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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Electric-vehicle battery second-life and recycling pathways: How economics depend on chemistry, processing, and application

We assess the economics of repurposing and recycling electric vehicle (EV) batteries by estimating the maximum acquisition price repurposers and recyclers could pay for used EV packs across cathode chemistries, first-life conditions, second-life applications, and recycling processes. We develop a novel open-source process-based cost model of a UL-1974-certified repurposing facility and leverage battery degradation models to estimate the maximum acquisition price repurposers could pay for used EV batteries while producing second-life battery energy storage systems with life-adjusted costs equivalent to new systems. We compare these maximum price estimates to maximum prices for recyclers based on cost and revenue estimates from the EverBatt model. We find that repurposing is more economical than recycling for lithium iron phosphate (LFP) batteries, due to their relatively long life and low value materials; recycling is generally more economical than repurposing for lithium nickel cobalt aluminum oxide (NCA) batteries, due to their shorter life and higher value materials; and the economics for lithium nickel manganese cobalt oxide (NMC) batteries depend more heavily on first life retirement conditions and second life application intensity. These results suggest an overall strategy: reuse LFP, recycle NCA, and sort NMC into recycling or repurposing pathways based on state of health and second-life application.

25 ENERGY STORAGE↗
DOE OSTI2023

Analysis of an optical imaging system prototype for autonomously monitoring zooplankton in an aquaculture facility

Traditional approaches to biomonitoring in aquatic systems, such as sample collection, sorting, and identification, require significant time and effort, thereby limiting the spatiotemporal resolution of sample collection. Additionally, collection and preservation of samples for subsequent taxonomic identification and enumeration leads to mortality of organisms. Recent advances in technologies that utilize optical imaging and machine learning have provided new opportunities to expedite biomonitoring and lead to significant cost savings. These technologies can be advantageous to scientists or managers that conduct routine biomonitoring to inform operations, as in the case of aquaculture facilities. The Small Aquatic Organism optical imaging system (SAO) is a high-throughput optical imaging and classification prototype system that relies on computer vision and machine learning (Support Vector Machines, or SVMs) to autonomously identify and enumerate aquatic organisms. The SAO provides a more sustainable method of collecting large volumes of data and has the benefit of being used in situ. In this study, we tested the performance of the SAO in providing comparable results to manual zooplankton community monitoring in ten ponds at an aquaculture facility. We performed a side-by-side study comparing the sampling methods of plankton tow nets, where major zooplankton taxonomic classes were manually identified and enumerated, to sampling with the SAO. Vouchered samples were used to develop a training library for the SAO, where classes consisted of water boatman and zooplankton groups: cladocerans, copepod adults, copepod nauplii, and rotifers. SAO imagery was manually classified and compared with predicted results for validation. Accuracy for the SVM classifier of the SAO was 37.4 %. Convolutional Neural Networks (CNN) and Random Forest classifiers were also applied to SAO imagery and image features for comparison. The best CNN model and our Random Forest model had accuracies of 80.4 % and 46.6 % respectively. Challenges faced included the small size of copepod nauplii and rotifers and the limited resolution of the imaging camera, although there are tradeoffs between imaging resolution and the sample processing rate. Furthermore, our comparison shows that advancement in both optical imaging and ML are needed in order for the SAO prototype to yield comparable results to manual community monitoring in an aquaculture facility.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Hybrid data-driven cement-stabilized soil design: An integration of machine learning, multi-objective optimization, and life cycle assessment

Soil stabilization is crucial in geotechnical engineering, yet conventional methods are often time-consuming, resource-intensive, and environmentally unsustainable. Despite growing interest in Machine Learning (ML) and optimization tools for mix design, few studies integrate these methods with decision-making techniques and environmental assessment to support practical implementation. This study proposes a hybrid data-driven framework for predicting strength, optimizing mix compositions, and evaluating environmental impacts via life cycle assessment of cement-stabilized soft soils. Six ML models were evaluated, and the top-performing eXtreme Gradient Boosting (XGB) model was further improved using the Grey Wolf Optimizer (GWO). The optimized XGB-GWO model, integrated with a polynomial cost function, served as the objective function in a multi-objective optimization problem solved via the Non-Dominated Sorting Genetic Algorithm II (NSGA-II), with final mix selection guided by the entropy-weighted TOPSIS method. Validation through a case study produced mix designs offering superior strength-cost trade-offs, with the optimal mix achieving 2243.2 kPa unconfined compressive strength and a 16.07 % reduction in carbon emissions compared to the highest-cost design. In conclusion, this study offers a sustainable, scalable approach to soil stabilization and supports informed decision-making in construction.

Life cycle assessment↗
DOE OSTI2021

Quantifying physical parameterization uncertainties associated with land-atmosphere interactions in the WRF model over Amazon

The Weather Research and Forecasting (WRF) model can be used to diagnose regional land-atmosphere (L-A) coupling strength in the absence of sufficient observations but subjected to uncertainties associated with model physical parameterizations. In this study, we propose a framework to quantify and reduce model physical parameterization uncertainties associated with surface fluxes and L-A coupling. An ensemble of WRF simulations with different physical schemes is used to simulate surface fluxes and land-atmosphere coupling strength over the Amazon region. The physical parameterizations investigated include cloud microphysics (MP), land surface processes (LSM), planetary boundary layer (PBL), surface layer (SL), and cumulus (CU). We perform 120 ensemble simulations using the WRF model and different combinations of six MPs, three LSMs, six PBLs and SLs and three CUs. The measurements from the GoAMAZON field campaign and satellite data are used to evaluate model performance. A Multi-way analysis of variance (ANOVA) approach is applied to quantify the relative importance of different physics processes on L-A coupling. The Tukey’s test is used to sort schemes that have no significant differences into one group. The suite of physics that result in the best simulations of the corresponding variables are selected based on the Taylor skill score. Results show that the relative importance of processes and their interaction vary with the variables of interest. For example, CU was the most important process in modulating soil moisture, 2 m-humidity, latent heat, and net radiation. LSM showed dominant effects on 2 m-temperature and also has the largest impact on sensible heat and the lifting condensation level. The best physical parameterization ensembles show much narrower ranges of the variables of interest than the priori ensemble. Results of this study show the roles of different physical processes in modulating L-A interactions, quantify model uncertainties from physical processes, and provide insights for improving the model physics parameterizations.

Wang, Chen↗
DOE OSTI2013

Loading and pre-loading processes generate a distinct siRNA population in Tetrahymena

Highlights: •The Tetrahymena Argonaute protein Twi1p binds to ∼28–30-nt siRNAs called scnRNAs. •The size of scnRNAs is determined during a pre-loading process. •The 5′ uracil bias of scnRNAs is attributed to pre-loading and loading processes. •The thermodynamic asymmetry of scnRNA duplex doesnot affect the guide strand decision. •scnRNAs may be produced non-sequentially from dsRNA substrates by Dicer. -- Abstract: The various properties of small RNAs, such as length, terminal nucleotide, thermodynamic asymmetry and duplex mismatches, can impact their sorting into different Argonaute proteins in diverse eukaryotes. The developmentally regulated 26- to 32-nt siRNAs (scnRNAs) are loaded to the Argonaute protein Twi1p and display a strong bias for uracil at the 5′ end. In this study, we used deep sequencing to analyze loaded and unloaded populations of scnRNAs. We show that the size of the scnRNA is determined during a pre-loading process, whereas their 5′ uracil bias is attributed to both pre-loading and loading processes. We also demonstrate that scnRNAs have a strong bias for adenine at the third base from the 3′ terminus, suggesting that most scnRNAs are direct Dicer products. Furthermore, we show that the thermodynamic asymmetry of the scnRNA duplex does not affect the guide and passenger strand decision. Finally, we show that scnRNAs frequently have templated uracil at the last base without a strong bias for adenine at the second base indicating non-sequential production of scnRNAs from substrates. These findings provide a biochemical basis for the varying attributes of scnRNAs, which should help improve our understanding of the production and turnover of scnRNAs in vivo.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

V-ATPase-dependent luminal acidification is required for endocytic recycling of a yeast cell wall stress sensor, Wsc1p

Highlights: •A targeted genome screen identified 5 gene groups affecting Wsc1p recycling. •V-ATPase-dependent luminal acidification is required for Wsc1p recycling. •Activity of V-ATPase might be required for cargo recognition by the retromer complex. -- Abstract: Wsc1p is a major cell wall sensor protein localized at the polarized cell surface. The localization of Wsc1p is maintained by endocytosis and recycling from endosomes back to the cell surface, but changes to the vacuole when cells are subjected to heat stress. Exploiting this unique property of Wsc1p, we screened for yeast single-gene deletion mutants exhibiting defects in Wsc1p trafficking. By expressing 3GFP-tagged Wsc1p in mutants with deleted genes whose function is related to intracellular trafficking, we identified 5 gene groups affecting Wsc1p trafficking, impaired respectively in endocytic internalization, multivesicular body sorting, the GARP complex, endosomal maturation/vacuolar fusion, and V-ATPase. Interestingly, deletion of the VPH1 gene, encoding the V{sub o} subunit of vacuolar-type H{sup +}-ATPase (V-ATPase), led to mis-localization of Wsc1p from the plasma membrane to the vacuole. In addition, disruption of other V-ATPase subunits (vma mutants) also caused defects of Wsc1p trafficking and vacuolar acidification similar to those seen in the vph1Δ mutant. Moreover, we found that deletion of the VPS26 gene, encoding a subunit of the retromer complex, also caused a defect in Wsc1p recycling and mis-localization of Wsc1p to the vacuole. These findings clarified the previously unidentified Wsc1p recycling pathway and requirement of V-ATPase-dependent luminal acidification for Wsc1p recycling.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Blocking the NOTCH pathway can inhibit the growth of CD133-positive A549 cells and sensitize to chemotherapy

Highlights: • Notch signaling pathway members are expressed lower levels in CD133+ cells. • CD133+ cells are not as sensitive as CD133− cells to chemotherapy. • GSI could inhibit the growth of both CD133+ and CD133− cells. • Blockade of Notch signaling pathway enhanced the effect of chemotherapy with CDDP. • DAPT/CDDP co-therapy caused G2/M arrest and elimination in CD133+ cells. - Abstract: Cancer stem cells (CSCs) are believed to play an important role in tumor growth and recurrence. These cells exhibit self-renewal and proliferation properties. CSCs also exhibit significant drug resistance compared with normal tumor cells. Finding new treatments that target CSCs could significantly enhance the effect of chemotherapy and improve patient survival. Notch signaling is known to regulate the development of the lungs by controlling the cell-fate determination of normal stem cells. In this study, we isolated CSCs from the human lung adenocarcinoma cell line A549. CD133 was used as a stem cell marker for fluorescence-activated cell sorting (FACS). We compared the expression of Notch signaling in both CD133+ and CD133− cells and blocked Notch signaling using the γ-secretase inhibitor DAPT (GSI-IX). The effect of combining GSI and cisplatin (CDDP) was also examined in these two types of cells. We observed that both CD133+ and CD133− cells proliferated at similar rates, but the cells exhibited distinctive differences in cell cycle progression. Few CD133+ cells were observed in the G{sub 2}/M phase, and there were half as many cells in S phase compared with the CD133− cells. Furthermore, CD133+ cells exhibited significant resistance to chemotherapy when treated with CDDP. The expression of Notch signaling pathway members, such as Notch1, Notch2 and Hes1, was lower in CD133+ cells. GSI slightly inhibited the proliferation of both cell types and exhibited little effect on the cell cycle. The inhibitory effects of DPP on these two types of cells were enhanced when combined with GSI. Interestingly, this effect was especially significant in CD133+ cells, suggesting that Notch pathway blockade may be a useful CSC-targeted therapy in lung cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

DDX4 (DEAD box polypeptide 4) colocalizes with cancer stem cell marker CD133 in ovarian cancers

Highlights: • Germ cell marker DDX4 was significantly increased in ovarian cancer. • Ovarian cancer stem cell marker CD133 was significantly increased in ovarian cancer. • DDX4 and CD133 were mostly colocalized in various types of ovarian cancer tissues. • CD133 positive ovarian cancer cells also express DDX4 whereas CD133-negative cells did not possess DDX4. • Germ cell marker DDX4 has the potential of ovarian cancer stem cell marker. - Abstract: DDX4 (DEAD box polypeptide 4), characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), is an RNA helicase which is implicated in various cellular processes involving the alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. DDX4 is known to be a germ cell-specific protein and is used as a sorting marker of germline stem cells for the production of oocytes. A recent report about DDX4 in ovarian cancer showed that DDX4 is overexpressed in epithelial ovarian cancer and disrupts a DNA damage-induced G2 checkpoint. We investigated the relationship between DDX4 and ovarian cancer stem cells by analyzing the expression patterns of DDX4 and the cancer stem cell marker CD133 in ovarian cancers via tissue microarray. Both DDX4 and CD133 were significantly increased in ovarian cancer compared to benign tumors, and showed similar patterns of expression. In addition, DDX4 and CD133 were mostly colocalized in various types of ovarian cancer tissues. Furthermore, almost all CD133 positive ovarian cancer cells also express DDX4 whereas CD133-negative cells did not possess DDX4, suggesting a strong possibility that DDX4 plays an important role in cancer stem cells, and/or can be used as an ovarian cancer stem cell marker.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Androgen-independent proliferation of LNCaP prostate cancer cells infected by xenotropic murine leukemia virus-related virus

Highlights: • XMRV infection induces androgen-independent growth in LNCaP cells. • XMRV infection reduces expression of androgen receptor. • XMRV promotes appearance of androgen blocker-resistant prostate cancer cells. - Abstract: Xenotropic murine leukemia virus-related virus (XMRV) is a novel gammaretrovirus that was originally isolated from human prostate cancer. It is now believed that XMRV is not the etiologic agent of prostate cancer. An analysis of murine leukemia virus (MLV) infection in various human cell lines revealed that prostate cancer cell lines are preferentially infected by XMRV, and this suggested that XMRV infection may confer some sort of growth advantage to prostate cancer cell lines. To examine this hypothesis, androgen-dependent LNCaP cells were infected with XMRV and tested for changes in certain cell growth properties. We found that XMRV-infected LNCaP cells can proliferate in the absence of the androgen dihydrotestosterone. Moreover, androgen receptor expression is significantly reduced in XMRV-infected LNCaP cells. Such alterations were not observed in uninfected and amphotropic MLV-infected LNCaP cells. This finding explains why prostate cancer cell lines are preferentially infected with XMRV.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Isorhynchophylline protects against pulmonary arterial hypertension and suppresses PASMCs proliferation

Highlights: • We focus on PASMCs proliferation in the pathogenesis of PAH. • Isorhynchophylline inhibited PASMCs proliferation and alleviated PAH. • IRN blocked PDGF-Rβ phosphorylation and its downstream signal transduction. • IRN regulated cyclins and CDKs to arrest cell cycle in the G0/G1 phase. • We reported IRN has the potential to be a candidate for PAH treatment. - Abstract: Increased pulmonary arterial smooth muscle cells (PASMCs) proliferation is a key pathophysiological component of pulmonary vascular remodeling in pulmonary arterial hypertension (PAH). Isorhynchophylline (IRN) is a tetracyclic oxindole alkaloid isolated from the Chinese herbal medicine Uncaria rhynchophylla. It has long been used clinically for treatment of cardiovascular and cerebrovascular diseases. However, very little is known about whether IRN can influence the development of PAH. Here we examined the effect of IRN on monocrotaline (MCT) induced PAH in rats. Our data demonstrated that IRN prevented MCT induced PAH in rats, as assessed by right ventricular (RV) pressure, the weight ratio of RV to (left ventricular + septum) and RV hypertrophy. IRN significantly attenuated the percentage of fully muscularized small arterioles, the medial wall thickness, and the expression of smooth muscle α-actin (α-SMA) and proliferating cell nuclear antigen (PCNA). In vitro studies, IRN concentration-dependently inhibited the platelet-derived growth factor (PDGF)-BB-induced proliferation of PASMCs. Fluorescence-activated cell-sorting analysis showed that IRN caused G0/G1 phase cell cycle arrest. IRN-induced growth inhibition was associated with downregulation of Cyclin D1 and CDK6 as well as an increase in p27Kip1 levels in PDGF-BB-stimulated PASMCs. Moreover, IRN negatively modulated PDGF-BB-induced phosphorylation of PDGF-Rβ, ERK1/2, Akt/GSK3β, and signal transducers and activators of transcription 3 (STAT3). These results demonstrate that IRN could inhibit PASMCs proliferation and attenuate pulmonary vascular remodeling after MCT induction. These beneficial effects were at least through the inhibition of PDGF-Rβ phosphorylation and its downstream signaling pathways. Therefore, IRN might be a potential candidate for the treatment of PAH.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Nascent histamine induces α-synuclein and caspase-3 on human cells

Highlights: • Nascent histamine alters cyclin expression pattern. • Nascent histamine increases expression of α-synuclein. • Nascent histamine activates caspase-3. - Abstract: Histamine (Hia) is the most multifunctional biogenic amine. It is synthetized by histidine decarboxylase (HDC) in a reduced set of mammalian cell types. Mast cells and histaminergic neurons store Hia in specialized organelles until the amine is extruded by exocytosis; however, other immune and cancer cells are able to produce but not store Hia. The intracellular effects of Hia are still not well characterized, in spite of its physiopathological relevance. Multiple functional relationships exist among Hia metabolism/signaling elements and those of other biogenic amines, including growth-related polyamines. Previously, we obtained the first insights for an inhibitory effect of newly synthetized Hia on both growth-related polyamine biosynthesis and cell cycle progression of non-fully differentiated mammalian cells. In this work, we describe progress in this line. HEK293 cells were transfected to express active and inactive versions of GFP-human HDC fusion proteins and, after cell sorting by flow cytometry, the relative expression of a large number of proteins associated with cell signaling were measured using an antibody microarray. Experimental results were analyzed in terms of protein–protein and functional interaction networks. Expression of active HDC induced a cell cycle arrest through the alteration of the levels of several proteins such as cyclin D1, cdk6, cdk7 and cyclin A. Regulation of α-synuclein and caspase-3 was also observed. The analyses provide new clues on the molecular mechanisms underlying the regulatory effects of intracellular newly synthetized Hia on cell proliferation/survival, cell trafficking and protein turnover. This information is especially interesting for emergent and orphan immune and neuroinflammatory diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Comparative proteomic analysis of outer membrane vesicles from Shigella flexneri under different culture conditions

Highlights: • We utilized mTRAQ-based quantification to study protein changes in Congo red-induced OMVs. • A total of 148 proteins were identified in S. flexneri-derived OMVs. • Twenty-eight and five proteins are significantly up- and down-regulated in the CR-induced OMV, respectively. • The result implied that a special sorting mechanism of particular proteins into OMVs may exist. • Key node proteins in the protein interaction network might be important for pathogenicity. - Abstract: The production of outer membrane vesicles (OMVs) is a common and regulated process of gram-negative bacteria. Nonetheless, the processes of Shigella flexneri OMV production still remain unclear. S. flexneri is the causative agent of endemic shigellosis in developing countries. The Congo red binding of strains is associated with increased infectivity of S. flexneri. Therefore, understanding the modulation pattern of OMV protein expression induced by Congo red will help to elucidate the bacterial pathogenesis. In the present study, we investigated the proteomic composition of OMVs and the change in OMV protein expression induced by Congo red using mTRAQ-based quantitative comparative proteomics. mTRAQ labelling increased the confidence in protein identification, and 148 total proteins were identified in S. flexneri-derived OMVs. These include a variety of important virulence factors, including Ipa proteins, TolC family, murein hydrolases, and members of the serine protease autotransporters of Enterobacteriaceae (SPATEs) family. Among the identified proteins, 28 and five proteins are significantly up- and down-regulated in the Congo red-induced OMV, respectively. Additionally, by comprehensive comparison with previous studies focused on DH5a-derived OMV, we identified some key node proteins in the protein–protein interaction network that may be involved in OMV biogenesis and are common to all gram-negative bacteria.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Chemoresistance of CD133{sup +} colon cancer may be related with increased survivin expression

CD133, putative cancer stem cell marker, deemed to aid chemoresistance. However, this claim has been challenged recently and we previously reported that patients with CD133{sup +} colon cancer have benefit from 5-fluorouracil (5-FU) chemotherapy incontrast to no benefit in patients with CD133{sup −} cancer. To elucidate the role of CD133 expression in chemoresistance, we silenced the CD133 expression in a colon cancer cell line and determined its effect on the biological characteristics downstream. We comparatively analyzed the sequential changes of MDR1, ABCG2, AKT1 and survivin expression and the result of proliferation assay (WST-1 assay) with 5-FU treatment in CD133{sup +} and siRNA-induced CD133{sup −} cells, derived from Caco-2 colon cancer cell line. 5-FU treatment induced significantly increase of the mRNA expression of MDR1, ABCG2 and AKT1genes, but not protein level. CD133 had little to no effect on the mRNA and protein expression of these genes. However, survivin expression at mRNA and protein level were significantly increased in CD133{sup +} cells compared with siRNA-induced CD133-cells and Mock (not sorted CD133{sup +} cells) at 96 h after siRNA transfection. The cytotoxicity assay demonstrated notable increase of chemoresistance to 5-FU treatment (10 μM) in CD133{sup +} cells at 96 h after siRNA transfection. From this study, we conclude that CD133{sup +} cells may have chemoresistance to 5-FU through the mechanism which is related with survivin expression, instead of MDR1, ABCG2 and AKT1 expression. Therefore a survivin inhibitor can be a new target for effective treatment of CD133{sup +} colon cancer. - Highlights: • We evaluate the role of CD133 in chemoresistance of colon cancer. • We compared the chemoresistance of CD133{sup +} cells and siRNA-induced CD133{sup −} cells. • CD133 had little to no effect on MDR1, ABCG2 and AKT1 expression. • Survivin expression and chemoresistance were increased in CD133{sup +} colon cancer cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Overexpression of miR-206 suppresses glycolysis, proliferation and migration in breast cancer cells via PFKFB3 targeting

miRNAs, sorting as non-coding RNAs, are differentially expressed in breast tumor and act as tumor promoters or suppressors. miR-206 could suppress the progression of breast cancer, the mechanism of which remains unclear. The study here was aimed to investigate the effect of miR-206 on human breast cancers. We found that miR-206 was down-regulated while one of its predicted targets, 6-Phosphofructo-2-kinase (PFKFB3) was up-regulated in human breast carcinomas. 17β-estradiol dose-dependently decreased miR-206 expression as well as enhanced PFKFB3 mRNA and protein expression in estrogen receptor α (ERα) positive breast cancer cells. Furthermore, we identified that miR-206 directly interacted with 3′-untranslated region (UTR) of PFKFB3 mRNA. miR-206 modulated PFKFB3 expression in MCF-7, T47D and SUM159 cells, which was influenced by 17β-estradiol depending on ERα expression. In addition, miR-206 overexpression impeded fructose-2,6-bisphosphate (F2,6BP) production, diminished lactate generation and reduced cell proliferation and migration in breast cancer cells. In conclusion, our study demonstrated that miR-206 regulated PFKFB3 expression in breast cancer cells, thereby stunting glycolysis, cell proliferation and migration. - Highlights: • miR-206 was down-regulated and PFKFB3 was up-regulated in human breast carcinomas. • 17β-estradiol regulated miR-206 and PFKFB3 expression in ERα+ cancer cells. • miR-206directly interacted with 3′-UTR of PFKFB3 mRNA. • miR-206 fructose-2,6-bisphosphate (F2,6BP) impeded production and lactate generation. • miR-206 reduced cell proliferation and migration in breast cancer cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Chameleon sequences in neurodegenerative diseases

Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

CD27{sup -}CD45{sup +} γδ T cells can be divided into two populations, CD27{sup -}CD45{sup int} and CD27{sup -}CD45{sup hi} with little proliferation potential

In addition to the majority of T cells which carry the αβ T cell receptor (TCR) for antigen, a distinct subset of about 1–5% of human peripheral blood T cells expressing the γδ TCR contributes to immune responses to infection, tissue damage and cancer. T cells with the Vδ2{sup +} TCR, usually paired with Vγ9, constitute the majority of these γδ T cells. Analogous to αβ T cells, they can be sorted into naive (CD27{sup +}CD45RA{sup +}), central memory (CD27{sup +}CD45RA{sup −}), effector memory (CD27{sup −}CD45RA{sup −}), and terminally-differentiated effector memory (CD27{sup −}CD45RA{sup +}) phenotypes. Here, we found that CD27{sup −}CD45RA{sup +} γδ T cells can be further divided into two populations based on the level of expression of CD45RA: CD27{sup −}CD45RA{sup int} and CD27{sup −}CD45RA{sup hi}. Those with the CD27{sup −}CD45RA{sup hi} phenotype lack extensive proliferative capacity, while those with the CD27{sup −}CD45RA{sup int} phenotype can be easily expanded by culture with zoledronate and IL-2. These CD27{sup -}CD45RA{sup hi} potentially exhausted γδ T cells were found predominantly in cancer patients but also in healthy subjects. We conclude that γδ T cells can be divided into at least 5 subsets enabling discrimination of γδ T cells with poor proliferative capacity. It was one of our goals to predict the feasibility of γδ T cell expansion to sufficient amounts for adoptive immunotherapy without the necessity for conducting small-scale culture tests. Fulfilling the ≥1.5% criterion for γδ T cells with phenotypes other than CD27{sup −}CD45RA{sup hi}, may help avoid small-scale culture testing and shorten the preparation period for adoptive γδ T cells by 10 days, which may be beneficial for patients with advanced cancer. - Highlights: • CD27{sup -}CD45{sup +} γδ T cells can be divided into two populations, CD27{sup -}CD45{sup hi} and CD27{sup -}CD45{sup int}. • CD27{sup -}CD45{sup hi} γδ T cells are detected in the peripheral blood of both cancer patients and healthy subjects. • CD27{sup -}CD45{sup hi} γδ T cells are distinct from so-called terminally differentiated CD27{sup -}CD45{sup int} γδ T cells. • CD27{sup -}CD45{sup hi} γδ T cells lack vigorous proliferative potential.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Integration of in silico approaches to determination of endocrine-disrupting perfluorinated chemicals binding potency with steroidogenic acute regulatory protein

A myriad of perfluorinated compounds (PFCs) have the ability to interfere with steroidogenic acute regulatory (StAR) protein. Consequently, PFCs breaches cholesterol biotransformation in mitochondria and cause fatal consequences in steroidogenesis, however, these were poorly characterized. In the present study, we have evaluated toxic potencies, nuclear mediated probabilities and interaction profiles with StAR of PFCs using computational system biology tools. Toxicity endpoints revealed that PFCs contain high carcinogenicity, developmental toxicity, skin sensitization effects with low mutagenic activity. Consensus qualitative nuclear receptor agonist models show higher probability rates towards ER and PPAR-γ receptor than AR and AhR models were observed. To poise the subtle fluctuations of actual predictions, balanced accuracy and MCC were computed, and they signify perfect correlation ranges in all models. Screening studies resulting protein-ligand interaction profiles showed that residues Asn148, Asn150, Glu169, Ala171, Arg182, Phe184, Arg188, Trp241, Thr263 and Phe267 were identified as novel hotspots, participated in halogen bonds, H-bonds, atomic π-stacking, π-cation interactions and salt-bridges formation. Thus, the additional bonds contribute conformer stability that holds the protein structure at flexible state, so that PFCs acts as a barrier to cholesterol binding. From docking outcomes, representation space was created, that specifies high and medium StAR binders were occupied in toxic endpoints space with active concern. PFCs restrain molecular features and mitochondrial membrane disruption functions were revealed by efficient toxicogenomics studies. These data indicate toxicity and StAR protein binding levels of PFCs, sorted pinpoints could be useful in a promising way to know the other environmental pollutants and health risks. - Highlights: • In this study, QSAR models were revealed that PFCs have greater adverse toxicity along with nuclear receptors interaction potencies. • Binding potencies of PFCs against the StAR protein revealed only potential novel residue hotspots showed various bond patterns, and they sustain stability and complexity of StAR. • Through that, PFCs acts as a barrier in cholesterol binding and leads fatal consequences in steroidogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Overexpression of SNX7 reduces Aβ production by enhancing lysosomal degradation of APP

Highlights: • SNX7 has been proposed to be linked with Alzheimer's disease. • Overexpression of SNX7 reduces the production of Aβ and sAPPβ. • It also reduces the cellular level of APP. • The reduction of APP is reversed by inhibitors of lysosomal degradation. • Our results suggest that SNX7 takes part in directing APP for degradation. Abnormal production of amyloid-β peptides (Aβ) by proteolytic processing of amyloid precursor protein (APP) is thought to be central to the pathogenesis of Alzheimer's disease (AD). Although many efforts have been made to investigate mechanisms that regulate APP processing, many details remain incompletely understood. Sorting nexins (SNXs) are a family of proteins which are involved in many intracellular trafficking events. Several SNXs have been implicated in APP processing and Aβ production. In this study, we extended the investigation to SNX7. We found that overexpression of SNX7 in HEK293T cells reduces the levels of secreted Aβ and β-cleaved N-terminal APP fragments (sAPPβ). Moreover, SNX7 overexpression caused a significant reduction of the steady-state levels of APP as well as of the cell surface APP levels. By using NH{sub 4}Cl and Bafilomycin A1 to inhibit the lysosomal degradative pathway, we found that the reduction of APP induced by SNX7 overexpression was prevented by such inhibition. No change in the cell surface distribution or steady-state levels of BACE1 was detected after overexpression of SNX7. Taken together, these results suggest that SNX7 regulates Aβ production by directing APP for degradation.

60 APPLIED LIFE SCIENCES↗