Search NASA⌕ Search

SEARCH · Search NASA

Results for “Animation”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,585 records · Page 88
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Conformal image-guided microbeam radiation therapy at the ESRF biomedical beamline ID17

Purpose: Upcoming veterinary trials in microbeam radiation therapy (MRT) demand for more advanced irradiation techniques than in preclinical research with small animals. The treatment of deep-seated tumors in cats and dogs with MRT requires sophisticated irradiation geometries from multiple ports, which impose further efforts to spare the normal tissue surrounding the target. Methods: This work presents the development and benchmarking of a precise patient alignment protocol for MRT at the biomedical beamline ID17 of the European Synchrotron Radiation Facility (ESRF). The positioning of the patient prior to irradiation is verified by taking x-ray projection images from different angles. Results: Using four external fiducial markers of 1.7 mm diameter and computed tomography-based treatment planning, a target alignment error of less than 2 mm can be achieved with an angular deviation of less than 2{sup ∘}. Minor improvements on the protocol and the use of smaller markers indicate that even a precision better than 1 mm is technically feasible. Detailed investigations concerning the imaging dose lead to the conclusion that doses for skull radiographs lie in the same range as dose reference levels for human head radiographs. A currently used online dose monitor for MRT has been proven to give reliable results for the imaging beam. Conclusions: The ESRF biomedical beamline ID17 is technically ready to apply conformal image-guided MRT from multiple ports to large animals during future veterinary trials.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-672: A Novel Kernel-Based Dose Engine for KeV Photon Beams

Purpose: Mimicking state-of-the-art patient radiotherapy with high precision irradiators for small animals allows advanced dose-effect studies and radiobiological investigations. One example is the implementation of pre-clinical IMRT-like irradiations, which requires the development of inverse planning for keV photon beams. As a first step, we present a novel kernel-based dose calculation engine for keV x-rays with explicit consideration of energy and material dependencies. Methods: We follow a superposition-convolution approach adapted to keV x-rays, based on previously published work on micro-beam therapy. In small animal radiotherapy, we assume local energy deposition at the photon interaction point, since the electron ranges in tissue are of the same order of magnitude as the voxel size. This allows us to use photon-only kernel sets generated by MC simulations, which are pre-calculated for six energy windows and ten base materials. We validate our stand-alone dose engine against Geant4 MC simulations for various beam configurations in water, slab phantoms with bone and lung inserts, and on a mouse CT with (0.275mm)3 voxels. Results: We observe good agreement for all cases. For field sizes of 1mm{sup 2} to 1cm{sup 2} in water, the depth dose curves agree within 1% (mean), with the largest deviations in the first voxel (4%) and at depths>5cm (<2.5%). The out-of-field doses at 1cm depth agree within 8% (mean) for all but the smallest field size. In slab geometries, the mean agreement was within 3%, with maximum deviations of 8% at water-bone interfaces. The γ-index (1mm/1%) passing rate for a single-field mouse irradiation is 71%. Conclusion: The presented dose engine yields an accurate representation of keV-photon doses suitable for inverse treatment planning for IMRT. It has the potential to become a significantly faster yet sufficiently accurate alternative to full MC simulations. Further investigations will focus on energy sampling as well as calculation times. Research at ICR is also supported by Cancer Research UK under Programme C33589/A19727 and NHS funding to the NIHR Biomedical Research Centre at RMH and ICR. MFF is supported by Cancer Research UK under Programme C33589/A19908.

43 PARTICLE ACCELERATORS↗
DOE OSTI2016

SU-G-TeP3-12: Retrospective Assessment of R2star Using Ultra-High Field MRI in a Rodent Model of Radiation Necrosis

Purpose: To establish a quantitative MRI method that would be capable of predicting radiation necrosis without using a contrast agent. Methods: Healthy male Fischer 344 rats were irradiated using an animal irradiator capable of delivering 2.3 Gy/min with a kVp of 225 V. A dose of 40 Gy was given to half the brain in a single session. Rats were scanned using a 9.4 T animal MRI before irradiation and every two weeks following radiation until either necrosis developed or they were sacrificed for health reasons. A multi-echo gradient-echo sequence was acquired at every time point and the apparent transverse relaxation rate R{sub 2}* was calculated based on the measured signal decay. At the last time point, an ROI mask with an R{sub 2}* value of greater than 45 s{sup −1} was applied in the area of the external and internal capsule where radiation necrosis was confirmed. A retrospective analysis was performed to determine whether R{sub 2}* values would be able to predict where radiation necrosis would occur. Results: Radiation necrosis was morphologically visible between weeks 22–24 following treatment. Gadolinium MRI and histology confirmed radiation necrosis in the area of MRI enhancement. Our data suggests that there is a trend towards significance in the lesion as early as 12 weeks prior to morphological changes on MRI with significance occurring 6 weeks prior (p≤0.05, p≤0.01 at week 24). Measurements of the R{sub 2}* in the hippocampus did not show any significant difference; however, there are areas of visible R{sub 2}* change within sub-hippocampal regions. Conclusion: R{sub 2}* is a promising method that could be able to predict an underlying disease process that occurs prior to radiation necrosis. The constant increase in R{sub 2}* values suggests a possible neuroinflammatory mechanism rather than an acute vascular event where R{sub 2}* would tend to decrease in the area.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-FG-BRB-02: The Impact of Using Dual-Energy CT for Determining Proton Stopping Powers: Comparison Between Theory and Experiments

Purpose: To evaluate the clinical performance of dual-energy CT (DECT) in determining proton stopping power ratios (SPR) and demonstrate advantages over conventional single-energy CT (SECT). Methods: SECT and DECT scans of tissue-equivalent plastics as well as animal meat samples are performed with a Siemens SOMATOM Definition Flash. The methods of Schneider et al. (1996) and Bourque et al. (2014) are used to determine proton SPR on SECT and DECT images, respectively. Waterequivalent path length (WEPL) measurements of plastics and tissue samples are performed with a 195 MeV proton beam. WEPL values are determined experimentally using the depth-dose shift and dose extinction methods. Results: Comparison between CT-based and experimental WEPL is performed for 12 tissue-equivalent plastic as well as 6 meat boxes containing animal liver, kidney, heart, stomach, muscle and bones. For plastic materials, results show a systematic improvement in determining SPR with DECT, with a mean absolute error of 0.4% compared to 1.7% for SECT. For the meat samples, preliminary results show the ability for DECT to determine WEPL with a mean absolute value of 1.1% over all meat boxes. Conclusion: This work demonstrates the potential in using DECT for determining proton SPR with plastic materials in a clinical context. Further work is required to show the benefits of DECT for tissue samples. While experimental uncertainties could be a limiting factor to show the benefits of DECT over SECT for the meat samples, further work is required to adapt the DECT formalism in the context of clinical use, where noise and artifacts play an important role.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

WE-FG-BRA-07: Theranostic Nanoparticles Improve Clinical MR-Guided Radiation Therapy

Purpose: MR-guided radiation therapy is a current and emerging clinical reality. We have designed and tested a silica-based gadolinium chelates nanoparticle (AGuIX) for integration with MR-guided radiation therapy. The AGuIX nanoparticles used in this study are a dual-modality probe with radiosensitization properties and better MRI contrast than current FDA-approved gadolinium chelates. In advance of an approved Phase I clinical trial, we report on the efficacy and safety in multiple animal models and clinically relevant radiation conditions. By modeling our study on current clinic workflows, we show compatibility with modern patient care, thus heightening the translational significance of this research. Methods: The dual imaging and therapy functionality of AGuIX was investigated in mice with clinical radiation beams while safety was evaluated in mice, and nonhuman primates after systemic injection of 0.25 mg/g of nanoparticles. MRI/ICP-MS were used to measure tumor uptake and biodistribution. Due to their small size (2–3 nm), AGuIX have good renal clearance (t1/2=19min). We performed in vitro cell uptake quantification and radiosensitization studies (clonogenic assays and DNA damage quantification). In vivo radiation therapy studies were performed with both 6MV and 6MV-FFF clinical radiation beams. Histology was performed to measure the increase in DNA damage in the tumor and to evaluate the toxicity in healthy tissues. Results: In vitro and in vivo results demonstrate statistically significant increase (P < 0.01) in DNA damage, tumor growth supression and survival (+100 days) compared to radiation alone. Negligible toxicity was observed in all of the animal models. The combination of 6MV-FFF/AGuIX demonstrated a substantial dose enhancement compared to 6MV/AGuIX (DEF = 1.36 vs. 1.22) due to the higher proportion of low energy photons. Conclusion: With demonstrated efficacy and negligible toxicity in mice and non-human primates, AGuIX is a biocompatible nanoplatform with strong translational potential for MR-guided radiation therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-FG-202-02: Exploration of High-Resolution Quantitative Ultrasonic Micro-Vascular Imaging for Early Assessment of Radiotherapy Tumor Response

Purpose: Currently, we cannot predict an individual patient’s response to a given radiotherapy which normally is not detected for weeks to months post-treatment. As a result, precious time is wasted for patients with unresponsive tumors who could have switched to an alternative treatment much earlier. Presently, no early treatment response detection method exists that is effective, low-cost, non-invasive, and safe. We hypothesize that changes in tumor microvasculature predict tumor response to radiotherapy earlier than tumor volume changes. Recent radiobiology research suggests tumors undergo vascular remodeling in response to radiation well before manifesting changes in tumor volume. We propose monitoring tumor microvasculature post-radiation using Acoustic Angiography (AA), a novel ultrasound imaging modality developed and patented in-house. In this study, we investigate whether changes in tumor microvasculature, measured using AA, can be an early indicator of high-dose radiotherapy success, compared to changes in tumor volume. Methods: Fibrosarcoma xenograft tumor tissue was subcutaneously implanted into rodent flanks (N=10). Animal tumors (N=8) were irradiated with a single treatment of 15Gy using a clinical LINAC at 100SSD and 2×2cm field size. Two untreated rats were left as tumor controls. AA imaging was performed immediately posttreatment and every third day thereafter for 30 days, or until tumors disappeared. Tumor volumes and vascular densities were measured from anatomical b-mode ultrasound and AA images, respectively. Results: Statistical differences in vascular density between treatment responders and non-responders were observed on Day 10 (p=0.005), whereas statistical differences in tumor volume were not observed until Day 19 (p=0.02). Conclusions: Tumor vascularity differences may be observed substantially earlier than differences in tumor size. In addition, significant early increases in vascular density were observed in non-responding tumors. This data is consistent with a similar study we completed using the same tumor and animal models (N=10) at 20Gy. The project described was supported by the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, through Grant Award Number UL1TR001111. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-FG-202-06: The Use of Hybrid PET MRI for Identifying the Presence of Cardiac Inflammation Following External Beam Irradiation

Purpose: To monitor the evolution of radiation-induced cardiac inflammation in a canine model using hybrid positron emission tomography (PET/magnetic resonance imaging (MRI). Methods: Research ethics approval was obtained for a longitudinal imaging study of 5 canines after cardiac irradiation. Animals were imaged at baseline, 3 months, 6 months, and 12 months post cardiac irradiation using a hybrid PET-MRI system (Biograph mMR, Siemens Healthcare). The imaging protocol was designed to assess changes in cardiac inflammation using {sup 18}F-fluorodeoxyglucose ({sup 18}F-FDG) PET tracer. In order to image cardiac inflammation, the normal myocardial uptake of glucose was suppressed prior to the injection of {sup 18}F-FDG. The suppression of glycolysis was achieved through; fasting (16–21 hours prior to the start of imaging) and an intravenous injection of heparin immediately followed by a 20% lipid infusion 20 min prior to the injection of {sup 18}F-FDG. The standard uptake value (SUV) obtained from 17 myocardial regions were used to compare FDG scans. All animals received a simulation CT scan (GE Medical Systems) for radiation treatment planning. Radiation treatment plans were created using the Pinncale3 treatment planning system (Philips Radiation Oncology Systems) and designed to resemble the typical cardiac exposure during left-sided breast cancer radiotherapy. Cardiac irradiations were performed in a single fraction using a TrueBeam linear accelerator (Varian Medical Systems). Results: The delivered dose (mean ± standard error) to heart, left ventricle, and left anterior descending artery were 1.7±0.1 Gy, 2.7±0.1 Gy, and 5.5±0.3 Gy respectively. At these doses, a significant increase in {sup 18}F-FDG uptake within the entire heart relative to baseline (1.1±0.02 g/ml) uptake was observed. {sup 18}F-FDG uptake at 3 months, 6 months, and 12 months post irradiation were 1.8±0.03 g/ml, 2.4±0.06 g/ml, and 2.6±0.11 g/ml respectively. Conclusion: Low doses of limited cardiac irradiation show evidence of a persistent global inflammatory response that can be detected using {sup 18}F-FDG PET imaging. This work was supported through the Translational Breast Cancer Studentship award, funded in part by the Breast Cancer Society of Canada. Additional financial support is provided by the London Regional Cancer Program Catalyst Grant and the Thames Valley Veterinary Services.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-EF-207A-07: An Integrated X-Ray/bioluminescence Tomography System for Radiation Guidance and Tumor Evaluation

Purpose: CT is not able to differentiate tumors from surrounding soft tissue. This study is to develop a bioluminescence tomography (BLT) system that is integrated onto our previously developed CT guided small animal arc radiation treatment system (iSMAART) to guide radiation, monitor tumor growth and evaluate therapeutic response. Methods: The BLT system employs a CCD camera coupled with a high speed lens, and is aligned orthogonally to the x-ray beam central axis. The two imaging modalities, CT and BLT, are physically registered through geometrical calibration. The CT anatomy provides an accurate contour of animal surface which is used to construct 3D mesh for BLT reconstruction. Bioluminescence projections are captured from multiple angles, once every 45 degree rotation. The diffusion equation based on analytical Kirchhoff approximation is adopted to model the photon propagation in tissues. A discrete cosine transform based reweighted L1-norm regularization (DCT-re-L1) algorithm is used for BLT reconstruction. Experiments are conducted on a mouse orthotopic prostate tumor model (n=12) to evaluate the BLT performance, in terms of its robustness and accuracy in locating and quantifying the bioluminescent tumor cells. Iodinated contrast agent was injected intravenously to delineate the tumor in CT. The tumor location and volume obtained from CT also serve as a benchmark against BLT. Results: With our cutting edge reconstruction algorithm, BLT is able to accurately reconstruct the orthotopic prostate tumors. The tumor center of mass in BLT is within 0.5 mm radial distance of that in CT. The tumor volume in BLT is significantly correlated with that in CT (R2 = 0.81). Conclusion: The BLT can differentiate, localize and quantify tumors. Together with CT, BLT will provide precision radiation guidance and reliable treatment assessment in preclinical cancer research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Marine energy converters: Potential acoustic effects on fishes and aquatic invertebrates

The potential effects of underwater anthropogenic sound and substrate vibration from offshore renewable energy development on the behavior, fitness, and health of aquatic animals is a continuing concern with increased deployments and installation of these devices. Initial focus of related studies concerned offshore wind. However, over the past decade, marine energy devices, such as a tidal turbines and wave energy converters, have begun to emerge as additional, scalable renewable energy sources. Because marine energy converters (MECs) are not as well-known as other anthropogenic sources of potential disturbance, their general function and what is known about the sounds and substrate vibrations that they produce are introduced. Furthermore, while most previous studies focused on MECs and marine mammals, this paper considers the potential of MECs to cause acoustic disturbances affecting nearshore and tidal fishes and invertebrates. In particular, the focus is on particle motion and substrate vibration from MECs because these effects are the most likely to be detected by these animals. Finally, an analysis of major data gaps in understanding the acoustics of MECs and their potential impacts on fishes and aquatic invertebrates and recommendations for research needed over the next several years to improve understanding of these potential impacts are provided.

16 TIDAL AND WAVE POWER↗
DOE OSTI2015

The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium

Surveillance of the extracellular environment by immune receptors is of central importance to eukaryotic survival. The rice receptor kinase XA21, which confers robust resistance to most strains of the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is representative of a large class of cell surface immune receptors in plants and animals. We report the identification of a previously undescribed Xoo protein, called RaxX, which is required for activation of XA21-mediated immunity. Xoo strains that lack RaxX, or carry mutations in the single RaxX tyrosine residue (Y41), are able to evade XA21-mediated immunity. Y41 of RaxX is sulfated by the prokaryotic tyrosine sulfotransferase RaxST. Sulfated, but not nonsulfated, RaxX triggers hallmarks of the plant immune response in an XA21-dependent manner. A sulfated, 21–amino acid synthetic RaxX peptide (RaxX21-sY) is sufficient for this activity. Xoo field isolates that overcome XA21-mediated immunity encode an alternate raxX allele, suggesting that coevolutionary interactions between host and pathogen contribute to RaxX diversification. RaxX is highly conserved in many plant pathogenic Xanthomonas species. The new insights gained from the discovery and characterization of the sulfated protein, RaxX, can be applied to the development of resistant crop varieties and therapeutic reagents that have the potential to block microbial infection of both plants and animals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Quantitative cross-species translators of cardiac myocyte electrophysiology: Model training, experimental validation, and applications

Animal experimentation is key in the evaluation of cardiac efficacy and safety of novel therapeutic compounds. However, interspecies differences in the mechanisms regulating excitation-contraction coupling can limit the translation of experimental findings from animal models to human physiology and undermine the assessment of drugs’ efficacy and safety. Here, we built a suite of translators for quantitatively mapping electrophysiological responses in ventricular myocytes across species. We trained these statistical operators using a broad dataset obtained by simulating populations of our biophysically detailed computational models of action potential and Ca 2+ transient in mouse, rabbit, and human. We then tested our translators against experimental data describing the response to stimuli, such as ion channel block, change in beating rate, and β-adrenergic challenge. We demonstrate that this approach is well suited to predicting the effects of perturbations across different species or experimental conditions and suggest its integration into mechanistic studies and drug development pipelines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Deeply conserved synteny and the evolution of metazoan chromosomes

Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Dynamic molecular architecture of the synaptonemal complex

During meiosis, pairing between homologous chromosomes is stabilized by the assembly of the synaptonemal complex (SC). The SC ensures the formation of crossovers between homologous chromosomes and regulates their distribution. However, how the SC regulates crossover formation remains elusive. We isolated an unusual mutation in Caenorhabditis elegans that disrupts crossover interference but not SC assembly. This mutation alters the unique C terminal domain of an essential SC protein, SYP-4, a likely ortholog of the vertebrate SC protein SIX6OS1. We use three-dimensional stochastic optical reconstruction microscopy (3D-STORM) to interrogate the molecular architecture of the SC from wild-type and mutant C. elegans animals. Using a probabilistic mapping approach to analyze super-resolution image data, we detect changes in the organization of the synaptonemal complex in wild-type animals that coincide with crossover designation. We also found that our syp-4 mutant perturbs SC architecture. Our findings add to growing evidence that the SC is an active material whose molecular organization contributes to chromosome-wide crossover regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structural basis for microRNA targeting

MicroRNAs (miRNAs) control expression of thousands of genes in plants and animals. miRNAs function by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. In this paper, we determined crystal structures of human Argonaute-2 (Ago2) bound to a defined guide RNA with and without target RNAs representing miRNA recognition sites. These structures suggest a stepwise mechanism, in which Ago2 primarily exposes guide nucleotides (nt) 2 to 5 for initial target pairing. Pairing to nt 2 to 5 promotes conformational changes that expose nt 2 to 8 and 13 to 16 for further target recognition. Interactions with the guide-target minor groove allow Ago2 to interrogate target RNAs in a sequence-independent manner, whereas an adenosine binding-pocket opposite guide nt 1 further facilitates target recognition. Spurious slicing of miRNA targets is avoided through an inhibitory coordination of one catalytic magnesium ion. Finally, these results explain the conserved nucleotide-pairing patterns in animal miRNA target sites first observed over two decades ago.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Chicken Production and Human Clinical Escherichia coli Isolates Differ in Their Carriage of Antimicrobial Resistance and Virulence Factors

Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A Rhizobiales-Specific Unipolar Polysaccharide Adhesin Contributes to Rhodopseudomonas palustris Biofilm Formation across Diverse Photoheterotrophic Conditions

Bacteria predominantly exist as members of surfaced-attached communities known as biofilms. Many bacterial species initiate biofilms and adhere to each other using cell surface adhesins. This is the case for numerous ecologically diverse Alphaprotebacteria , which use polar exopolysaccharide adhesins for cell-cell adhesion and surface attachment. Here, we show that Rhodopseudomonas palustris , a metabolically versatile member of the alphaproteobacterial order Rhizobiales , contains a functional unipolar polysaccharide (UPP) biosynthesis gene cluster. Deletion of genes predicted to be critical for UPP biosynthesis and export abolished UPP production. We also found that R. palustris uses UPP to mediate biofilm formation across diverse photoheterotrophic growth conditions, wherein light and organic substrates are used to support growth. However, UPP was less important for biofilm formation during photoautotrophy, where light and CO 2 support growth, and during aerobic respiration with organic compounds. Expanding our analysis beyond R. palustris , we examined the phylogenetic distribution and genomic organization of UPP gene clusters among Rhizobiales species that inhabit diverse niches. Our analysis suggests that UPP is a conserved ancestral trait of the Rhizobiales but that it has been independently lost multiple times during the evolution of this clade, twice coinciding with adaptation to intracellular lifestyles within animal hosts. Bacteria are ubiquitously found as surface-attached communities and cellular aggregates in nature. Here, we address how bacterial adhesion is coordinated in response to diverse environments using two complementary approaches. First, we examined how Rhodopseudomonas palustris , one of the most metabolically versatile organisms ever described, varies its adhesion to surfaces in response to different environmental conditions. We identified critical genes for the production of a unipolar polysaccharide (UPP) and showed that UPP is important for adhesion when light and organic substrates are used for growth. Looking beyond R. palustris , we performed the most comprehensive survey to date on the conservation of UPP biosynthesis genes among a group of closely related bacteria that occupy diverse niches. Our findings suggest that UPP is important for free-living and plant-associated lifestyles but dispensable for animal pathogens. Additionally, we propose guidelines for classifying the adhesins produced by various Alphaprotebacteria , facilitating future functional and comparative studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates

While most Vibrionaceae are considered generalists that thrive on diverse substrates, including animal-derived material, we show that Vibrio breoganii has specialized for the consumption of marine macroalga-derived substrates. Genomic and physiological comparisons of V. breoganii with other Vibrionaceae isolates revealed the ability to degrade alginate, laminarin, and additional glycans present in algal cell walls. Moreover, the widely conserved ability to hydrolyze animal-derived polymers, including chitin and glycogen, was lost, along with the ability to efficiently grow on a variety of amino acids. Ecological data showing associations with particulate algal material but not zooplankton further support this shift in niche preference, and the loss of motility appears to reflect a sessile macroalga-associated lifestyle. Altogether, these findings indicate that algal polysaccharides have become a major source of carbon and energy in V. breoganii , and these ecophysiological adaptations may facilitate transient commensal associations with marine invertebrates that feed on algae.

59 BASIC BIOLOGICAL SCIENCES↗