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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗
DOE OSTI2022

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Thylakoid Assembly and Folded Protein Transport by the Tat Pathway

Assembly of functional photosystems complete with necessary intrinsic and extrinsic proteins requires the function of at least three protein transport pathways in thylakoid membranes. Our research focuses on one of those pathways, a unique and essential protein transport pathway found in the chloroplasts of plants, bacteria, and some archaebacteria, the Twin arginine translocation (Tat) system. The chloroplast Tat (cpTat) system is thought to be responsible for the proper localization of ~50% of thylakoid lumen proteins, several of which are necessary for proper photosystem assembly, maintenance, and function. For example, two components of the extrinsic oxygen evolving complex, PsbP and PsbQ, are transported to the thylakoid lumen via the cpTat system. PsbP and PsbQ have been shown to be important in photosystem II function and maintenance (Yi et al. 2006; Yi et al. 2007). The current project addresses the issues of what forms the translocation conduit, how the translocon complex is arranged and what role Hcf106 and cpTatC may have in the process of forming the conduit.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

KS4A-Omics1.0_FspDS682

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. Here, we observed how a representative of common saprotrophic soil fungi, Fusarium sp. DS 682, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals.This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment, using a high-throughput multi-omic analysis approach. Data package KS4A-Omics.1.0_FspDS682 (Publication: Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization) contents reported here are the first version (1.0) and contain pre- and post-processed data using high throughput data capture technologies for multi-omic analysis and integration, this data package contains raw and post-processed experimental data for X-Ray Absorption Near Edge Structure Spectroscopy (XANES/XRF), Optical Microscopy, Proteomics, Scanning Electron Microscope (SEM), Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS), X-Ray Diffraction Spectroscopy (XRD) files, and X- Ray Photoelectron Spectroscopy (XPS) using EMSL capabilities. This data package DOI contains a comprehensive collection of high-throughput multi-omics data and process metadata catalog. Support files include additional data download contents “Read Me” with dataset descriptor information and data source method application ontologies (see data dictionary section). Reported data download content is structured for compliance with reported guidelines provided by community standard initiatives and publisher stakeholder policies supporting FAIR data principles.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Role of different organic and inorganic amendments in the biofortification of iodine in Coriandrum sativum crop

Iodine deficiency disorder (IDDs) is one of the most prevailing and common health issues in mountainous communities. An effective way to control the prevalence and emergence of IDDs in remote areas is to use iodized salt. However, recent studies indicated that iodized salt is mostly lost during the cooking process. The current study of iodine biofortification differed from the previous studies in two main aspects: it involved exogenous organic iodine (OI), and inorganic iodine such as potassium iodide (KI), added in the amended soils, which previous studies did not consider. Moreover, the translocation, transformation, and distribution of iodine from soil to plants are poorly understood in amended soil. Thus, identifying an effective management option to enhance iodine (I) bioavailability in nutrient-deficient soils is currently a significant challenge. Therefore, a greenhouse study was conducted to investigate the effects of organic and inorganic soil amendments on the uptake of different iodine sources in coriander crops. Results showed that applying an inorganic iodine source significantly enhanced the iodine edible part of the crop compared to the control ( p < 0.05). The application of soil amendments relatively improved iodine uptake by the coriander crop compared to the control. The highest iodine was found in crop tissues grown in wood ash-amended soil supplemented with KI (291.97 μg kg −1 ). The KI uptake was significantly higher than the OI ( p < 0.05). Compared to OI, a higher translocation factor (0.96) and distribution coefficient (3.51) were found for plants treated with KI. Thus, this study indicates that a suitable soil amendment can be a better option for iodine biofortification and that it can serve as an alternative to iodized salt in preventing IDDs.

Tianyi, Yan↗
DOE OSTI2021

pH Homeostasis and Sodium Ion Pumping by Multiple Resistance and pH Antiporters in Pyrococcus furiosus

Multiple Resistance and pH (Mrp) antiporters are seven-subunit complexes that couple transport of ions across the membrane in response to a proton motive force (PMF) and have various physiological roles, including sodium ion sensing and pH homeostasis. The hyperthermophilic archaeon Pyrococcus furiosus contains three copies of Mrp encoding genes in its genome. Two are found as integral components of two respiratory complexes, membrane bound hydrogenase (MBH) and the membrane bound sulfane sulfur reductase (MBS) that couple redox activity to sodium translocation, while the third copy is a stand-alone Mrp. Sequence alignments show that this Mrp does not contain an energy-input (PMF) module but contains all other predicted functional Mrp domains. The P. furiosus Mrp deletion strain exhibits no significant changes in optimal pH or sodium ion concentration for growth but is more sensitive to medium acidification during growth. Cell suspension hydrogen gas production assays using the deletion strain show that this Mrp uses sodium as the coupling ion. Mrp likely maintains cytoplasmic pH by exchanging protons inside the cell for extracellular sodium ions. Deletion of the MBH sodium-translocating module demonstrates that hydrogen gas production is uncoupled from ion pumping and provides insights into the evolution of this Mrp-containing respiratory complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

A grand challenge facing society is climate change caused mainly by rising CO 2 concentration in Earth’s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO 2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO 2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO 2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ecological connectivity and in-kind mitigation in a regulatory decision framework: A case study with an amphibian habitat specialist

Ecological connectivity is critical to the survival and long-term viability of populations but is often overlooked in regulatory frameworks. We integrated landscape-level processes into a mitigation strategy for impacts to aquatic resources on the U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) in eastern Tennessee. Wetlands on the ORR, which contain significant breeding populations of the imperiled four-toed salamander (Hemidactylium scutatum) and tubercled rein orchid (Platanthera flava var. herbiola), will be impacted by construction of an environmental waste disposal facility under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA). Here, we used a modified Kepner-Tregoe decision analysis to select general mitigation options that balanced regulatory requirements and interest group perspectives. We emphasized habitat connectivity through models that prioritized an area's importance to natural area connectivity (centrality) and maintenance of population structure for an affected habitat specialist (four-toed salamanders). We also emphasized in-kind mitigation through the preservation and enhancement of ecologically similar resources and the translocation and establishment of a new subpopulation of four-toed salamanders elsewhere on the ORR. We ultimately released over 500 juvenile salamanders that originated from the impacted site into the chosen mitigation wetlands. By doing so under the constraints of a time-sensitive CERCLA remediation effort and exceeding its substantive requirements, this work underscores feasibility. Ecological connectivity and the conservation of species that are not afforded explicit regulatory processes can be effectively and efficiently integrated into environmental decision-making and land use planning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Exosomes derived from hypoxic bone marrow mesenchymal stem cells rescue OGD-induced injury in neural cells by suppressing NLRP3 inflammasome-mediated pyroptosis

Exosomes have been shown to have therapeutic potential for cerebral ischemic diseases. In this study, we investigated the neuroprotective effects of normoxic and hypoxic bone marrow mesenchymal stromal cells-derived exosomes (N-BM-MSCs-Exo and H-BM-MSCs-Exo, respectively) on oxygen-glucose deprivation (OGD) injury in mouse neuroblastoma N2a cells and rat primary cortical neurons. The proportions of dead cells in N2a and primary cortical neurons after OGD injury were significantly increased, and N-BM-MSCs-Exo (40 μg/ml) could reduce the ratios, noteworthily, the protective effects of H-BM-MSCs-Exo (40 μg/ml) were more potent. Western blotting analysis indicated that N-BM-MSCs-Exo decreased the expression of NLRP3, ASC, Caspase-1, GSDMD-N, cleaved IL-1β and IL-18 in N2a cells. However, H-BM-MSCs-Exo (40 μg/ml) was more powerful in inhibiting the expression of these proteins in comparison with N-BM-MSCs-Exo. Similar results were obtained in primary cortical neurons. Immunofluorescence assays showed that after N-BM-MSCs-Exo and H-BM-MSCs-Exo treatment, the co-localization of NLRP3, ASC, Caspase-1 and the GSDMD translocation from the nucleus to the cytoplasm and membrane after OGD injury were reduced in N2a cells and primary cortical neurons, and H-BM-MSCs-Exo had a more obvious effect. In addition, N-BM-MSCs-Exo and H-BM-MSCs-Exo significantly reduced lactate dehydrogenase (LDH) release and the IL-18 levels in cell culture medium in N2a cells and primary cortical neurons. Once again H-BM-MSCs-Exo induced these effects more potently than N-BM-MSCs-Exo. All of these results demonstrated that N-BM-MSCs-Exo and H-BM-MSCs-Exo have significant neuroprotective effects against NLRP3 inflammasome-mediated pyroptosis. H-BM-MSCs-Exo has a more pronounced protective effect than N-BM-MSCs-Exo and may be used to ameliorate the progression of cerebral ischemia and hypoxia injury in patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Vimentin loss promotes cancer proliferation through up-regulating Rictor/AKT/β-catenin signaling pathway

Vimentin protein is one of the main cytoskeleton and plays an important role in cell motility and metastasis. Nowadays, vimentin is widely studied as an epithelial-mesenchymal transition (EMT) marker of cancer cells while its involvement in cancer proliferation is poorly understood. In this study, we investigated the participation of vimentin in regulating cancer proliferation by silencing VIM gene in four cancer cell lines. Our results demonstrated that vimentin loss significantly induced cancer cell proliferation both in vitro and in vivo, which has not been reported so far. Mechanistically, knockdown of vimentin expression activated AKT phosphorylation and its downstream β-catenin signaling. Nuclear translocation and transcriptional activity of β-catenin was enhanced after silencing vimentin expression. Furthermore, vimentin loss could prevent Rictor from autophagy-dependent degradation via reducing AMPK-mediated autophagy signaling. AICAR, an AMPK activator, down-regulated Rictor and p-AKT levels while vimentin knockdown could rescue the effects. In vivo, it was also found that Ki67 expression and p-AKT/β-catenin signaling pathway were obviously up-regulated in the tumor tissues in which vimentin was silenced compared to control groups. Taken together, these data showed the novel function of vimentin in regulating cancer proliferation via Rictor/AKT/β-catenin signaling pathway, which suggested that it need more careful consideration before inhibiting metastatic cancers through targeting vimentin.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Glucocorticoids activate Yes-associated protein in human vocal fold fibroblasts

Fibrosis of the vocal folds poses a substantive clinical challenge potentially underlying the rapid proliferation of direct steroid injections into the upper airway. The variable clinical response to glucocorticoids (GCs) in the vocal folds is likely related to diversity inherent to GCs and patient-specific, and upstream, cell-specific responses to GCs. Broadly, we hypothesize the disparity in clinical outcomes are due to undesirable effects of GCs on resident fibroblasts. Transcriptome analysis identified significant GC-mediated modulation of Hippo signaling, a known regulator of fibrotic gene expression. Subsequent analysis confirmed GC-mediated YAP activation, a transcriptional co-factor in the Hippo signaling pathway. YAP inhibition attenuated ACTA2 expression in GC-treated human vocal fold fibroblasts. Nuclear localization and phosphorylation at Ser211, however, was not affected by YAP inhibition, suggesting nuclear translocation of YAP is indirectly driven by GR. RNA-seq analysis confirmed the influence of GCs on Wnt signaling, and canonical Wnt signaling target genes were upregulated by GCs. These data implicate YAP and its downstream targets as putative mediators of a pro-fibrotic response to GCs. Therapeutic YAP inhibition may ultimately be clinically relevant and warrants further consideration.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

AGTR1 blocker attenuates activation of Tenon's capsule fibroblasts after glaucoma filtration surgery via the NF-κB signaling pathway

Activation of Tenon's capsule fibroblasts limits the success rate of glaucoma filtration surgery (GFS), the most efficacious therapy for patients with glaucoma. Angiotensin type 1 receptor (AGTR1) is involved in tissues remodeling and fibrogenesis. However, whether AGTR1 is involved in the progress of fibrogenesis after GFS is not fully elucidated. The aim of this study was to investigate the role of an AGTR1 in scar formation after GFS and the potential anti-fibrosis effect of AGTR1 blocker. AGTR1 expression level was increased in subconjunctival tissues in a rat model of GFS and transforming growth factor-beta 2 (TGF-β2)-induced human Tenon's capsule fibroblasts (HTFs). AGTR1 blocker treatment suppressed TGF-β2-induced HTF migration and α-smooth muscle actin (α-SMA) and fibronectin (FN) expression. AGTR1 blocker treatment also attenuated collagen deposition and α-SMA and FN expression in subconjunctival tissues of the rat model after GFS. Moreover, AGTR1 blocker decreased TGF-β2-induced P65 phosphorylation, P65 nuclear translocation, and nuclear factor kappa B (NF-κB) luciferase activity. Additionally, BAY 11–7082 (an NF-κB inhibitor) significantly suppressed HTF fibrosis. In conclusion, our results indicate that AGTR1 is involved in scar formation after GFS. The AGTR1 blocker attenuates subconjunctival fibrosis after GFS by inhibiting the NF-κB signaling pathway. These findings indicate that targeting AGTR1 is a potential approach to attenuate fibrosis after GFS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Alleviation of CCCP-induced mitochondrial injury by augmenter of liver regeneration via the PINK1/Parkin pathway-dependent mitophagy

The occurrence of liver diseases is attributed to mitochondrial damage. Mitophagy selectively removes dysfunctional mitochondria, thereby preserving mitochondrial function. Augmenter of liver regeneration (ALR) protects the mitochondria from injury. However, whether ALR protection is associated with mitophagy remains unclear. In this study, mitochondrial damage was induced by carbonyl cyanide 3-chlorophenylhydrazone (CCCP), and long-form ALR (lfRNA)-mediated protection against this damage was investigated. Treatment of HepG2 cells with CCCP elevated the level of intracellular ROS, inhibited ATP production, and increased the mitochondrial membrane potential and cell apoptotic rate. However, in lfALR-transfected cells, CCCP-induced cell injury was clearly alleviated, the apoptosis and ROS levels clearly declined, and the ATP production was significantly enhanced as compared with that in vector-Tx cells. Furthermore, lfALR overexpression promoted autophagy and mitophagy via a PINK1/Parkin-dependent pathway, whereas knockdown of ALR suppressed mitophagy. In lfALR-transfected cells, the phosphorylation of AKT was decreased, thus, downregulating the phosphorylation of the transcription factor FOXO3a at Ser315. In contrast, the phosphorylation of AMPK was enhanced, thereby upregulating the phosphorylation of FOXO3a at Ser413. Consequently, FOXO3a′s nuclear translocation and binding to the promoter region of PINK1 was enhanced, and the accumulation of PINK1/Parkin in mitochondria increased. Meanwhile, short-form ALR (sfALR) also increased PINK1 expression through FOXO3a with the similar pathway to lfALR. In conclusion, our data suggest a novel mechanism through which both lfALR and sfALR protect mitochondria by promoting PINK1/Parkin-dependent mitophagy through FOXO3a activation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Updates to a Preliminary Probabilistic Performance Assessment Model for Radiological and Chemical Contamination at the West Valley Site, New York - 20420

The New York State Energy Research and Development Authority (NYSERDA) is the owner of the Western New York Nuclear Service Center (WNYNSC), a 1,351-ha site located approximately 48 km south of Buffalo, New York. In 1962, Nuclear Fuel Services, Inc. (NFS) entered into agreements with the Atomic Energy Commission and New York State to construct the first commercial reprocessing plant of nuclear fuel in the United States at the WNYNSC. NFS built and operated the spent fuel reprocessing plant and waste disposal facilities, processing 640 Mg (640 metric tons) of spent nuclear fuel from 1966 to 1972 under an Atomic Energy Commission license. Nuclear fuel reprocessing operations halted in 1972 and never restarted, leaving behind radioactive and chemical wastes. The U.S. Department of Energy (DOE) was required to complete certain waste management activities under the West Valley Demonstration Project (WVDP) Act of 1980 including decommissioning of WVDP facilities. As collaborating agencies, NYSERDA and the DOE are tasked with making decisions about decommissioning and risk reduction for the West Valley Site. Neptune and Company, Inc. (Neptune) was contracted to develop a probabilistic performance assessment (PPA) model to assist the agencies in their decision making process for decommissioning the WVDP and WNYNSC. One important tool that is needed in order to inform the decision-making process is a science-based model of the West Valley Site that evaluates potential future consequences for human health and the environment. This forms the core of the spatial domain of the West Valley PPA Model. The PPA Model, developed using the GoldSim system modeling software, is a tool intended to provide support for decision making that evaluates uncertainty, in a manner that is transparent, defensible, and robust. The PPA Model includes contaminant transport and health effects components, and is organized around geographically-grouped contaminated facilities. These include the waste disposal areas licensed by the U.S. Nuclear Regulatory Commission and the State of New York, a waste tank farm for storage of high level radioactive waste resulting from reprocessing operations, and several areas contaminated with radioactive and chemical constituents. The PPA Model evaluates contaminant transport from these sources to points of exposure across the site and into receiving surface waters and sediments. Hypothetical people and wildlife could be exposed to contamination at these locations, and the effects of these exposures are evaluated. Contaminant transport processes to be evaluated in the PPA Model include groundwater and surface water transport, contaminant translocation by plants and animals, diffusion, and erosion. The evaluation of exposures to people in this preliminary model is limited to a resident farmer scenario, and ecological assessment is performed at the level of a screening analysis. The results of these preliminary evaluations inform future model developments. PPA Model results are subjected to sensitivity analysis in order to determine those pathways and parameters that are most significant in influencing the results. This information allows analysts and decision makers to focus on those aspects of Site behavior and processes. With this information, the decision makers can drive informed, defensible decisions regarding decommissioning of the Site. This paper includes an update of the information presented at WM2019 [1]. (authors)

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

A Dose Assessment Model for Radioactive Waste Exposed by Gully Erosion at West Valley - 20513

The Western New York Nuclear Service Center (WNYNSC), located approximately 48 km south of Buffalo, New York, is the site of a former nuclear fuel reprocessing and radioactive waste disposal facility. Spent nuclear fuel was processed there from 1966 to 1972, leaving behind radioactive and chemical wastes in two disposal areas and a waste tank farm. Site operations also resulted in releases of radioactivity to site soils, groundwater, and to surface waters draining the site. The New York State Energy Research and Development Authority (NYSERDA) and the U.S. Department of Energy (DOE) are collaborating in a process of decision making for decommissioning those facilities remaining at the WNYNSC following the completion of Phase 1 decommissioning. Neptune and Company, Inc. (Neptune) was contracted to develop a probabilistic performance assessment (PPA) computer model to assist the agencies in this process. The PPA Model includes a contaminant transport component focusing on the movement of contaminants within and among environmental media including groundwater and surface water transport, contaminant translocation by plants and animals, diffusion, and erosion. The model also includes evaluation of potential exposure and health effects for a Resident Farmer exposure scenario, where the Resident Farmer represents a critical group, described as that group of individuals reasonably expected to receive the greatest exposure to residual radioactivity for any applicable set of circumstances. The West Valley Site is located in the glaciated Allegheny Plateau region of western New York State. The waste reprocessing and disposal areas were constructed on a relatively fat area of plateau dissected by drainages of Buttermilk Creek, including Erdman Brook, Franks Creek, and Quarry Creek. An important aspect of the contaminant transport component of the PPA model is consideration of erosive processes such as slumping of the stream slopes and the advance of gullies from these streams. These erosion processes remove material from the plateau, growing the size of the creek valleys and making them wider and deeper. Of particular interest for the impact of erosion is radioactive waste contained in the Nuclear Regulatory Commission (NRC)-Licensed Disposal Area (NDA), the New York State-Licensed Disposal Area (SDA), and residual radiological inventory in the underground storage tanks at the Waste Tank Farm (WTF). The PPA Model is organized around geographically-defined facilities which were constructed upon the plateau, including the NDA, SDA, and WTF. Ongoing stream erosion processes will potentially transfer radioactive waste and residual inventory from these facilities to the ground surface on adjacent hillslope areas where erosion has breached the facility. Hence, it is important to evaluate the consequences of potential exposures to a Resident Farmer on the hillslopes below a breached facility. Two interrelated aspects of the dose assessment model related to hillslope exposure are discussed: 1) representation of the physical processes related to transport of radionuclides from facilities onto the hillslopes, and from the hillslopes into adjoining creeks where contaminated material migrates downstream with surface water and sediment, and; 2) adaptation of the activities associated with the Resident Farmer scenario to assess potential exposures to contamination in the hillslope areas. This discussion will cover the conceptual basis of the hillslope exposure and transport models, and also implementation in the PPA computer model. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Exploring inflammation‐related protein expression and its relationship with TSPO PET in Alzheimer's disease

Abstract INTRODUCTION To understand the role of neuroinflammation in Alzheimer's disease (AD), we characterized immune‐related proteins in central and peripheral biofluids. METHODS Selection of participants from the Translational Biomarker of Aging and Dementia (TRIAD) cohort with available translocator protein (TSPO) positron emission tomography (PET), cerebrospinal fluid (CSF) (n = 97), and plasma (n = 165). Biofluid samples analyzed with Olink technology (368 inflammation proteins). RESULTS Elevated proteins levels in CSF of TSPO‐positive individuals were identified. Functional enrichment analysis of CSF proteins revealed processes implicated in AD (MAPK, ERK cascades, cytokine, and leukocyte signaling). Selected candidates (CXCL1 and TNFRSF11B) showed high correlation with each other in CSF and with TSPO PET signal, but weaker associations with amyloid and tau PET. No significantly changed proteins in plasma between TSPO groups were found. DISCUSSION This explorative study identified two potential targets in CSF showing correlations with TSPO, amyloid and tau PET, suggesting a direct link between neuroinflammation, expression of these proteins and their potential implication in AD. Highlights Several proteins are elevated in CSF of TSPO PET‐positive individuals, linking them to neuroinflammation. Elevated CSF proteins were enriched in pathways such as MAPK, ERK, and cytokine signaling, linking them to the AD pathophysiology. Candidate proteins (CXCL1 and TNFRSF11B) correlated strongly with TSPO PET, particularly in brain regions known to be affected in AD. Although none of the plasma proteins remained significant after multiple comparisons correction when comparing their expression between TSPO groups, as done for CSF, candidate CSF proteins were found to correlate with plasmatic proteins, highlighting the complexity of the immune system.

Neurosciences & Neurology↗
DOE OSTI2023

Mammalian Chromosome Analysis and Sorting by Flow Cytometry

The analysis of chromosomes by flow cytometry is termed flow cytogenetics, and it involves the analysis and sorting of single mitotic chromosomes in suspension. The study of flow karyograms provides insight into chromosome number and structure to provide information on chromosomal DNA content and can enable the detection of deletions, translocations, or any forms of aneuploidy. Beyond its clinical applications, flow cytogenetics greatly contributed to the Human Genome Project through the ability to sort pure populations of chromosomes for gene mapping, cloning, and the construction of DNA libraries. Maximizing the potential of these important applications of flow cytogenetics relies on precise instrument setup and optimal sample processing, both of which impact the accuracy and quality of the data that are generated. This article is a compilation of the existing protocols that describe the stepwise methodology of accumulating, isolating, and staining metaphase chromosomes to prepare single-chromosome suspensions for flow cytometric analysis and sorting. Although the chromosome preparation protocols have remained largely unchanged, cytometer technology has advanced dramatically since these protocols were originally developed. Advances in cytometry technologies offer new and exciting approaches for understanding and monitoring chromosomal aberrations, but the hallmark of these protocols remains their simplicity in methodologies and reagent requirements and the accuracy of data resolvable to every chromosome of the cell.

59 BASIC BIOLOGICAL SCIENCES↗