Results for “Comprehensive” — Page 92

DOE OSTI2016

TH-C-204-01: Vision for Medical Physics and Status of Current Initiatives

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-C-204-02: Improving Manuscript Quality Via Structured Reviews, Enhanced Scientific Category Taxonomy, and Outreach

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-C-204-03: Writing Good Scientific Papers and Responding to Critiques

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-CD-207B-07: Noise Modeling of Single Photon Avalanche Diode (SPAD) for Photon Counting CT Applications

Purpose: Silicon photomultiplier (SiPM) has recently emerged as a promising photodetector for biomedical imaging applications. Due to its high multiplication gain (comparable to PMT), fast timing, low cost and compactness, it is considered a good candidate for photon counting CT. Dark noise is a limiting factor which impacts both energy resolution and detection dynamic range. Our goal is to develop a comprehensive model for noise sources for SiPM sensors. Methods: The physical parameters used in this work were based upon a test SPAD fabricated in 130nm CMOS process. The SPAD uses an n+/p-well junction, which is isolated from the p-substrate by a deep n-well junction. Inter-avalanche time measurement was used to record the time interval between two adjacent avalanche pulses. After collecting 1×106 counts, the histogram was obtained and multiple exponential fitting process was used to extract the lifetime associated with the traps within the bandgap. Results: At room temperature, the breakdown voltage of the SPAD is ∼11.4V and shows a temperature coefficient of 7.7mV/°C. The dark noise of SPAD increases with both the excess biasing voltage and temperature. The primary dark counts from the model were validated against the measurement results. A maximum relative error of 8.7% is observed at 20 °C with an excess voltage of 0.5V. The probabilities of after-pulsing are found to be dependent of both temperature and excess voltage. With 0.5V excess voltage, the after-pulsing probability is 63.5% at - 30 °C and drops to ∼6.6% at 40 °C. Conclusion: A comprehensive noise model for SPAD sensor was proposed. The model takes into account of static, dynamic and statistical behavior of SPADs. We believe that this is the first SPAD circuit simulation model that includes the band-to-band tunneling dark noise contribution and temporal dependence of the after-pulsing probability.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2016

Technical Report: Evaluation of peripheral dose for flattening filter free photon beams

Purpose: To develop a comprehensive peripheral dose (PD) dataset for the two unflattened beams of nominal energy 6 and 10 MV for use in clinical care. Methods: Measurements were made in a 40 × 120 × 20 cm{sup 3} (width × length × depth) stack of solid water using an ionization chamber at varying depths (dmax, 5, and 10 cm), field sizes (3 × 3 to 30 × 30 cm{sup 2}), and distances from the field edge (5–40 cm). The effects of the multileaf collimator (MLC) and collimator rotation were also evaluated for a 10 × 10 cm{sup 2} field. Using the same phantom geometry, the accuracy of the analytic anisotropic algorithm (AAA) and Acuros dose calculation algorithm was assessed and compared to the measured values. Results: The PDs for both the 6 flattening filter free (FFF) and 10 FFF photon beams were found to decrease with increasing distance from the radiation field edge and the decreasing field size. The measured PD was observed to be higher for the 6 FFF than for the 10 FFF for all field sizes and depths. The impact of collimator rotation was not found to be clinically significant when used in conjunction with MLCs. AAA and Acuros algorithms both underestimated the PD with average errors of −13.6% and −7.8%, respectively, for all field sizes and depths at distances of 5 and 10 cm from the field edge, but the average error was found to increase to nearly −69% at greater distances. Conclusions: Given the known inaccuracies of peripheral dose calculations, this comprehensive dataset can be used to estimate the out-of-field dose to regions of interest such as organs at risk, electronic implantable devices, and a fetus. While the impact of collimator rotation was not found to significantly decrease PD when used in conjunction with MLCs, results are expected to be machine model and beam energy dependent. It is not recommended to use a treatment planning system to estimate PD due to the underestimation of the out-of-field dose and the inability to calculate dose at extended distances due to the limits of the dose calculation matrix.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Exploration of metastability and hidden phases in correlated electron crystals visualized by femtosecond optical doping and electron crystallography

Characterizing and understanding the emergence of multiple macroscopically ordered electronic phases through subtle tuning of temperature, pressure, and chemical doping has been a long-standing central issue for complex materials research. We report the first comprehensive studies of optical doping–induced emergence of stable phases and metastable hidden phases visualized in situ by femtosecond electron crystallography. The electronic phase transitions are triggered by femtosecond infrared pulses, and a temperature–optical density phase diagram is constructed and substantiated with the dynamics of metastable states, highlighting the cooperation and competition through which the macroscopic quantum orders emerge. These results elucidate key pathways of femtosecond electronic switching phenomena and provide an important new avenue to comprehensively investigate optical doping–induced transition states and phase diagrams of complex materials with wide-ranging applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

Global carbon intensity of crude oil production

Producing, transporting, and refining crude oil into fuels such as gasoline and diesel accounts for ~15 to 40% of the “well-to-wheels” life-cycle greenhouse gas (GHG) emissions of transport fuels. Reducing emissions from petroleum production is of particular importance, as current transport fleets are almost entirely dependent on liquid petroleum products, and many uses of petroleum have limited prospects for near-term substitution (e.g., air travel). Better understanding of crude oil GHG emissions can help to quantify the benefits of alternative fuels and identify the most cost-effective opportunities for oil-sector emissions reductions. Yet, while regulations are beginning to address petroleum sector GHG emissions, and private investors are beginning to consider climate-related risk in oil investments, such efforts have generally struggled with methodological and data challenges. First, no single method exists for measuring the carbon intensity (CI) of oils. Second, there is a lack of comprehensive geographically rich datasets that would allow evaluation and monitoring of life-cycle emissions from oils. We have previously worked to address the first challenge by developing open-source oil-sector CI modeling tools [OPGEE, supplementary materials (SM) 1.1]. Furthermore, we address the second challenge by using these tools to model well-to-refinery CI of all major active oil fields globally—and to identify major drivers of these emissions.

02 PETROLEUM↗

DOE OSTI2020

Absence of evidence for chiral Majorana modes in quantum anomalous Hall-superconductor devices

A quantum anomalous Hall (QAH) insulator coupled to an s-wave superconductor is predicted to harbor chiral Majorana modes. A recent experiment interprets the half-quantized two-terminal conductance plateau as evidence for these modes in a millimeter-size QAH-niobium hybrid device. However, non-Majorana mechanisms can also generate similar signatures, especially in disordered samples. Here, we studied similar hybrid devices with a well-controlled and transparent interface between the superconductor and the QAH insulator. When the devices are in the QAH state with well-aligned magnetization, the two-terminal conductance is always half-quantized. Our experiment provides a comprehensive understanding of the superconducting proximity effect observed in QAH-superconductor hybrid devices and shows that the half-quantized conductance plateau is unlikely to be induced by chiral Majorana fermions in samples with a highly transparent interface.

Science & Technology - Other Topics↗

DOE OSTI2025

RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling

Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive data set of functional evidence for the genetic basis of dicarboxylic and fatty acid metabolism using randomly barcoded transposon sequencing (RB-TnSeq). We identified four β-proteobacteria that displayed robust growth with dicarboxylic acid sole carbon source and cultured their mutant libraries with dicarboxylic and fatty acids with carbon chain lengths from C3 to C12. The resulting fitness data suggested that dicarboxylic and fatty acid metabolisms are largely distinct, and different sets of β-oxidation genes are required for catabolizing dicarboxylic versus fatty acids of the same carbon chain lengths. In addition, we identified transcriptional regulators and transporters with strong fitness phenotypes related to dicarboxylic acid utilization. In Ralstonia sp. UNC404CL21Col (R. CL21), we deleted two transcriptional repressors to improve its utilization of short-chain dicarboxylic acids. We exploited the diacid-utilizing catabolism of R. CL21 to upcycle a mock mixture of the dicarboxylic acids produced when polyethylene is oxidized. After introducing a heterologous indigoidine production pathway, this engineered Ralstonia produced 0.56 ± 0.02 g/L indigoidine from a mixture of dicarboxylic acids as a carbon source, demonstrating the potential of R. CL21 to upcycle plastic wastes to products derived from tricarboxylic acid (TCA) cycle intermediates. IMPORTANCE: Upcycling the carbon in plastic wastes to value-added products is a promising approach to address the plastic waste and climate crises, and dicarboxylic acid metabolism is an important facet of several approaches. Improving our understanding of the genetic basis of this metabolism has the potential to uncover new enzymes and genetic parts for engineered pathways involving dicarboxylic acids. Our data set is the most comprehensive interrogation of dicarboxylic acid catabolism to date, and this work will be of utility to researchers interested in both plastics bioproduction and upcycling applications.

Pearson, Allison N↗

DOE OSTI2018

Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota

ABSTRACT Several studies monitoring alterations in the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene sequencing, metaproteomics, and metabolomics on fecal samples from individuals subjected to high and low doses of type 2 RS (RS2; 48 g and 3 g/2,500 kcal, respectively, daily for 2 weeks) in a crossover intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals ( n = 12) from that study to obtain additional detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes , with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for the growth of various major butyrate producers exhibiting the enzyme butyryl-coenzyme A (CoA):acetate CoA-transferase. H 2 -scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted, where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome, emphasizing a constant substrate supply for maintaining specific functional communities. IMPORTANCE Manipulation of gut microbiota is increasingly recognized as a promising approach to reduce various noncommunicable diseases, such as obesity and type 2 diabetes. Specific dietary supplements, including resistant starches (RS), are often a focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific more-downstream-acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on an individual's microbiota.

Vital, Marius↗

DOE OSTI2017

RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA

ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF , proP , tnaC , dctA , pheM , sdhC , yhhQ , glpT , aceK , and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF , pflB , and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. IMPORTANCE The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli . Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307

Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for K. pneumoniae, it is imperative to understand the population genomic structure of strains causing human infections. To address this knowledge gap, we sequenced the genomes of 1,777 extended-spectrum beta-lactamase-producing K. pneumoniae strains cultured from patients in the 2,000-bed Houston Methodist Hospital system between September 2011 and May 2015, representing a comprehensive, population-based strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused more infections than those of well-studied epidemic CG258. Strains varied markedly in gene content and had an extensive array of small and very large plasmids, often containing antimicrobial resistance genes. Some patients with multiple strains cultured over time were infected with genetically distinct clones. We identified 15 strains expressing the New Delhi metallo-beta-lactamase 1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse strains showed that the global transcriptome of each strain was unique and highly variable. Experimental mouse infection provided new information about immunological parameters of host-pathogen interaction. We exploited the large data set to develop whole-genome sequence-based classifiers that accurately predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We conclude that analysis of large, comprehensive, population-based strain samples can assist understanding of the molecular diversity of these organisms and contribute to enhanced translational research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggest that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.

Nakayasu, Ernesto S.↗

DOE OSTI2018

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. Here, this study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Transcriptome Analysis of Neisseria gonorrhoeae during Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants between Men and Women

Neisseria gonorrhoeae is a bacterial pathogen responsible for the sexually transmitted infection gonorrhea. Emergence of antimicrobial resistance (AMR) of N. gonorrhoeae worldwide has resulted in limited therapeutic choices for this infection. Men who seek treatment often have symptomatic urethritis; in contrast, gonococcal cervicitis in women is usually minimally symptomatic, but may progress to pelvic inflammatory disease. Previously, we reported the first analysis of gonococcal transcriptome expression determined in secretions from women with cervical infection. Here, we defined gonococcal global transcriptional responses in urethral specimens from men with symptomatic urethritis and compared these with transcriptional responses in specimens obtained from women with cervical infections and in vitro-grown N. gonorrhoeae isolates. This is the first comprehensive comparison of gonococcal gene expression in infected men and women. RNA sequencing analysis revealed that 9.4% of gonococcal genes showed increased expression exclusively in men and included genes involved in host immune cell interactions, while 4.3% showed increased expression exclusively in women and included phage-associated genes. Infected men and women displayed comparable antibiotic-resistant genotypes and in vitro phenotypes, but a 4-fold higher expression of the Mtr efflux pump-related genes was observed in men. These results suggest that expression of AMR genes is programed genotypically and also driven by sex-specific environments. Collectively, our results indicate that distinct N. gonorrhoeae gene expression signatures are detected during genital infection in men and women. We propose that therapeutic strategies could target sex-specific differences in expression of antibiotic resistance genes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample.

Nakayasu, Ernesto S.↗

DOE OSTI2016

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO 2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated ( P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO 2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Identification of hidden N4-like viruses and their interactions with hosts

The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.

60 APPLIED LIFE SCIENCES↗