells and the protein expression of TNT were increased in the ES cell-derived CMs with apela treatment. Functionally, the contractile frequency of the ES-derived CMs responded appropriately to the vasoactive drugs isoprenaline and carbachol. Our work presented a protocol for specially labelling and enriching CMs by combining transgenic human ES cell lines and exogenous growth factor treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Identification of potent inhibitors of JUN N-terminal kinases for treatment of endometriosis and associated pain

Endometriosis, defined as the ectopic growth of endometrial tissue outside of the uterine cavity, is an inflammatory and hormone-dependent disease that causes excruciating pelvic pain, infertility, and significantly decreases quality of life in affected patients. The JUN N-terminal kinases (JNKs) are a leading class of nonhormonal therapeutic targets that have been validated in preclinical models of endometriosis and in a Phase 1/2 clinical trial. Despite their therapeutic potential, JNK inhibitors with increased potency and specificity are needed to address the inflammatory pathology of endometriosis and to prevent disease progression. Leveraging a DNA-encoded chemical library collection of ~4 billion compounds, we identified lead inhibitor CDD-2428 and optimized derivatives, CDD-2728 and CDD-3013, with excellent binding affinity to JNK1-3 (K d = 0.12 to 3.7 nM), enhanced selectivity, metabolic stability, and cellular permeability. Crystallographic and biochemical studies confirmed that CDD-3013 exhibited superior kinase selectivity with improved efficacy compared to existing JNK inhibitors. In primary endometriosis cell models, CDD-2728 and CDD-3013 suppressed JNK-dependent inflammatory signaling, dampening pathways linked to pain, invasion, angiogenesis, and macrophage recruitment. In an endometriosis mouse model, both CDD-2728 and CDD-3013 reduced endometriotic lesion size, macrophage infiltration, and cellular proliferation, showing in vivo efficacy. When tested in a lipopolysaccharide-induced hyperalgesia model, CDD-2728 and CDD-3013 decreased markers of induced pain, as measured by changes in a dynamic weight bearing test and Grimace scores. These findings nominate CDD-2728 and CDD-3013 as potent, nonhormonal therapeutic candidates for endometriosis with broad anti-inflammatory and analgesic activity, addressing a critical unmet clinical need.

Madasu, Chandrashekhar [Department of Pathology an↗
DOE OSTI2023

SPRUCE Climate Warming and Elevated CO2 Rapidly Alter Peatland Soil Carbon Sources and Stability: Supporting Data

This data set reports a suite of complementary biogeochemical analyses of peat samples from the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experiment. Results were collected using quantitative molecular analysis of bulk soil carbon to assess the stability of soil organic carbon following whole-ecosystem warming and exposure to elevated carbon dioxide concentrations (eCO2). Targeted soil organic carbon components include solvent-extractable compounds (alkanoic acids, alkanols, alkanes, steroids, and terpenoids), ester-bound hydrolysable biopolymers (cutin and suberin markers), lignin phenols, and pyrogenic carbon. Bulk peat samples were analysed by Soxhlet extraction and solid phase separation for solvent-extractable compounds, alkaline hydrolysis to extract hydrolysable biopolymers, copper (II) oxide oxidation to extract lignin phenols and benzene polycarboxylic acids (BPCAs) as an approximation of pyrogenic carbon. Samples were analysed by gas chromatography (GC) equipped with a flame ionization detector (GC-FID) and compound identification was performed on GC coupled to mass selective detector (MS) for solvent-extractable compounds, ester-bound hydrolysable biopolymers and lignin phenols, and high-performance liquid chromatograph (HPLC) for pyrogenic carbon. Results are presented in Ofiti et al. (accepted). The experimental work was conducted on samples collected in August 2018 at the SPRUCE climate manipulation experiment in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). Samples were collected and later analysed in a 10 cm increments over 0 to 50 cm depth and 25 cm intervals from 50 to 75 cm. Samples were analyzed for lignin phenols over 0 to 30 cm depth. This data set contains one file in comma separate (*.csv) format. This dataset contains data used to produce: Ofiti, N.O.E., Schmidt, M.W.I., Abiven, S., Hanson, P.J., Iversen, C.M., Wilson, R.M., Kostka, J.E., Wiesenberg, G.L.B., Malhotra, A. 2023. Climate warming and elevated CO2 rapidly alter peatland soil carbon sources and stability. Nat Commun 14, 7533. https://doi.org/10.1038/s41467-023-43410-z.

SPRUCE experiment, Marcell Experimental Forest, so↗
DOE OSTI2023

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs

Abstract Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis “pyrifera” and M. “integrifolia” are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. “pyrifera” and M. “integrifolia” across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. “pyrifera” and M. “integrifolia” are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent “integrifolia” morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.

Environmental Sciences & Ecology↗
NASA NTRS1988

Drosophila geotaxis as a tool for the study of aging

Age dependent changes in geotaxis profiles were examined in 27 wild-type populations of Drosophila, representing a diversity of species, semispecies and strains. In addition, four strains of D. melanogaster were tested. Tests were carried out at a minimum of three test ages, and involve the use of a calibrated, adjustable inclined plane that can be set at any angle between 0 and 85 deg. Among selected lines, decline in geotactic response occurs later in the long lived flies than in the controls. Longer lived flies continue to show an increase in negative geotactic response through age 14 days. These results suggest that common processes may be influencing the rate of decline in geotactic response and longevity. Further analysis of the mechanisms underlying age dependent changes in geotaxis may reveal factors which influence the aging process itself. The use of geotaxis aging markers in a broad range of Drosophila species reflecting varying degrees of genetic relatedness is proposed to test the universality vs. specificity of aging processes.

Schnebel, Edgar M.↗