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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise

Exercise provides a robust physiological stimulus that evokes cross-talk between a wide range of tissues via hormonal, cellular and molecular signals that when repeated regularly over time (i.e., training) improves physiological capacity, benefits numerous organ systems and decreases the risk for premature mortality. In spite of its fundamental importance, a gap remains in identifying the detailed molecular signals and responses to exercise and its benefits for health and disease prevention. To further knowledge in this emerging area, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to generate a molecular map of the effects of acute and chronic exercise. MoTrPAC investigators are conducting preclinical and clinical studies to better understand the systemic effects of exercise across multiple tissues. The preclinical studies were performed on more than 700 rats with the analysis of twenty or more organs per rat. The clinical study involves a large cohort of ~2600 individuals with a range of ages and fitness levels (untrained, trained, highly trained) who will be evaluated physiologically and by molecular probing of blood, muscle and adipose tissues before and after acute and chronic endurance or resistance exercise. Multi-omic analyses (genomics, epigenomics, transcriptomics, proteomics and metabolomics/lipidomics) will be performed followed by state-of-the-art bioinformatics to create a molecular map of exercise. This mapping project will provide a public database that is expected to enhance our understanding of the health benefits of physical activity in many organ systems and potentially provide insight into mitigating diseases through activity.

Sanford, James A.↗
DOE OSTI2025

The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism

Bacteria exist in competitive and rapidly changing environments in which the nature of future threats cannot be easily predicted. Streptomyces coelicolor produces three antibacterial umbrella particles that harbor distinct polymorphic toxin domains and an overlapping set of six diversified lectins. Here, we show that the exquisite specificity of umbrella particles derives from lectin-mediated species-specific binding to previously undescribed hypervariable surface glycoconjugates. A cryo-electron microscopy (cryo-EM) structure of one such lectin in complex with its oligosaccharide substrate defines the molecular basis for targeting through the coordinated recognition of multiple glycan features. Biochemical and genetic studies of several target species, in conjunction with lectin-swapping experiments, support a model whereby S. coelicolor umbrella toxin diversification at the levels of lectin composition and toxin polymorphism represents a unique, two-tiered bet-hedging strategy. Bioinformatic analyses support this as a means by which the unusual architecture of umbrella toxins offers Streptomyces a generalizable strategy to antagonize an unpredictable array of competitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

SILAC Analysis Reveals Increased Secretion of Hemostasis-Related Factors by Senescent Cells

Cellular senescence irreversibly arrests cell proliferation, accompanied by a multi-component senescence-associated secretory phenotype (SASP) that participates in several age-related diseases. Using stable isotope labeling with amino acids (SILACs) and cultured cells, we identify 343 SASP proteins that senescent human fibroblasts secrete at 2-fold or higher levels compared with quiescent cell counterparts. Bioinformatic analysis reveals that 44 of these proteins participate in hemostasis, a process not previously linked with cellular senescence. We validated the expression of some of these SASP factors in cultured cells and in vivo. Mice treated with the chemotherapeutic agent doxorubicin, which induces widespread cellular senescence in vivo, show increased blood clotting. Conversely, selective removal of senescent cells using transgenic p16-3MR mice showed that clearing senescent cells attenuates the increased clotting caused by doxorubicin. Our study provides an in-depth, unbiased analysis of the SASP and unveils a function for cellular senescence in hemostasis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

The interactions of peripheral membrane proteins with biological membranes

The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approaches continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Microbial communities for bioprocessing: lessons learned from nature

Microbial bioprocessing has evolved from the use of undefined natural consortia to the construction of synthetic communities tailored to specific processes and bioproducts. This evolution is enabled by recent advances in biotechnology, including cultivation of non-model microbes, metabolic engineering, bioinformatics, and numerical modeling. Equipped with these powerful tools, engineers have designed co-cultures and consortia with an expanded set of capabilities, mainly via ‘bottom-up’ approaches that tether isolates together in culture. We present a brief review of the opportunities, challenges, and recent developments in consortia-based bioprocessing with a focus on lignocellulosic biomass conversion. With improved understanding of microbial community composition and function, we further present a vision to harness defined consortia down-selected from nature via ‘top down’ approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi

Fungi generate a wide range of extracellular hydrolytic and oxidative enzymes and reactive metabolites, collectively known as the secretome, that synergistically drive plant litter decomposition in the environment. While secretome studies of model organisms have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or directly compared temporal patterns of enzyme utilization among diverse species. Thus, the mechanisms of carbon (C) degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of iTRAQ proteomics and custom bioinformatic analyses to compare the protein composition of the secretomes of four manganese(II)-oxidizing Ascomycete fungi over a three-week time course. We demonstrate that although the fungi produce a similar suite of extracellular enzymes, they exhibit striking differences in the regulation of these enzymes among species and over time, revealing species-specific and temporal shifts in C utilization strategies as they degrade the same substrate. Specifically, our findings suggest that Paraconiothyrium sporulosum AP3s5-JAC2a and Alternaria alternata SRC1lrK2f employ sequential enzyme secretion patterns concomitant with decreasing resource availability, Stagonospora sp. SRC1lsM3a preferentially degrades proteinaceous substrate before switching to carbohydrates, and Pyrenochaeta sp. DS3sAY3a utilizes primarily peptidases to aggressively attack carbon sources in a concentrated burst. This work highlights the diversity of operative metabolic strategies among cellulose-degrading Ascomycetes and enhances our understanding of their role in C turnover in the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Using simple PID-inspired controllers for online resilient resource management of distributed scientific workflows

Scientific workflows have become mainstream for conducting large-scale scientific research. As a result, many workflow applications and Workflow Management Systems (WMSs) have been developed as part of the cyberinfrastructure to allow scientists to execute their applications seamlessly on a range of distributed platforms. Although the scientific community has addressed this challenge from both theoretical and practical approaches, failure prediction, detection, and recovery still raise many research questions. In this paper, we propose an approach inspired by the control theory developed as part of autonomic computing to predict failures before they happen, and mitigated them when possible. The proposed approach is inspired on the proportional–integral–derivative controller (PID controller) control loop mechanism, which is widely used in industrial control systems, where the controller will react to adjust its output to mitigate faults. PID controllers aim to detect the possibility of a non-steady state far enough in advance so that an action can be performed to prevent it from happening. To demonstrate the feasibility of the approach, we tackle two common execution faults of large scale data-intensive workflows—data storage overload and memory overflow. We developed a simulator, which implements and evaluates simple standalone PID-inspired controllers to autonomously manage data and memory usage of a data-intensive bioinformatics workflow that consumes/produces over 4.4 TB of data, and requires over 24 TB of memory to run all tasks concurrently. Experimental results obtained via simulation indicate that workflow executions may significantly benefit from the controller-inspired approach, in particular under online and unknown conditions. Simulation results show that nearly-optimal executions (slowdown of 1.01) can be attained when utilizing our proposed method, and faults are detected and mitigated far in advance of their occurrence.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

miR-15a/16 Enhances Radiation Sensitivity of Non-Small Cell Lung Cancer Cells by Targeting the TLR1/NF-κB Signaling Pathway

Purpose: Many miRNAs have been identified as essential issues and core determining factors in tumor radiation. Recent reports have demonstrated that miRNAs and Toll-like receptors could exert reciprocal effects to control cancer development in various ways. However, a novel role of miR-15a/16 in enhancing radiation sensitivity by directly targeting TLR1 has not been reported, to our knowledge. Methods and Materials: Bioinformatic analyses, luciferase reporter assay, biochemical assays, and subcutaneous tumor establishment were used to characterize the signaling pathways of miRNA-15a/16 in response to radiation treatment. Results: First, an inverse correlation between the expression of miR-15a/16 and TLR1 protein was revealed in non-small cell lung cancer (NSCLC) and normal lung tissues. Next, we corroborated that miR-15a/16 specifically bound to TLR1 3′UTR and inhibited the expression of TLR1 in H358 and A549 cells. Furthermore, miR-15a/16 downregulated the activity of the NF-κB signaling pathway through TLR1. In addition, overexpression of miR-15a/16 inhibited survival capability and increased radiation-induced apoptosis, resulting in enhancement of radiosensitivity in H358 and A549 cells. Finally, subcutaneous tumor bearing NSCLC cells in a nude mice model was established, and the results showed that combined groups (miR-15a/16 + radiation) inhibited tumor growth more significantly than did radiation alone. Conclusions: We mainly elucidate that miRNA-15a/16 can enhance radiation sensitivity by regulating the TLR1/NF-κB signaling pathway and act as a potential therapeutic approach to overcome radioresistance for lung cancer treatment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

MiR-20a Induces Cell Radioresistance by Activating the PTEN/PI3K/Akt Signaling Pathway in Hepatocellular Carcinoma

Purpose: To investigate the role of miR-20a in hepatocellular carcinoma (HCC) cell radioresistance, which may reveal potential strategies to improve treatment. Methods and Materials: The expression of miR-20a and PTEN were detected in HCC cell lines and paired primary tissues by quantitative real-time polymerase chain reaction. Cell radiation combined with colony formation assays was administrated to discover the effect of miR-20a on radiosensitivity. Bioinformatics prediction and luciferase assay were used to identify the target of miR-20a. The phosphatidylinositol 3-kinase inhibitor LY294002 was used to inhibit phosphorylation of Akt, to verify whether miR-20a affects HCC cell radioresistance through activating the PTEN/PI3K/Akt pathway. Results: MiR-20a levels were increased in HCC cell lines and tissues, whereas PTEN was inversely correlated with it. Overexpression of miR-20a in Bel-7402 and SMMC-7721 cells enhances their resistance to the effect of ionizing radiation, and the inhibition of miR-20a in HCCLM3 and QGY-7701 cells sensitizes them to it. PTEN was identified as a direct functional target of miR-20a for the induction of radioresistance. Overexpression of miR-20a activated the PTEN/PI3K/Akt signaling pathway. Additionally, the kinase inhibitor LY294002 could reverse the effect of miR-20a–induced radioresistance. Conclusion: MiR-20a induces HCC cell radioresistance by activating the PTEN/PI3K/Akt pathway, which suggests that miR-20a/PTEN/PI3K/Akt might represent a target of investigation for developing effective therapeutic strategies against HCC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Proteomic Profiling of Radiation-Induced Skin Fibrosis in Rats: Targeting the Ubiquitin-Proteasome System

Purpose: To investigate the molecular changes underlying the pathogenesis of radiation-induced skin fibrosis. Methods and Materials: Rat skin was irradiated to 30 or 45 Gy with an electron beam. Protein expression in fibrotic rat skin and adjacent normal tissues was quantified by label-free protein quantitation. Human skin cells HaCaT and WS-1 were treated by x-ray irradiation, and the proteasome activity was determined with a fluorescent probe. The effect of proteasome inhibitors on Transforming growth factor Beta (TGF-B) signaling was measured by Western blot and immunofluorescence. The efficacy of bortezomib in wound healing of rat skin was assessed by the skin injury scale. Results: We found that irradiation induced epidermal and dermal hyperplasia in rat and human skin. One hundred ninety-six preferentially expressed and 80 unique proteins in the irradiated fibrotic skin were identified. Through bioinformatic analysis, the ubiquitin-proteasome pathway showed a significant fold change and was investigated in greater detail. In vitro experiments demonstrated that irradiation resulted in a decline in the activity of the proteasome in human skin cells. The proteasome inhibitor bortezomib suppressed profibrotic TGF-β downstream signaling but not TGF-β secretion stimulated by irradiation in HaCaT and WS-1 cells. Moreover, bortezomib ameliorated radiation-induced skin injury and attenuated epidermal hyperplasia. Conclusion: Our findings illustrate the molecular changes during radiation-induced skin fibrosis and suggest that targeting the ubiquitin-proteasome system would be an effective countermeasure.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Challenges and Promises of PET Radiomics

Radiomics describes the extraction of multiple, otherwise invisible, features from medical images that, with bioinformatic approaches, can be used to provide additional information that can predict underlying tumor biology and behavior.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Expression, purification, and characterization of diacylated Lipo-YcjN from Escherichia coli

YcjN is a putative substrate binding protein expressed from a cluster of genes involved in carbohydrate import and metabolism in Escherichia coli. Here, we determine the crystal structure of YcjN to a resolution of 1.95 Å, revealing that its three-dimensional structure is similar to substrate binding proteins in subcluster D-I, which includes the well-characterized maltose binding protein. Furthermore, we found that recombinant overexpression of YcjN results in the formation of a lipidated form of YcjN that is posttranslationally diacylated at cysteine 21. Comparisons of size-exclusion chromatography profiles and dynamic light scattering measurements of lipidated and nonlipidated YcjN proteins suggest that lipidated YcjN aggregates in solution via its lipid moiety. Additionally, bioinformatic analysis indicates that YcjN-like proteins may exist in both Bacteria and Archaea, potentially in both lipidated and nonlipidated forms. Together, our results provide a better understanding of the aggregation properties of recombinantly expressed bacterial lipoproteins in solution and establish a foundation for future studies that aim to elucidate the role of these proteins in bacterial physiology.

Escherichia coli↗
DOE OSTI2024

Functional diversification within the heme-binding split-barrel family

Due to neofunctionalization, a single fold can be identified in multiple proteins that have distinct molecular functions. Depending on the time that has passed since gene duplication and the number of mutations, the sequence similarity between functionally divergent proteins can be relatively high, eroding the value of sequence similarity as the sole tool for accurately annotating the function of uncharacterized homologs. Here, we combine bioinformatic approaches with targeted experimentation to reveal a large multifunctional family of putative enzymatic and nonenzymatic proteins involved in heme metabolism. This family (homolog of HugZ (HOZ)) is embedded in the “FMN-binding split barrel” superfamily and contains separate groups of proteins from prokaryotes, plants, and algae, which bind heme and either catalyze its degradation or function as nonenzymatic heme sensors. In prokaryotes these proteins are often involved in iron assimilation, whereas several plant and algal homologs are predicted to degrade heme in the plastid or regulate heme biosynthesis. In the plant Arabidopsis thaliana, which contains two HOZ subfamilies that can degrade heme in vitro (HOZ1 and HOZ2), disruption of AtHOZ1 (AT3G03890) or AtHOZ2A (AT1G51560) causes developmental delays, pointing to important biological roles in the plastid. In the tree Populus trichocarpa, a recent duplication event of a HOZ1 ancestor has resulted in localization of a paralog to the cytosol. Structural characterization of this cytosolic paralog and comparison to published homologous structures suggests conservation of heme-binding sites. This study unifies our understanding of the sequence-structure-function relationships within this multilineage family of heme-binding proteins and presents new molecular players in plant and bacterial heme metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Antibacterial ADP-ribosyl cyclase toxins inhibit bacterial growth by rapidly depleting NAD(P) +

In metazoans, enzymes belonging to the bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose (cADPr) hydrolase family regulate diverse cellular processes by synthesizing and hydrolyzing the intracellular second messenger cADPr, derived from the electron carrier NAD+. However, bacterial enzymes belonging to this family have not been characterized. Here, we identify a bacterial ADP-ribosyl cyclase that is associated with the type VII secretion system and functions as an antibacterial toxin. This enzyme, which we name Tac1, inhibits bacterial growth by rapidly hydrolyzing NAD+ and NADP+. We determine the X-ray crystal structure of Tac1 to a resolution of 1.4 Å, which reveals that this protein adopts the core catalytic fold of metazoan ADP-ribosyl cyclase enzymes such as CD38. Using a combination of biochemical and mutagenesis approaches, we identify catalytic residues within the active site of Tac1, which are responsible for the formation of a cADPr catalytic intermediate and subsequent hydrolysis of this intermediate into linear ADP-ribose. A bioinformatic analysis reveals that Tac1 is the founding member of a widespread family of bacterial ADP-ribosyl cyclase enzymes, many of which are associated with interbacterial conflict systems. We also identify enzymes in this family that are not associated with biological conflict systems and demonstrate that they produce cADPr as their major product rather than linear ADP-ribose, suggesting that these enzymes serve a biological function distinct from interbacterial antagonism. Together, these findings demonstrate that ADP-ribosyl cyclase/cADPr hydrolase enzymes function as toxins in diverse bacterial conflict systems and suggest that cADPr may play a previously overlooked role in bacterial physiology.

Colautti, Jake↗
DOE OSTI2014

Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function

Bacterial microconnpartnnents (BMCs) sequester enzymes from the cytoplasmic environment by encapsulation inside a selectively permeable protein shell. Bioinformatic analyses indicate that many bacteria encode BMC clusters of unknown function and with diverse combinations of shell proteins. The genome of the halophilic myxobacterium Haliangium ochraceum encodes one of the most atypical sets of shell proteins in terms of composition and primary structure. We found that microconnpartnnent shells could be purified in high yield when all seven H. ochraceum BMC shell genes were expressed from a synthetic operon in Escherichia coll. These shells differ substantially from previously isolated shell systems in that they are considerably smaller and more homogeneous, with measured diameters of 39 2 nm. The size and nearly uniform geometry allowed the development of a structural model for the shells composed of 260 hexagonal units and 13 hexagons per icosahedral face. We found that new proteins could be recruited to the shells by fusion to a predicted targeting peptide sequence, setting the stage for the use of these remarkably homogeneous shells for applications such as three-dimensional scaffolding and the construction of synthetic BMCs. Our results demonstrate the value of selecting from the diversity of BMC shell building blocks found in genomic sequence data for the construction of novel compartments. (C) 2014 Elsevier Ltd. All rights reserved.

Lassila, JK↗
DOE OSTI2019

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps

Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. Here, we used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a “key in a keyhole” pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.

59 BASIC BIOLOGICAL SCIENCES↗