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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Systemic clearance of p16 INK4a -positive senescent cells mitigates age-associated intervertebral disc degeneration

RATIONALE:Age-related changes in the intervertebral discs are the predominant contributors to back pain, a common physical and functional impairment experienced by older persons. Cellular senescence, a process wherein cells undergo growth arrest and chronically secrete numerous inflammatory molecules and proteases, has been reported to cause decline in the health and function of multiple tissues with age. Although senescent cells have been reported to increase in intervertebral degeneration (IDD), it is not known whether they are causative in age-related IDD. OBJECTIVE:The study aimed to elucidate whether a causal relationship exists between cellular senescence and age-related IDD. METHODS AND RESULTS:To examine the impact of senescent cells on age-associated IDD, we used p16-3MR transgenic mice, which enables the selective removal of p16 INK4a -positive senescent cells by the drug ganciclovir. Disc cellularity, aggrecan content and fragmentation alongside expression of inflammatory cytokine (IL-6) and matrix proteases (ADAMTS4 and MMP13) in discs of p16-3MR mice treated with GCV and untreated controls were assessed. In aged mice, reducing the per cent of senescent cells decreased disc aggrecan proteolytic degradation and increased overall proteoglycan matrix content along with improved histological disc features. Additionally, reduction of senescent cells lowered the levels of MMP13, which is purported to promote disc degenerative changes during aging. CONCLUSIONS:The findings of this study suggest that systemic reduction in the number of senescent cells ameliorates multiple age-associated changes within the disc tissue. Cellular senescence could therefore serve as a therapeutic target to restore the health of disc tissue that deteriorates with age.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Targeting senescent cells alleviates obesity-induced metabolic dysfunction

Adipose tissue inflammation and dysfunction are associated with obesity-related insulin resistance and diabetes, but mechanisms underlying this relationship are unclear. Although senescent cells accumulate in adipose tissue of obese humans and rodents, a direct pathogenic role for these cells in the development of diabetes remains to be demonstrated. Here, we show that reducing senescent cell burden in obese mice, either by activating drug-inducible "suicide" genes driven by the p 16Ink4a promoter or by treatment with senolytic agents, alleviates metabolic and adipose tissue dysfunction. These senolytic interventions improved glucose tolerance, enhanced insulin sensitivity, lowered circulating inflammatory mediators, and promoted adipogenesis in obese mice. Elimination of senescent cells also prevented the migration of transplanted monocytes into intra-abdominal adipose tissue and reduced the number of macrophages in this tissue. In addition, microalbuminuria, renal podocyte function, and cardiac diastolic function improved with senolytic therapy. Our results implicate cellular senescence as a causal factor in obesity-related inflammation and metabolic derangements and show that emerging senolytic agents hold promise for treating obesity-related metabolic dysfunction and its complications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Inhibition of USP7 activity selectively eliminates senescent cells in part via restoration of p53 activity

The accumulation of senescent cells (SnCs) is a causal factor of various age-related diseases as well as some of the side effects of chemotherapy. Pharmacological elimination of SnCs (senolysis) has the potential to be developed into novel therapeutic strategies to treat these diseases and pathological conditions. Here we show that ubiquitin-specific peptidase 7 (USP7) is a novel target for senolysis because inhibition of USP7 with an inhibitor or genetic depletion of USP7 by RNA interference induces apoptosis selectively in SnCs. The senolytic activity of USP7 inhibitors is likely attributable in part to the promotion of the human homolog of mouse double minute 2 (MDM2) ubiquitination and degradation by the ubiquitin–proteasome system. This degradation increases the levels of p53, which in turn induces the pro-apoptotic proteins PUMA, NOXA, and FAS and inhibits the interaction of BCL-XL and BAK to selectively induce apoptosis in SnCs. Further, we show that treatment with a USP7 inhibitor can effectively eliminate SnCs and suppress the senescence-associated secretory phenotype (SASP) induced by doxorubicin in mice. These findings suggest that small molecule USP7 inhibitors are novel senolytics that can be exploited to reduce chemotherapy-induced toxicities and treat age-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Age-related telomere attrition causes aberrant gene expression in sub-telomeric regions

Telomere attrition has been proposed as a biomarker and causal factor in aging. In addition to causing cellular senescence and apoptosis, telomere shortening has been found to affect gene expression in subtelomeric regions. Here, we analyzed the distribution of age-related differentially expressed genes from the GTEx RNA sequencing database of 54 tissue types from 979 human subjects and found significantly more upregulated than downregulated genes in subtelomeric regions as compared to the genome-wide average. Our data demonstrate spatial relationships between telomeres and gene expression in aging.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Rapid assessment of beech leaf disease in Fagus sylvatica buds

Abstract The European beech (Fagus sylvatica) is threatened by the foliar nematodeLitylenchus crenataesubsp.mccannii(Lcm), the causal agent of beech leaf disease (BLD). Thus far, the majority of studies regarding BLD have focused on American beech (F. grandifolia). To better determine the impact of Lcm in buds of European beech, a total of 54 buds were collected from naturally symptomatic trees. Here, we characterized for the first time the bud scale morphology of two different cultivars ofF. sylvaticainfected with Lcm. Detailed observations of asymptomatic and symptomatic bud scales provided insight into the physical changes and arrangements of cells in the bud scale, shedding light on the dynamic processes occurring during Lcm infection. In addition, we evaluated the suitability of using the bud scale morphology for the early detection of BLD and Lcm in naturally infected buds. The distinct cellular arrangement of symptomatic bud scales cells (i.e., asymmetric pattern of enlarged cells) provides a rapid and visual, user‐friendly methodology to prematurely diagnose BLD symptoms within the buds, as well as the detection of associated nematodes.

Forestry↗
DOE OSTI2014

When should species richness be energy-limited, and how would we know?

Energetic constraints are fundamental to ecology and evolution, and empirical relationships between species richness and estimates of available energy have led some to suggest that richness is energetically constrained. However, the mechanism linking energy with richness is rarely specified and predictions of secondary patterns consistent with energy-constrained richness are lacking. Here we lay out the necessary and sufficient assumptions of a causal relationship linking energy gradients to richness gradients. We then describe an eco-evolutionary simulation model that combines spatially-explicit diversification with trait evolution, resource availability, and assemblage-level carrying capacities. Our model identified patterns in richness and phylogenetic structure expected when a spatial gradient in energy availability determines the number of individuals supported in a given area. A comparison to patterns under alternative scenarios, in which fundamental assumptions behind energetic explanations were violated, revealed patterns that are useful for evaluating the importance of energetic constraints in empirical systems. We find that clades arising at the low-energy end of a gradient provide the most powerful inferences regarding whether assumptions are met, and use rockfish (Sebastes) from the northeastern Pacific to show how empirical data can be coupled with model predictions to evaluate the role of energetic constraints in generating observed richness gradients.

diversification↗
DOE OSTI2023

Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Abstract With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes of both Chinook Salmon and Steelhead, several subsequent studies have investigated the effect size and distribution of early and late migration alleles among populations in the Columbia River. Here, we synthesize the results of these studies for the major lineages of Chinook Salmon and Steelhead that include highly distinct groups in the interior Columbia River that exhibit atypical life histories from most coastal lineage populations of these two species. Whole‐genome studies with high marker density have provided extensive insight into SNPs most associated with adult migration timing, and suites of markers for each species have been genotyped in large numbers of individuals to further validate phenotypic effects. For Steelhead, the largest phenotypic effect sizes have been observed in the coastal lineage (36% of variation for passage timing at Bonneville Dam; 43% of variation for tributary arrival timing) compared to the inland lineage (7.5% of variation for passage timing at Bonneville Dam; 8.4% of variation for tributary arrival timing) that overwinter in freshwater prior to spawning. For Chinook Salmon, large effect sizes have been observed in all three lineages for multiple adult migration phenotypes (Coastal lineage: percentage of variation of 27.9% for passage timing at Bonneville Dam, 28.7% for arrival timing for spawning; Interior ocean type: percentage of variation of 47.6% for passage timing at Bonneville Dam, 39.6% for tributary arrival timing, 77.9% for arrival timing for spawning; Interior stream type: percentage of variation of 35.3% for passage at Bonneville Dam, 9.8% for tributary arrival timing, 4.7% for arrival timing for spawning). Together, these results have extended our understanding of genetic variation associated with life history diversity in distinct populations of the Columbia River, however, much research remains necessary to determine the causal mechanism for this major effect region on migration timing in these species.

Narum, Shawn R.↗
DOE OSTI2019

The flagella of ‘ Candidatus Liberibacter asiaticus’ and its movement in planta

Summary Citrus huanglongbing (HLB) is the most devastating citrus disease worldwide. ‘ Candidatus Liberibacter asiaticus’ (Las) is the most prevalent HLB causal agent that is yet to be cultured. Here, we analysed the flagellar genes of Las and Rhizobiaceae and observed two characteristics unique to the flagellar proteins of Las: (i) a shorter primary structure of the rod capping protein FlgJ than other Rhizobiaceae bacteria and (ii) Las contains only one flagellin‐encoding gene flaA (CLIBASIA_02090), whereas other Rhizobiaceae species carry at least three flagellin‐encoding genes. Only flgJ Atu but not flgJ Las restored the swimming motility of Agrobacterium tumefaciens flgJ mutant. Pull‐down assays demonstrated that FlgJ Las interacts with FlgB but not with FliE. Ectopic expression of flaA Las in A. tumefaciens mutants restored the swimming motility of ∆ flaA mutant and ∆ flaAD mutant, but not that of the null mutant ∆ flaABCD . No flagellum was observed for Las in citrus and dodder. The expression of flagellar genes was higher in psyllids than in planta . In addition, western blotting using flagellin‐specific antibody indicates that Las expresses flagellin protein in psyllids, but not in planta . The flagellar features of Las in planta suggest that Las movement in the phloem is not mediated by flagella. We also characterized the movement of Las after psyllid transmission into young flush. Our data support a model that Las remains inside young flush after psyllid transmission and before the flush matures. The delayed movement of Las out of young flush after psyllid transmission provides opportunities for targeted treatment of young flush for HLB control.

Andrade, Maxuel O.↗
DOE OSTI2023

Plant defensin MtDef4–derived antifungal peptide with multiple modes of action and potential as a bio–inspired fungicide

Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). The sequence-divergent cysteine-rich antifungal defensins with multisite MoA are promising starting templates for design of novel peptide-based fungicides. Here, we experimentally tested such a set of 17-amino-acid peptides containing the γ-core motif of the antifungal plant defensin MtDef4. These designed peptides exhibited antifungal properties different from those of MtDef4. Focused analysis of a lead peptide, GMA4CG_V6, showed that it was a random coil in solution with little or no secondary structure elements. Additionally, it exhibited potent cation-tolerant antifungal activity against the plant fungal pathogen Botrytis cinerea, the causal agent of grey mould disease in fruits and vegetables. Its multisite MoA involved localization predominantly to the plasma membrane, permeabilization of the plasma membrane, rapid internalization into the vacuole and cytoplasm, and affinity for the bioactive phosphoinositides phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. The sequence motif RRRW was identified as a major determinant of the antifungal activity of this peptide. While topical spray application of GMA4CG_V6 on Nicotiana benthamiana and tomato plants provided preventive and curative suppression of grey mould disease symptoms, the peptide was not internalized into plant cells. Our findings open the possibility that truncated and modified defensin-derived peptides containing the γ-core sequence could serve as promising candidates for further development of bio-inspired fungicides.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Defining the scope for altering rice leaf anatomy to improve photosynthesis: a modelling approach

Summary Leaf structure plays an important role in photosynthesis. However, the causal relationship and the quantitative importance of any single structural parameter to the overall photosynthetic performance of a leaf remains open to debate. In this paper, we report on a mechanistic model, eLeaf, which successfully captures rice leaf photosynthetic performance under varying environmental conditions of light and CO 2 . We developed a 3D reaction‐diffusion model for leaf photosynthesis parameterised using a range of imaging data and biochemical measurements from plants grown under ambient and elevated CO 2 and then interrogated the model to quantify the importance of these elements. The model successfully captured leaf‐level photosynthetic performance in rice. Photosynthetic metabolism underpinned the majority of the increased carbon assimilation rate observed under elevated CO 2 levels, with a range of structural elements making positive and negative contributions. Mesophyll porosity could be varied without any major outcome on photosynthetic performance, providing a theoretical underpinning for experimental data. eLeaf allows quantitative analysis of the influence of morphological and biochemical properties on leaf photosynthesis. The analysis highlights a degree of leaf structural plasticity with respect to photosynthesis of significance in the context of attempts to improve crop photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

BUZZ : an essential gene for postinitiation root hair growth and a mediator of root architecture in Brachypodium distachyon

Here, we discover a player in root development. Recovered from a forward-genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild-type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole-genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin-dependent kinase (CDK)-like gene. The buzz mutant phenotypes are rescued by the wild-type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T-DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA-Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX-1 and -2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Soybean ( Glycine max ) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics

Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Validation in the Absence of Observed Events

Here our paper addresses the problem of validating models in the absence of observed events, in the area of Weapons of Mass Destruction terrorism risk assessment. We address that problem with a broadened definition of “Validation,” based on “backing up” to the reason why modelers and decision makers seek validation, and from that basis re-define validation as testing how well the model can advise decision makers in terrorism risk management decisions. We develop that into two conditions: Validation must be based on cues available in the observable world; and it must focus on what can be done to affect that observable world, i.e. risk management. That in turn leads to two foci: 1.) the risk generating process, 2.) best use of available data. Based on our experience with nine WMD terrorism risk assessment models, we then describe three best use of available data pitfalls: SME confidence bias, lack of SME cross-referencing, and problematic initiation rates. Those two foci and three pitfalls provide a basis from which we define validation in this context in terms of four tests -- Does the model: … capture initiation? … capture the sequence of events by which attack scenarios unfold? … consider unanticipated scenarios? … consider alternative causal chains? Finally, we corroborate our approach against three key validation tests from the DOD literature: Is the model a correct representation of the simuland? To what degree are the model results comparable to the real world? Over what range of inputs are the model results useful?

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2019

Construction and comparison of three reference-quality genome assemblies for soybean

Here, we report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A common resequencing‐based genetic marker data set for global maize diversity

SUMMARY Maize ( Zea mays ssp. mays ) populations exhibit vast ranges of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole‐genome resequencing strategies, identifying millions of segregating single‐nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here, we employ resequencing data from 1276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of approximately 366 million segregating variants and approximately 46 million high‐confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering‐time genes using previously published trait data sets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

A high-fidelity harmonic drive model.

In this paper, a new model of the harmonic drive transmission is presented. The purpose of this work is to better understand the transmission hysteresis behavior while constructing a new type of comprehensive harmonic drive model. The four dominant aspects of harmonic drive behavior - nonlinear viscous friction, nonlinear stiffness, hysteresis, and kinematic error - are all included in the model. The harmonic drive is taken to be a black box, and a dynamometer is used to observe the input/output relations of the transmission. This phenomenological approach does not require any specific knowledge of the internal kinematics. In a novel application, the Maxwell resistive-capacitor hysteresis model is applied to the harmonic drive. In this model, sets of linear stiffness elements in series with Coulomb friction elements are arranged in parallel to capture the hysteresis behavior of the transmission. The causal hysteresis model is combined with nonlinear viscous friction and spectral kinematic error models to accurately represent the harmonic drive behavior. Empirical measurements are presented to quantify all four aspects of the transmission behavior. These measurements motivate the formulation of the complete model. Simulation results are then compared to additional measurements of the harmonic drive performance.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2012

COMPARISON OF EXPERIMENTS TO CFD MODELS FOR MIXING USING DUAL OPPOSING JETS IN TANKS WITH AND WITHOUT INTERNAL OBSTRUCTIONS

This paper documents testing methods, statistical data analysis, and a comparison of experimental results to CFD models for blending of fluids, which were blended using a single pump designed with dual opposing nozzles in an eight foot diameter tank. Overall, this research presents new findings in the field of mixing research. Specifically, blending processes were clearly shown to have random, chaotic effects, where possible causal factors such as turbulence, pump fluctuations, and eddies required future evaluation. CFD models were shown to provide reasonable estimates for the average blending times, but large variations -- or scatter -- occurred for blending times during similar tests. Using this experimental blending time data, the chaotic nature of blending was demonstrated and the variability of blending times with respect to average blending times were shown to increase with system complexity. Prior to this research, the variation in blending times caused discrepancies between CFD models and experiments. This research addressed this discrepancy, and determined statistical correction factors that can be applied to CFD models, and thereby quantified techniques to permit the application of CFD models to complex systems, such as blending. These blending time correction factors for CFD models are comparable to safety factors used in structural design, and compensate variability that cannot be theoretically calculated. To determine these correction factors, research was performed to investigate blending, using a pump with dual opposing jets which re-circulate fluids in the tank to promote blending when fluids are added to the tank. In all, eighty-five tests were performed both in a tank without internal obstructions and a tank with vertical obstructions similar to a tube bank in a heat exchanger. These obstructions provided scale models of vertical cooling coils below the liquid surface for a full scale, liquid radioactive waste storage tank. Also, different jet diameters and different horizontal orientations of the jets were investigated with respect to blending. Two types of blending tests were performed. The first set of eighty-one tests blended small quantities of tracer fluids into solution. Data from these tests were statistically evaluated to determine blending times for the addition of tracer solution to tanks, and blending times were successfully compared to Computational Fluid Dynamics (CFD) models. The second set of four tests blended bulk quantities of solutions of different density and viscosity. For example, in one test a quarter tank of water was added to a three quarters of a tank of a more viscous salt solution. In this case, the blending process was noted to significantly change due to stratification of fluids, and blending times increased substantially. However, CFD models for stratification and the variability of blending times for different density fluids was not pursued, and further research is recommended in the area of blending bulk quantities of fluids. All in all, testing showed that CFD models can be effectively applied if statistically validated through experimental testing, but in the absence of experimental validation CFD model scan be extremely misleading as a basis for design and operation decisions.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Understanding Laser Powder Bed Fusion Surface Roughness

Abstract Surface roughness is a well-known consequence of additive manufacturing methods, particularly powder bed fusion processes. To properly design parts for additive manufacturing, a comprehensive understanding of the inherent roughness is necessary. While many researchers have measured different surface roughness resultant from a variety of parameters in the laser powder bed fusion process, few have succeeded in determining causal relationships due to the large number of variables at play. To assist the community in understanding the roughness in laser powder bed fusion processes, this study explored several studies from the literature to identify common trends and discrepancies amongst roughness data. Then, an experimental study was carried out to explore the influence of certain process parameters on surface roughness. Through these comparisons, certain local and global roughness trends have been identified and discussed, as well as a new framework for considering the effect of process parameters on surface roughness.

Engineering↗