Results for “Cellular” — Page 87

DOE OSTI2017

Efficacy of atmospheric pressure dielectric barrier discharge for inactivating airborne pathogens

Atmospheric pressure plasmas have gained attention in recent years for several environmental applications. This technology could potentially be used to deactivate airborne microorganisms, surface-bound microorganisms, and biofilms. Here, the authors explore the efficacy of the atmospheric pressure dielectric barrier discharge (DBD) to inactivate airborne Staphylococcus epidermidis and Aspergillus niger that are opportunistic pathogens associated with nosocomial infections. This technology uses air as the source of gas and does not require any process gas such as helium, argon, nitrogen, or hydrogen. Moreover, the effect of DBD was studied on aerosolized S. epidermidis and aerosolized A. niger spores via scanning electron microscopy (SEM). The morphology observed on the SEM micrographs showed deformations in the cellular structure of both microorganisms. Cell structure damage upon interaction with the DBD suggests leakage of vital cellular materials, which is a key mechanism for microbial inactivation. The chemical structure of the cell surface of S. epidermidis was also analyzed by near edge x-ray absorption fine structure spectroscopy before and after DBD exposure. Our results from surface analysis revealed that reactive oxygen species from the DBD discharge contributed to alterations on the chemistry of the cell membrane/cell wall of S. epidermidis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Targeting mitochondria in cancer cells using gold nanoparticle-enhanced radiotherapy: A Monte Carlo study

Purpose: Radiation damage to mitochondria has been shown to alter cellular processes and even lead to apoptosis. Gold nanoparticles (AuNPs) may be used to enhance these effects in scenarios where they collect on the outer membranes of mitochondria. A Monte Carlo (MC) approach is used to estimate mitochondrial dose enhancement under a variety of conditions. Methods: The PENELOPE MC code was used to generate dose distributions resulting from photons striking a 13 nm diameter AuNP with various thicknesses of water-equivalent coatings. Similar dose distributions were generated with the AuNP replaced by water so as to estimate the gain in dose on a microscopic scale due to the presence of AuNPs within an irradiated volume. Models of mitochondria with AuNPs affixed to their outer membrane were then generated—considering variation in mitochondrial size and shape, number of affixed AuNPs, and AuNP coating thickness—and exposed (in a dose calculation sense) to source spectra ranging from 6 MV to 90 kVp. Subsequently dose enhancement ratios (DERs), or the dose with the AuNPs present to that for no AuNPs, for the entire mitochondrion and its components were tallied under these scenarios. Results: For a representative case of a 1000 nm diameter mitochondrion affixed with 565 AuNPs, each with a 13 nm thick coating, the mean DER over the whole organelle ranged from roughly 1.1 to 1.6 for the kilovoltage sources, but was generally less than 1.01 for the megavoltage sources. The outer membrane DERs remained less than 1.01 for the megavoltage sources, but rose to 2.3 for 90 kVp. The voxel maximum DER values were as high as 8.2 for the 90 kVp source and increased further when the particles clustered together. The DER exhibited dependence on the mitochondrion dimensions, number of AuNPs, and the AuNP coating thickness. Conclusions: Substantial dose enhancement directly to the mitochondria can be achieved under the conditions modeled. If the mitochondrion dose can be directly enhanced, as these simulations show, this work suggests the potential for both a tool to study the role of mitochondria in cellular response to radiation and a novel avenue for radiation therapy in that the mitochondria may be targeted, rather than the nuclear DNA.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Quantitative single-particle digital autoradiography with α-particle emitters for targeted radionuclide therapy using the iQID camera

Purpose: Alpha-emitting radionuclides exhibit a potential advantage for cancer treatments because they release large amounts of ionizing energy over a few cell diameters (50–80 μm), causing localized, irreparable double-strand DNA breaks that lead to cell death. Radioimmunotherapy (RIT) approaches using monoclonal antibodies labeled with α emitters may thus inactivate targeted cells with minimal radiation damage to surrounding tissues. Tools are needed to visualize and quantify the radioactivity distribution and absorbed doses to targeted and nontargeted cells for accurate dosimetry of all treatment regimens utilizing α particles, including RIT and others (e.g., Ra-223), especially for organs and tumors with heterogeneous radionuclide distributions. The aim of this study was to evaluate and characterize a novel single-particle digital autoradiography imager, the ionizing-radiation quantum imaging detector (iQID) camera, for use in α-RIT experiments. Methods: The iQID camera is a scintillator-based radiation detection system that images and identifies charged-particle and gamma-ray/x-ray emissions spatially and temporally on an event-by-event basis. It employs CCD-CMOS cameras and high-performance computing hardware for real-time imaging and activity quantification of tissue sections, approaching cellular resolutions. In this work, the authors evaluated its characteristics for α-particle imaging, including measurements of intrinsic detector spatial resolutions and background count rates at various detector configurations and quantification of activity distributions. The technique was assessed for quantitative imaging of astatine-211 ({sup 211}At) activity distributions in cryosections of murine and canine tissue samples. Results: The highest spatial resolution was measured at ∼20 μm full width at half maximum and the α-particle background was measured at a rate as low as (2.6 ± 0.5) × 10{sup −4} cpm/cm{sup 2} (40 mm diameter detector area). Simultaneous imaging of multiple tissue sections was performed using a large-area iQID configuration (ø 11.5 cm). Estimation of the {sup 211}At activity distribution was demonstrated at mBq/μg-levels. Conclusions: Single-particle digital autoradiography of α emitters has advantages over traditional film-based autoradiographic techniques that use phosphor screens, in terms of spatial resolution, sensitivity, and activity quantification capability. The system features and characterization results presented in this study show that the iQID is a promising technology for microdosimetry, because it provides necessary information for interpreting alpha-RIT outcomes and for predicting the therapeutic efficacy of cell-targeted approaches using α emitters.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2015

TU-CD-303-02: Beyond Radiation Induced Double Strand Breaks - a New Horizon for Radiation Therapy Research

Recent advances in cancer research have shed new light on the complex processes of how therapeutic radiation initiates changes at cellular, tissue, and system levels that may lead to clinical effects. These new advances may transform the way we use radiation to combat certain types of cancers. For the past two decades many technological advancements in radiation therapy have been largely based on the hypothesis that direct radiation-induced DNA double strand breaks cause cell death and thus tumor control and normal tissue damage. However, new insights have elucidated that in addition to causing cellular DNA damage, localized therapeutic radiation also initiates cascades of complex downstream biological responses in tissue that extend far beyond where therapeutic radiation dose is directly deposited. For instance, studies show that irradiated dying tumor cells release tumor antigens that can lead the immune system to a systemic anti-cancer attack throughout the body of cancer patient; targeted irradiation to solid tumor also increases the migration of tumor cells already in bloodstream, the seeds of potential metastasis. Some of the new insights may explain the long ago discovered but still unexplained non-localized radiation effects (bystander effect and abscopal effect) and the efficacy of spatially fractionated radiation therapy (microbeam radiation therapy and GRID therapy) where many “hot” and “cold” spots are intentionally created throughout the treatment volume. Better understanding of the mechanisms behind the non-localized radiation effects creates tremendous opportunities to develop new and integrated cancer treatment strategies that are based on radiotherapy, immunology, and chemotherapy. However, in the multidisciplinary effort to advance new radiobiology, there are also tremendous challenges including a lack of multidisciplinary researchers and imaging technologies for the microscopic radiation-induced responses. A better grasp of the essence of these advances in cancer biology research will give medical physicists a new perspective in daily clinical physics practice and in future radiation therapy technological development. Furthermore, academic medical physics should continue to be an integral part of the multidisciplinary cancer research community, harnessing our newly acquired understanding of radiation effects, and developing novel cost-effective treatment strategies to better combat cancer. Learning Objectives: Understand that localized radiation can lead to non-localized secondary effects such as radiation-induced immune response, bystander effect, and abscopal effect. Understand that the non-localized radiation effects may be harnessed to improve cancer treatment. Learn examples of physics participation in multidisciplinary research to advance cancer biology. Recognize the challenges and possibilities of physics applications in cancer research. Chang: NIH 5RC2CA148487-02 and 1U54CA151652-01 Graves: IDEA award (19IB-0106) from the California Breast Cancer Research Program (CBCRP), and by NIH P01 CA67166.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

TU-CD-303-03: Localized Radiation Can Induce Systemic Anti-Cancer Immune and Non-Immune Responses and How We Might Utilize It

Recent advances in cancer research have shed new light on the complex processes of how therapeutic radiation initiates changes at cellular, tissue, and system levels that may lead to clinical effects. These new advances may transform the way we use radiation to combat certain types of cancers. For the past two decades many technological advancements in radiation therapy have been largely based on the hypothesis that direct radiation-induced DNA double strand breaks cause cell death and thus tumor control and normal tissue damage. However, new insights have elucidated that in addition to causing cellular DNA damage, localized therapeutic radiation also initiates cascades of complex downstream biological responses in tissue that extend far beyond where therapeutic radiation dose is directly deposited. For instance, studies show that irradiated dying tumor cells release tumor antigens that can lead the immune system to a systemic anti-cancer attack throughout the body of cancer patient; targeted irradiation to solid tumor also increases the migration of tumor cells already in bloodstream, the seeds of potential metastasis. Some of the new insights may explain the long ago discovered but still unexplained non-localized radiation effects (bystander effect and abscopal effect) and the efficacy of spatially fractionated radiation therapy (microbeam radiation therapy and GRID therapy) where many “hot” and “cold” spots are intentionally created throughout the treatment volume. Better understanding of the mechanisms behind the non-localized radiation effects creates tremendous opportunities to develop new and integrated cancer treatment strategies that are based on radiotherapy, immunology, and chemotherapy. However, in the multidisciplinary effort to advance new radiobiology, there are also tremendous challenges including a lack of multidisciplinary researchers and imaging technologies for the microscopic radiation-induced responses. A better grasp of the essence of these advances in cancer biology research will give medical physicists a new perspective in daily clinical physics practice and in future radiation therapy technological development. Furthermore, academic medical physics should continue to be an integral part of the multidisciplinary cancer research community, harnessing our newly acquired understanding of radiation effects, and developing novel cost-effective treatment strategies to better combat cancer. Learning Objectives: Understand that localized radiation can lead to non-localized secondary effects such as radiation-induced immune response, bystander effect, and abscopal effect. Understand that the non-localized radiation effects may be harnessed to improve cancer treatment. Learn examples of physics participation in multidisciplinary research to advance cancer biology. Recognize the challenges and possibilities of physics applications in cancer research. Chang: NIH 5RC2CA148487-02 and 1U54CA151652-01 Graves: IDEA award (19IB-0106) from the California Breast Cancer Research Program (CBCRP), and by NIH P01 CA67166.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

TU-CD-303-04: Radiation-Induced Long Distance Tumor Cell Migration Into and Out of the Radiation Field and Its Clinical Implication

Recent advances in cancer research have shed new light on the complex processes of how therapeutic radiation initiates changes at cellular, tissue, and system levels that may lead to clinical effects. These new advances may transform the way we use radiation to combat certain types of cancers. For the past two decades many technological advancements in radiation therapy have been largely based on the hypothesis that direct radiation-induced DNA double strand breaks cause cell death and thus tumor control and normal tissue damage. However, new insights have elucidated that in addition to causing cellular DNA damage, localized therapeutic radiation also initiates cascades of complex downstream biological responses in tissue that extend far beyond where therapeutic radiation dose is directly deposited. For instance, studies show that irradiated dying tumor cells release tumor antigens that can lead the immune system to a systemic anti-cancer attack throughout the body of cancer patient; targeted irradiation to solid tumor also increases the migration of tumor cells already in bloodstream, the seeds of potential metastasis. Some of the new insights may explain the long ago discovered but still unexplained non-localized radiation effects (bystander effect and abscopal effect) and the efficacy of spatially fractionated radiation therapy (microbeam radiation therapy and GRID therapy) where many “hot” and “cold” spots are intentionally created throughout the treatment volume. Better understanding of the mechanisms behind the non-localized radiation effects creates tremendous opportunities to develop new and integrated cancer treatment strategies that are based on radiotherapy, immunology, and chemotherapy. However, in the multidisciplinary effort to advance new radiobiology, there are also tremendous challenges including a lack of multidisciplinary researchers and imaging technologies for the microscopic radiation-induced responses. A better grasp of the essence of these advances in cancer biology research will give medical physicists a new perspective in daily clinical physics practice and in future radiation therapy technological development. Furthermore, academic medical physics should continue to be an integral part of the multidisciplinary cancer research community, harnessing our newly acquired understanding of radiation effects, and developing novel cost-effective treatment strategies to better combat cancer. Learning Objectives: Understand that localized radiation can lead to non-localized secondary effects such as radiation-induced immune response, bystander effect, and abscopal effect. Understand that the non-localized radiation effects may be harnessed to improve cancer treatment. Learn examples of physics participation in multidisciplinary research to advance cancer biology. Recognize the challenges and possibilities of physics applications in cancer research. Chang: NIH 5RC2CA148487-02 and 1U54CA151652-01 Graves: IDEA award (19IB-0106) from the California Breast Cancer Research Program (CBCRP), and by NIH P01 CA67166.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

TU-CD-303-05: Unveiling Tumor Heterogeneity by Molecular Imaging

Recent advances in cancer research have shed new light on the complex processes of how therapeutic radiation initiates changes at cellular, tissue, and system levels that may lead to clinical effects. These new advances may transform the way we use radiation to combat certain types of cancers. For the past two decades many technological advancements in radiation therapy have been largely based on the hypothesis that direct radiation-induced DNA double strand breaks cause cell death and thus tumor control and normal tissue damage. However, new insights have elucidated that in addition to causing cellular DNA damage, localized therapeutic radiation also initiates cascades of complex downstream biological responses in tissue that extend far beyond where therapeutic radiation dose is directly deposited. For instance, studies show that irradiated dying tumor cells release tumor antigens that can lead the immune system to a systemic anti-cancer attack throughout the body of cancer patient; targeted irradiation to solid tumor also increases the migration of tumor cells already in bloodstream, the seeds of potential metastasis. Some of the new insights may explain the long ago discovered but still unexplained non-localized radiation effects (bystander effect and abscopal effect) and the efficacy of spatially fractionated radiation therapy (microbeam radiation therapy and GRID therapy) where many “hot” and “cold” spots are intentionally created throughout the treatment volume. Better understanding of the mechanisms behind the non-localized radiation effects creates tremendous opportunities to develop new and integrated cancer treatment strategies that are based on radiotherapy, immunology, and chemotherapy. However, in the multidisciplinary effort to advance new radiobiology, there are also tremendous challenges including a lack of multidisciplinary researchers and imaging technologies for the microscopic radiation-induced responses. A better grasp of the essence of these advances in cancer biology research will give medical physicists a new perspective in daily clinical physics practice and in future radiation therapy technological development. Furthermore, academic medical physics should continue to be an integral part of the multidisciplinary cancer research community, harnessing our newly acquired understanding of radiation effects, and developing novel cost-effective treatment strategies to better combat cancer. Learning Objectives: Understand that localized radiation can lead to non-localized secondary effects such as radiation-induced immune response, bystander effect, and abscopal effect. Understand that the non-localized radiation effects may be harnessed to improve cancer treatment. Learn examples of physics participation in multidisciplinary research to advance cancer biology. Recognize the challenges and possibilities of physics applications in cancer research. Chang: NIH 5RC2CA148487-02 and 1U54CA151652-01 Graves: IDEA award (19IB-0106) from the California Breast Cancer Research Program (CBCRP), and by NIH P01 CA67166.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-G-TeP3-10: Radiation Induces Prompt Live-Cell Metabolic Fluxes

Purpose: To compare metabolic dynamics and HIF-1α expression following radiation between a cancerous cell line (UM-SCC-22B) and a normal, immortalized cell line, NOK (Normal Oral Keratinocyte). HIF-1 is a key factor in metabolism and radiosensitivity. A better understanding of how radiation affects the interplay of metabolism and HIF-1 might give a better understanding of the mechanisms responsible for radiosensitivity. Methods: Changes in cellular metabolism in response to radiation are tracked by fluorescence lifetime of NADH. Expression of HIF-1α was measured by immunofluorescence for both cell lines with and without irradiation. Radiation response is also monitored with additional treatment of a HIF-1α inhibitor (chrysin) as well as a radical scavenger (glutathione). Changes in oxygen consumption and respiratory capacity are also monitored using the Seahorse XF analyzer. Results: An increase in HIF-1α was found to be in response to radiation for the cancer cell line, but not the normal cell line. Radiation was found to shift metabolism toward glycolytic pathways in cancer cells as measured by oxygen consumption and respiratory capacity. Radiation response was found to be muted by addition of glutathione to cell media. HIF-1α inhibition similarly muted radiation response in cancer. Conclusion: The HIF-1 protein complex is a key regulator cellular metabolism through the regulation of glycolysis and glucose transport enzymes. Moreover, HIF-1 has shown radio-protective effects in tumor vascular endothelia, and has been implicated in metastatic aggression. Monitoring interplay between metabolism and the HIF-1 protein complex can give a more fundamental understanding of radiotherapy response.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

MO-FG-209-02: Development of a Virtual Breast Phantom From a Multi-Modality Perspective

This symposium will review recent advances in the simulation methods for evaluation of novel breast imaging systems – the subject of AAPM Task Group TG234. Our focus will be on the various approaches to development and validation of software anthropomorphic phantoms and their use in the statistical assessment of novel imaging systems using such phantoms along with computational models for the x-ray image formation process. Due to the dynamic development and complex design of modern medical imaging systems, the simulation of anatomical structures, image acquisition modalities, and the image perception and analysis offers substantial benefits of reduced cost, duration, and radiation exposure, as well as the known ground-truth and wide variability in simulated anatomies. For these reasons, Virtual Clinical Trials (VCTs) have been increasingly accepted as a viable tool for preclinical assessment of x-ray and other breast imaging methods. Activities of TG234 have encompassed the optimization of protocols for simulation studies, including phantom specifications, the simulated data representation, models of the imaging process, and statistical assessment of simulated images. The symposium will discuss the state-of-the-science of VCTs for novel breast imaging systems, emphasizing recent developments and future directions. Presentations will discuss virtual phantoms for intermodality breast imaging performance comparisons, extension of the breast anatomy simulation to the cellular level, optimized integration of the simulated imaging chain, and the novel directions in the observer models design. Learning Objectives: Review novel results in developing and applying virtual phantoms for inter-modality breast imaging performance comparisons; Discuss the efforts to extend the computer simulation of breast anatomy and pathology to the cellular level; Summarize the state of the science in optimized integration of modules in the simulated imaging chain; Compare novel directions in the design of observer models for task based validation of imaging systems. PB: Research funding support from the NIH, NSF, and Komen for the Cure; NIH funded collaboration with Barco, Inc. and Hologic, Inc.; Consultant to Delaware State Univ. and NCCPM, UK. AA: Employed at Barco Healthcare.; P. Bakic, NIH: (NIGMS P20 #GM103446, NCI R01 #CA154444); M. Das, NIH Research grants.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

MO-FG-209-05: Towards a Feature-Based Anthropomorphic Model Observer

This symposium will review recent advances in the simulation methods for evaluation of novel breast imaging systems – the subject of AAPM Task Group TG234. Our focus will be on the various approaches to development and validation of software anthropomorphic phantoms and their use in the statistical assessment of novel imaging systems using such phantoms along with computational models for the x-ray image formation process. Due to the dynamic development and complex design of modern medical imaging systems, the simulation of anatomical structures, image acquisition modalities, and the image perception and analysis offers substantial benefits of reduced cost, duration, and radiation exposure, as well as the known ground-truth and wide variability in simulated anatomies. For these reasons, Virtual Clinical Trials (VCTs) have been increasingly accepted as a viable tool for preclinical assessment of x-ray and other breast imaging methods. Activities of TG234 have encompassed the optimization of protocols for simulation studies, including phantom specifications, the simulated data representation, models of the imaging process, and statistical assessment of simulated images. The symposium will discuss the state-of-the-science of VCTs for novel breast imaging systems, emphasizing recent developments and future directions. Presentations will discuss virtual phantoms for intermodality breast imaging performance comparisons, extension of the breast anatomy simulation to the cellular level, optimized integration of the simulated imaging chain, and the novel directions in the observer models design. Learning Objectives: Review novel results in developing and applying virtual phantoms for inter-modality breast imaging performance comparisons; Discuss the efforts to extend the computer simulation of breast anatomy and pathology to the cellular level; Summarize the state of the science in optimized integration of modules in the simulated imaging chain; Compare novel directions in the design of observer models for task based validation of imaging systems. PB: Research funding support from the NIH, NSF, and Komen for the Cure; NIH funded collaboration with Barco, Inc. and Hologic, Inc.; Consultant to Delaware State Univ. and NCCPM, UK. AA: Employed at Barco Healthcare.; P. Bakic, NIH: (NIGMS P20 #GM103446, NCI R01 #CA154444); M. Das, NIH Research grants.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-FG-BRA-11: Theranostic Platinum Nanoparticle for Radiation Sensitization in Breast Cancer Radiotherapy

Purpose: We have developed a novel receptor-targeted theranostic platinum nanoparticle (HER-PtNP) for enhanced radiation sensitization in HER2-positive breast cancer radiation treatment. This study aims to evaluate receptor-targeting specificity, and radiation sensitization of the nanoparticle. Methods: The platinum nanoparticle (PtNP) was synthesized with the diameter of 2nm, and capped with cysteine. The nanoparticle was tagged with a fluorescent dye (cy5) for the fluoresence detection, and conjuated with HER2/3 targeted protein (HerPBK10) for HER2-targeting specificity. We evaluated the theranostic features using in vitro breast cancer cell models: HER2-positive BT-474, and HER2-negative MDA-MB-231. The HER2-targeting specificity was evaluated using immunofluorescence and confocal microscopy. For each cell line, three sets of samples, including non-stained control, fluorescence stained PtNP-cy5 treated, and HER-PtNP treated, were imaged by confocal microscopy. Two breast cancer cell lineages were incubated with PtNP and HER-PtNP at 10 µg/mL, and then irradiated with X-rays for 2 Gy dose at 50 kVp. A colonogenic assay was used to determine cellular survival fractions by immediately reseeding 300 cells after irradiation in growth media and allowing colonies to grow for 2 weeks. Results: The results of confocal images show that no apparent nanoparticle cellular uptake was observed in the HER2-(MDA-MB-231) cells with 1% for PtNP-cy5 and 0.5% for HER-PtNP. Similarly no apparent PtNP-cy5 uptake (<1%) for BT474 cells was observed. However, there was significant HER-PtNP uptake (73%) for the HER2+(BT474) cells. The clonogenic assay showed that BT474 cells treated with HER-PtNP had significantly lower survival compared to those treated with PtNP (32% vs 81%, p=0.01). However, no significant radiosensitivity enhancement was observed for MDA-MB-231 cell treated with PtNP and HER-PtNP (89% vs 92%, p=0.78). Conclusion: Our studies suggest that the HER2-targeted platinum nanoparticle has excellent receptor targeting specificity and enhanced radiation sensitization compared to nanoparticle alone, suggesting potential for clinical applications in breast cancer radiotherapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

HU multimerization shift controls nucleoid compaction

Molecular mechanisms controlling functional bacterial chromosome (nucleoid) compaction and organization are surprisingly enigmatic but partly depend on conserved, histone-like proteins HUαα and HUαβ and their interactions that span the nanoscale and mesoscale from protein-DNA complexes to the bacterial chromosome and nucleoid structure. We determined the crystal structures of these chromosome-associated proteins in complex with native duplex DNA. Distinct DNA binding modes of HUαα and HUαβ elucidate fundamental features of bacterial chromosome packing that regulate gene transcription. By combining crystal structures with solution x-ray scattering results, we determined architectures of HU-DNA nucleoproteins in solution under near-physiological conditions. These macromolecular conformations and interactions result in contraction at the cellular level based on in vivo imaging of native unlabeled nucleoid by soft x-ray tomography upon HUβ and ectopic HUα38 expression. Structural characterization of charge-altered HUαα-DNA complexes reveals an HU molecular switch that is suitable for condensing nucleoid and reprogramming noninvasive Escherichia coli into an invasive form. Collective findings suggest that shifts between networking and cooperative and noncooperative DNA-dependent HU multimerization control DNA compaction and supercoiling independently of cellular topoisomerase activity. By integrating x-ray crystal structures, x-ray scattering, mutational tests, and x-ray imaging that span from protein-DNA complexes to the bacterial chromosome and nucleoid structure, we show that defined dynamic HU interaction networks can promote nucleoid reorganization and transcriptional regulation as efficient general microbial mechanisms to help synchronize genetic responses to cell cycle, changing environments, and pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBβ

Heme is the endogenous ligand for the constitutively repressive REV-ERB nuclear receptors, REV-ERBα (NR1D1) and REV-ERBβ (NR1D2), but how heme regulates REV-ERB activity remains unclear. Cellular studies indicate that heme is required for the REV-ERBs to bind the corepressor NCoR and repress transcription. However, fluorescence-based biochemical assays suggest that heme displaces NCoR; here, we show that this is due to a heme-dependent artifact. Using ITC and NMR spectroscopy, we show that heme binding remodels the thermodynamic interaction profile of NCoR receptor interaction domain (RID) binding to REV-ERBβ ligand-binding domain (LBD). We solved two crystal structures of REV-ERBβ LBD cobound to heme and NCoR peptides, revealing the heme-dependent NCoR binding mode. ITC and chemical cross-linking mass spectrometry reveals a 2:1 LBD:RID stoichiometry, consistent with cellular studies showing that NCoR-dependent repression of REV-ERB transcription occurs on dimeric DNA response elements. Our findings should facilitate renewed progress toward understanding heme-dependent REV-ERB activity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Stiffness anisotropy coordinates supracellular contractility driving long-range myotube-ECM alignment

The ability of cells to organize into tissues with proper structure and function requires the effective coordination of proliferation, migration, polarization, and differentiation across length scales. Skeletal muscle is innately anisotropic; however, few biomaterials can emulate mechanical anisotropy to determine its influence on tissue patterning without introducing confounding topography. Here, we demonstrate that substrate stiffness anisotropy coordinates contractility-driven collective cellular dynamics resulting in C2C12 myotube alignment over millimeter-scale distances. When cultured on mechanically anisotropic liquid crystalline polymer networks (LCNs) lacking topography, C2C12 myoblasts collectively polarize in the stiffest direction. Cellular coordination is amplified through reciprocal cell-ECM dynamics that emerge during fusion, driving global myotube-ECM ordering. Conversely, myotube alignment was restricted to small local domains with no directional preference on mechanically isotropic LCNs of the same chemical formulation. These findings provide valuable insights for designing biomaterials that mimic anisotropic microenvironments and underscore the importance of stiffness anisotropy in orchestrating tissue morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Composition and in situ structure of the Methanospirillum hungatei cell envelope and surface layer

Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo–electron tomography, we visualized the S-layer lattice surroundingMethanospirillum hungatei, a methanogenic archaeon. Though more compact than known structures,M. hungatei’s S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer’s cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment.M. hungateicell’s end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.

Science & Technology - Other Topics↗

DOE OSTI2020

Ancient origins of allosteric activation in a Ser-Thr kinase

A myriad of cellular events are regulated by allostery; therefore, evolution of this process is of fundamental interest. Here, we use ancestral sequence reconstruction to resurrect ancestors of two colocalizing proteins, Aurora A kinase and its allosteric activator TPX2 (targeting protein for Xklp2), to experimentally characterize the evolutionary path of allosteric activation. Autophosphorylation of the activation loop is the most ancient activation mechanism; it is fully developed in the oldest kinase ancestor and has remained stable over 1 billion years of evolution. As the microtubule-associated protein TPX2 appeared, efficient kinase binding to TPX2 evolved, likely owing to increased fitness by virtue of colocalization. Subsequently, TPX2-mediated allosteric kinase regulation gradually evolved. Surprisingly, evolution of this regulation is encoded in the kinase and did not arise by a dominating mechanism of coevolution.

Science & Technology - Other Topics↗

DOE OSTI2020

The histone H3-H4 tetramer is a copper reductase enzyme

Eukaryotic histone H3-H4 tetramers contain a putative copper (Cu 2+ ) binding site at the H3-H3′ dimerization interface with unknown function. The coincident emergence of eukaryotes with global oxygenation, which challenged cellular copper utilization, raised the possibility that histones may function in cellular copper homeostasis. We report that the recombinant Xenopus laevis H3-H4 tetramer is an oxidoreductase enzyme that binds Cu 2+ and catalyzes its reduction to Cu 1+ in vitro. Loss- and gain-of-function mutations of the putative active site residues correspondingly altered copper binding and the enzymatic activity, as well as intracellular Cu 1+ abundance and copper-dependent mitochondrial respiration and Sod1 function in the yeast Saccharomyces cerevisiae . The histone H3-H4 tetramer, therefore, has a role other than chromatin compaction or epigenetic regulation and generates biousable Cu 1+ ions in eukaryotes.

Attar, Narsis↗

DOE OSTI2021

Structural analysis of the PTEN:P-Rex2 signaling complex reveals how cancer-associated mutations coordinate to hyperactivate Rac1

The dual-specificity phosphatase PTEN functions as a tumor suppressor by hydrolyzing PI(3,4,5)P 3 to PI(4,5)P 2 to inhibit PI3K-AKT signaling and cellular proliferation. P-Rex2 is a guanine nucleotide exchange factor for Rho GTPases and can be activated by Gβγ subunits downstream of G protein–coupled receptor signaling and by PI(3,4,5)P 3 downstream of receptor tyrosine kinases. The PTEN:P-Rex2 complex is a commonly mutated signaling node in metastatic cancer. Assembly of the PTEN:P-Rex2 complex inhibits the activity of both proteins, and its dysregulation can drive PI3K-AKT signaling and cellular proliferation. Here, using cross-linking mass spectrometry and functional studies, we gained mechanistic insights into PTEN:P-Rex2 complex assembly and coinhibition. We found that PTEN was anchored to P-Rex2 by interactions between the PDZ-interacting motif in the PTEN C-terminal tail and the second PDZ domain of P-Rex2. This interaction bridged PTEN across the P-Rex2 surface, preventing PI(3,4,5)P 3 hydrolysis. Conversely, PTEN both allosterically promoted an autoinhibited conformation of P-Rex2 and blocked its binding to Gβγ. In addition, we observed that the PTEN-deactivating mutations and P-Rex2 truncations combined to drive Rac1 activation to a greater extent than did either single variant alone. These insights enabled us to propose a class of gain-of-function, cancer-associated mutations within the PTEN:P-Rex2 interface that uncouple PTEN from the inhibition of Rac1 signaling.

D’Andrea, Laura↗