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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Subtask 4.8 - Fate and Control of Mercury and Trace Elements

The Center for Air Toxic Metals® (CATM®) Program at the Energy & Environmental Research Center (EERC) continues to focus on vital basic and applied research related to the fate, behavior, measurement, and control of trace metals, especially mercury, and the impact that these trace metals have on human health and the environment. For years, the CATM Program has maintained an international perspective, performing research and providing results that apply to both domestic and international audiences, with reports distributed in the United States and abroad. In addition to trace metals, CATM’s research focuses on other related emissions and issues that impact trace metal releases to the environment, such as SO x , NO x , CO 2 , ash, and wastewater streams. Of paramount interest and focus has been performing research that continues to enable the power and industrial sectors to operate in an environmentally responsible manner to meet regulatory standards. The research funded by the U.S. Department of Energy’s (DOE’s) National Energy Technology Laboratory (NETL) through CATM has allowed significant strides to be made to gain a better understanding of trace metals and other emissions, improve sampling and measurement techniques, fill data gaps, address emerging technical issues, and develop/test control technologies that allow industry to cost-effectively meet regulatory standards. The DOE NETL–CATM research specifically focused on the fate and control of mercury and trace elements in power systems that use CO 2 control technologies, such as oxycombustion and gasification systems, which are expected to be among those technologies that will be used to address climate change issues. In addition, research addressed data gaps for systems that use conventional and multipollutant control technologies, such as electrostatic precipitators, selective catalytic reduction units, flue gas desulfurization systems, and flue gas-conditioning methods, to understand mercury interactions, develop better control strategies and, in some cases, prevent mercury from being reemitted. This research also addressed stakeholder concerns and questions related to sampling and analytical methods for mercury, especially for continuous mercury monitors and sorbent trap methods for future compliance. Advancements were made toward the development of a much simpler dry-based method for measurement of halogens and trace metals. Finally, this research resulted in significant outcomes related to mercury and selenium concentrations in freshwater fish and how it is associated with other elements, thereby potentially impacting health; this has greatly enhanced the understanding of the second-order mechanism of mercury toxicity. The outcomes of this research have been shared with stakeholders in various domestic and international forums, working groups, conferences, educational settings, and published documents, with information available and accessible to those most impacted or interested in timely and current results on toxic metals. This subtask was funded through the EERC–DOE Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FC26-08NT43291.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

An Extended Group Additivity Method for Polycyclic Thermochemistry Estimation

Automatic kinetic mechanism generation, virtual high-throughput screening, and automatic transition state search are currently trending applications requiring exploration of a large molecule space. Large-scale search requires fast and accurate estimation of molecules’ properties of interest, such as thermochemistry. Existing approaches are not satisfactory for large polycyclic molecules: considering the number of molecules being screened, quantum chemistry (even cheap density functional theory methods) can be computationally expensive, and group additivity, though fast, is not sufficiently accurate. Here, this paper provides a fast and moderately accurate alternative by proposing a polycyclic thermochemistry estimation method that extends the group additivity method with two additional algorithms: similarity match and bicyclic decomposition. It significantly reduces H f (298 K) estimation error from over 60 kcal/mol (group additivity method) to around 5 kcal/mol, C p (298 K) error from 9 to 1 cal/mol/K,and S(298 K) error from 70 to 7 cal/mol/K. This method also works well for heteroatomic polycyclics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1994

National facilities study. Volume 4: Space operations facilities task group

The principal objectives of the National Facilities Study (NFS) were to: (1) determine where U.S. facilities do not meet national aerospace needs; (2) define new facilities required to make U.S. capabilities 'world class' where such improvements are in the national interest; (3) define where consolidation and phase-out of existing facilities is appropriate; and (4) develop a long-term national plan for world-class facility acquisition and shared usage. The Space Operations Facilities Task Group defined discrete tasks to accomplish the above objectives within the scope of the study. An assessment of national space operations facilities was conducted to determine the nation's capability to meet the requirements of space operations during the next 30 years. The mission model used in the study to define facility requirements is described in Volume 3. Based on this model, the major focus of the Task Group was to identify any substantive overlap or underutilization of space operations facilities and to identify any facility shortfalls that would necessitate facility upgrades or new facilities. The focus of this initial study was directed toward facility recommendations related to consolidations, closures, enhancements, and upgrades considered necessary to efficiently and effectively support the baseline requirements model. Activities related to identifying facility needs or recommendations for enhancing U.S. international competitiveness and achieving world-class capability, where appropriate, were deferred to a subsequent study phase.

Source record↗
DOE OSTI2018

Evolution and expression of core SWI / SNF genes in red algae

Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue‐specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI / SNF chromatin‐remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI / SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI / SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI / SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI 3 and SNF 5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins.

Stiller, John W.↗
DOE OSTI2015

L-Tryptophan on Cu(111): engineering a molecular labyrinth driven by indole groups

The present article investigates the adsorption and molecular orientation of L-Tryptophan, which is both an essential amino acid important for protein synthesis and of particular interest for the development of chiral molecular electronics and biocompatible processes and devices, on Cu(111) using scanning tunneling microscopy and spectroscopy at 55 K and at room temperature. The arrangement of chemisorbed L-Tryptophan on the copper surface varies with both temperature and surface coverage. At low coverage, small clusters form on the surface irrespective of temperature, while at high coverage an ordered chain structure emerges at room temperature, and a tightly packed structure forms a molecular labyrinth at low temperature. The dominating superstructure of the adsorbates arises from intermolecular hydrogen bonding, and pi-bonding interactions between the indole groups of neighboring molecules and the Cu surface.

Yitamben, E. N.↗
DOE OSTI2016

Nanomaterials in Extreme Environments: Fundamentals and Applications Rostislav A. Andrievski and Arsen V. Khatchoyan

Nanomaterials in Extreme Environments Rostislav A. Andrievski and Arsen V. Khatchoyan Springer, 2016 106 pages, $99.00 (e-book $69.99) ISBN 978–3-319–25331–2 This slim volume is an extensive review of our current understanding of the response of nanostructured materials to extreme operating conditions, such as high temperature, flux of high energy neutrons, high pressure, mechanical stress, and oxidizing environments. The emphasis is on metallic materials, especially Cu alloys. Graphene-based materials, fullerenes, polymeric materials, nano-glasses and glass-ceramics are not covered by this review. The book has six chapters including an introduction and a brief conclusion. The introduction documents the growth of scientific interest in nanostructured materials and stresses the need to study the behavior of nanomaterials under extreme conditions. This chapter also presents Herbert Gleiter’s classification of nanomaterials into twelve groups based on the shapes of the nanoscale features and chemical composition of the components of the nanostructure. The second chapter deals with the high temperature environment and the thermodynamics and kinetics of grain growth. The authors identify the lack of reliable thermodynamic data as a key limitation in this field. The discussion brings out the interplay of structural relaxation, redistribution of excess free volume, diffusion, and recrystallization in multicomponent nanostructures at elevated temperature. Chapter 3 focuses on the effects of ion and neutron irradiation on the structure and properties of nanomaterials. The authors do a good job of highlighting recent studies on the radiation tolerance of nanocrystalline oxides and rapid grain growth under irradiation. The material addresses both fission and fusion reactor applications. Chapter 4 reviews the effects of severe plastic deformation and cyclic loading on nanostructure formation and phase transformation. This chapter also explores the challenge of achieving high density while retaining nanostructural features during processing under extreme loads and high temperatures. Chapter 5 discusses the effects of corrosion on nanomaterials. The behavior of a variety of alloys and high melting point compounds in liquid media and high temperature oxidizing environments is reviewed. The concluding chapter identifies areas for further research. The book would have benefited from careful copy editing for use of the English language. Moreover, the excessive use of acronyms makes the text difficult to read. Each chapter ends with a section on the application of nanomaterials and a long list of references. The integration of theoretical approaches and simulation results with experimental data offers fresh insights into the behavior of nanomaterials. Overall, this book will serve as useful reference material for researchers interested in nanomaterials driven to extremes. Reviewer: Ram Devanathan is Technical Group Manager of Reactor Materials and Mechanical Design, Pacific Northwest National Laboratory, USA.

Devanathan, Ram↗
DOE OSTI2013

Social impact assessment in mining projects in Northern Finland: Comparing practice to theory

The paper discusses social impact assessments (SIA) for mining projects in light of the international principles and guidelines for such assessments and the academic literature in the field. The data consist of environmental impact assessment (EIA) programmes and reports for six mining projects that have started up in northern Finland in the 2000s. A first observation is that the role of the SIAs in the EIA programmes and reports studied was quite minor: measured in number of pages, the assessments account for three or four percent of the total. This study analyses the data collection, research methodology and conceptual premises used in the SIAs. It concludes that the assessments do not fully meet the high standards of the international principles and guidelines set out for them: for example, elderly men are over-represented in the data and no efforts were made to identify and bring to the fore vulnerable groups. Moreover, the reliability of the assessments is difficult to gauge, because the qualitative methods are not described and where quantitative methods were used, details such as non-response rates to questionnaires are not discussed. At the end of the paper, the SIAs are discussed in terms of Jürgen Habermas' theory of knowledge interests, with the conclusion that the assessments continue the empirical analytical tradition of the social sciences and exhibit a technical knowledge interest. -- Highlights: • Paper investigates social impact assessments in Finnish mining projects. • Role of social impact assessment is minor in whole EIA-process. • Mining SIAs give the voice for elderly men, vulnerable groups are not identified. • Assessment of SIAs is difficult because of lacking transparency in reporting. • SIAs belong to empirical analytical tradition with technical knowledge interest.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Anchoring Groups for Dye-Sensitized Solar Cells

The dyes in dye-sensitized solar cells (DSSCs) require one or more chemical substituents that can act as an anchor, enabling their adsorption onto a metal oxide substrate. This adsorption provides a means for electron injection, which is the process that initiates the electrical circuit in a DSSC. Understanding the structure of various DSSC anchors and the search for new anchors are critical factors for the development of improved DSSCs. Traditionally, carboxylic acid and cyanoacrylic acid groupsare employed as dye anchors in DSSCs. In recent years, novel anchor groups have emerged, which make a larger pool of materials available for DSSC dyes, and their associated physical and chemical characteristics offer interesting effects at the interface between dye and metal oxide. This review focuses especially on the structural aspects of these novel dye anchors for TiO2-based DSSCs, including pyridine, phosphonic acid, tetracyanate, perylene dicarboxylic acid anhydride, 2-hydroxylbenzonitrile, 8-hydroxylquinoline, pyridine-N-oxide, hydroxylpyridium, catechol, hydroxamate, sulfonic acid, acetylacetanate, boronic acid, nitro, tetrazole, rhodanine, and salicylic acid substituents. We anticipate that further exploration and understanding of these new types of anchoring groups for TiO2 substrates will not only contribute to the development of advanced DSSCs, but also of quantum dot-sensitized solar cells, water splitting systems, and other self-assembled monolayer-based technologies.

Adsorption↗
DOE OSTI2020

N-Terminal Decarboxylation as a Probe for Intramolecular Contact Formation in $γ$-Glu-(Pro) n -Met Peptides

The kinetics of intramolecular-contact formation between remote functional groups in peptides with restricted conformational flexibility were examined using designed peptides with variable-length proline bridges. As probes for this motion, free radicals were produced using the • OH-induced oxidation at the C-terminal methionine residue of γ-Glu-(Pro) n -Met peptides ( n = 0–3). The progress of the radicals’ motion along the proline bridges was monitored as the radicals underwent reactions along the peptides’ backbones. Of particular interest was the reaction between the sulfur atom located in the side chain of the oxidized Met residue and the unprotonated amino group of the glutamic acid moiety. Interactions between them were probed by the radiation-chemical yields (expressed as G values) of the formation of C-centered, α-aminoalkyl radicals (αN) on the Glu residue. These radicals were monitored directly or via their reaction with p -nitroacetophenone (PNAP) to generate the optically detected PNAP •– radical anions. The yields of these αN radicals were found to be linearly dependent on the number of Pro residues. A constant decrease by 0.09 μM J –1 per spacing Pro residue of the radiation-chemical yields of G (αN) was observed. Previous reports support the conclusion that the αN radicals in these cases would have to result from (S$\therefore$N) + -bonded cyclic radical cations that arose as a result from direct contact between the ends of the peptides. Furthermore, by analogy with the rate constants for the formation of intramolecularly (S$\therefore$S) + -bonded radical cations in Met-(Pro) n -Met peptides ( J. Phys. Chem. B 2016 , 120 , 9732), the rate constants for the formation of intramolecularly (S$\therefore$N) + -bonded radical cations are activated to the same extent for all of the γ-Glu-(Pro) n -Met peptides. Thus, the continuous decrease of G (αN) with the number of Pro residues (from 0 to 3) suggests that the formation of a contact between the S-atom in the C-terminal Met residue and the N-atom of a deprotonated N-terminal amino group of Glu is controlled in peptides with 0 to 3 Pro residues by the relative diffusion of the S •+ and unoxidized N-atom. The overall rate constants of cyclization to form the (S$\therefore$N)-bonded radical cations were estimated to be 3.8 × 10 6 , 1.8 × 10 6 , and 8.1 × 10 5 s –1 for peptides with n = 0, 1, and 2 Pro residues, respectively. If activation is the same for all of the peptides, then these rate constants are a direct indication for the end-to-end dynamics along the chain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

MR texture analysis: potential imaging biomarker for predicting the chemotherapeutic response of patients with colorectal liver metastases

Purpose: The purpose of the study was to determine whether the pre-treated MR texture features of colorectal liver metastases (CRLMs) are predictive of therapeutic response after chemotherapy. Methods: The study included twenty-six consecutive patients (a total of 193 liver metastasis) with unrespectable CRLMs at our institution from August 2014 to February 2016. Lesions were categorized into either responding group or non-responding group according to changes in size. Texture analysis was quantified on T2-weighted images by two radiologists with consensus on regions of interest which were manually drawn on the largest cross-sectional area of the lesions. Five histogram features (mean, variance, skewness, kurtosis, and entropy{sup 1}) and five gray level co-occurrence matrix features (GLCM; angular second moment (ASM), entropy{sup 2}, contrast, correlation, and inverse difference moment (IDM)) were extracted. The texture parameters were statistically analyzed to identify the differences between the two groups, and the potential predictive parameters to differentiate the responding group from the non-responding group were subsequently tested using multivariable logistic regression analysis. Results: A total of 107 responding and 86 non-responding lesions were evaluated. A higher variance, entropy{sup 1}, contrast, entropy{sup 2} and a lower ASM, correlation, IDM were independently (P < 0.05) associated with a good response to chemotherapy with the areas under the ROC curves (AUCs) of 0.602–0.784. Variance (P < 0.001) and ASM (P = 0.001) remained potential predictive values to discriminate responding lesions from non-responding lesions when tested using multivariable logistic regression analysis. The highest AUC of the predictors from the association of variance and ASM was 0.814. Conclusion: MR texture features on pre-treated T2 images have the potential to predict the therapeutic response of colorectal liver metastases.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Comparison of Shallow and Deep Learning Methods on Classifying the Regional Pattern of Diffuse Lung Disease

This study aimed to compare shallow and deep learning of classifying the patterns of interstitial lung diseases (ILDs). Using high-resolution computed tomography images, two experienced radiologists marked 1200 regions of interest (ROIs), in which 600 ROIs were each acquired using a GE or Siemens scanner and each group of 600 ROIs consisted of 100 ROIs for subregions that included normal and five regional pulmonary disease patterns (ground-glass opacity, consolidation, reticular opacity, emphysema, and honeycombing). We employed the convolution neural network (CNN) with six learnable layers that consisted of four convolution layers and two fully connected layers. The classification results were compared with the results classified by a shallow learning of a support vector machine (SVM). The CNN classifier showed significantly better performance for accuracy compared with that of the SVM classifier by 6–9%. As the convolution layer increases, the classification accuracy of the CNN showed better performance from 81.27 to 95.12%. Especially in the cases showing pathological ambiguity such as between normal and emphysema cases or between honeycombing and reticular opacity cases, the increment of the convolution layer greatly drops the misclassification rate between each case. Conclusively, the CNN classifier showed significantly greater accuracy than the SVM classifier, and the results implied structural characteristics that are inherent to the specific ILD patterns.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2017

Mass Spectral Library Quality Assurance by Inter-Library Comparison

A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three or more entries for the same compound are compared, the outlier as determined by visual inspection was almost always found to contain the error. These errors were either in the spectrum itself or in the chemical descriptors that accompanied it. The method is demonstrated on finding errors in compounds of forensic interest in the NIST/EPA/NIH Mass Spectral Library. The target list of compounds checked was the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) mass spectral library. Some examples of errors found are described. A checklist of errors that curators should look for when performing inter-library comparisons is provided. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

A mouse model of alcoholic liver fibrosis-associated acute kidney injury identifies key molecular pathways

Clinical data strongly indicate that acute kidney injury (AKI) is a critical complication in alcoholic hepatitis, an acute-on-chronic form of liver failure in patients with advanced alcoholic fibrosis. Development of targeted therapies for AKI in this setting is hampered by the lack of an animal model. To enable research into molecular drivers and novel therapies for fibrosis- and alcohol-associated AKI, we aimed to combine carbon tetrachloride (CCl{sub 4})-induced fibrosis with chronic intra-gastric alcohol feeding. Male C57BL/6J mice were administered a low dose of CCl{sub 4} (0.2 ml/kg 2 × week/6 weeks) followed by alcohol intragastrically (up to 25 g/kg/day for 3 weeks) and with continued CCl{sub 4}. We observed that combined treatment with CCl{sub 4} and alcohol resulted in severe liver injury, more pronounced than using each treatment alone. Importantly, severe kidney injury was evident only in the combined treatment group. This mouse model reproduced distinct pathological features consistent with AKI in human alcoholic hepatitis. Transcriptomic analysis of kidneys revealed profound effects in the combined treatment group, with enrichment for damage-associated pathways, such as apoptosis, inflammation, immune-response and hypoxia. Interestingly, Havcr1 and Lcn2, biomarkers of AKI, were markedly up-regulated. Overall, this study established a novel mouse model of fibrosis- and alcohol-associated AKI and identified key mechanistic pathways. - Highlights: • Acute kidney injury (AKI) is a critical complication in alcoholic hepatitis • We developed a novel mouse model of fibrosis- and alcohol-associated AKI • This model reproduces key molecular and pathological features of human AKI • This animal model can help identify new targeted therapies for alcoholic hepatitis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Quantification of the Electrostatic Effect on Redox Potential by Positive Charges in a Catalyst Microenvironment

Charged functional groups in the secondary coordination sphere (SCS) of a heterogeneous nanoparticle or homogeneous electrocatalyst are of growing interest due to enhancements in reactivity that derive from specific interactions that stabilize substrate binding or charged intermediates. At the same time, accurate benchmarking of electrocatalyst systems most often depends on the development of linear free-energy scaling relationships. Furthermore, the thermodynamic axis in those kinetic–thermodynamic correlations is most often obtained by a direct electrochemical measurement of the catalyst redox potential and might be influenced by electrostatic effects of a charged SCS. In this report, we systematically probe positive charges in a SCS and their electrostatic contributions to the electrocatalyst redox potential. A series of 11 iron carbonyl clusters modified with charged and uncharged ligands was probed, and a linear correlation between the ν CO absorption band energy and electrochemical redox potentials is observed except where the SCS is positively charged.

14 SOLAR ENERGY↗
DOE OSTI2021

Two-Dimensional 2M-WS 2 Nanolayers for Superconductivity

Recently, a newly discovered VIB group transition metal dichalcogenide (TMD) material, 2M-WS 2 , has attracted extensive attention due to its interesting physical properties such as topological superconductivity, nodeless superconductivity, and anisotropic Majorana bound states. However, the techniques to grow high-quality 2M-WS 2 bulk crystals and the study of their physical properties at the nanometer scale are still limited. In this work, we report a new route to grow high-quality 2M-WS 2 single crystals and the observation of superconductivity in its thin layers. The crystal structure of the as-grown 2M-WS 2 crystals was determined by X-ray diffraction (XRD) and scanning tunneling microscopy (STM). The chemical composition of the 2M-WS 2 crystals was determined by energy dispersive X-ray spectroscopy (EDS) analysis. At 77 K, we observed the spatial variation of the local tunneling conductance (dI/dV) of the 2M-WS2 thin flakes by scanning tunneling spectroscopy (STS). Our low temperature transport measurements demonstrate clear signatures of superconductivity of a 25 nm-thick 2M-WS 2 flake with a critical temperature (T C ) of ~8.5 K and an upper critical field of ~2.5 T at T = 1.5 K. Our work may pave new opportunities in studying the topological superconductivity at the atomic scale in simple 2D TMD materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

NEUWAVE-12 at ESS: Workshop Series on Wavelength Dependent Neutron Imaging Back in Full Swing

The NEUWAVE workshop series, a cornerstone for advancements in energy- or wavelength-resolved neutron imaging, held its 12th meeting at the European Spallation Source (ESS) in Lund from September 1 to 5, 2024. The participants can be seen in Figure 1 during the site visit. The series focuses on developments in techniques using phenomena such as Bragg-edges, incoherent and inelastic scattering, or neutron absorption resonances as contrast mechanisms and is therefore far more specialized than more general conferences for neutron imaging such as the WCNR or ITMNR series [Citation1]. After a break during the pandemic and record attendance at NEUWAVE-11 in Tokyo in 2023, which underscored the immense interest in wavelength dependent neutron imaging, NEUWAVE returned to its roots with a focus on a smaller group of specialists meeting in a workshop format, allowing for in-depth discussions and the exchange of new ideas.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

Small molecule annotation for the Protein Data Bank

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100 000 structures contain more than 20 000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genomic insights into local adaptation and migration success in reintroduced Coho Salmon of the Wenatchee River basin

ABSTRACT Objective Reintroduction of salmonids into regions where they have been extirpated is a common conservation strategy that is often implemented through natural recolonization, translocation of natural populations, or hatchery-based programs. Locally adapting to specific environmental conditions is critical for long-term population viability, particularly for species like Coho Salmon Oncorhynchus kisutch, which face diverse selective pressures during their migration. This study focused on the mid-Columbia River Coho Salmon reintroduction program managed by Yakama Nation Fisheries, which has successfully reintroduced Coho Salmon into the Wenatchee and Methow River basins, Washington. Notably, these populations have adapted to the longer migration route than those in the founding stock, with selection favoring individuals with an earlier arrival time and that can navigate a 15-km, high-gradient canyon to reach optimal spawning grounds. The objectives of this study were to investigate whether specific genomic regions are under selection for traits associated with return location and timing in Coho Salmon. Methods Low-coverage whole-genome resequencing data were used to screen for genomic regions associated with the phenotypes of interest. Results A weak polygenic signal in female Coho Salmon was found to be associated with return group, with a subset of candidate adaptive regions occurring across eight chromosomes. Conclusions These findings provide insights into the genomic mechanisms underlying local adaptation in reintroduced salmon populations and inform broodstock selection strategies aimed at promoting natural production and long-term population sustainability.

Horn, Rebekah L.↗