A Novel Waveguide Concept for Ultrasonic Thermometry Applications
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Cetiner, Nesrin↗
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The Mechanical Response of High Burnup 17x17 PWR Fuel Rods Under Bending
As a part of the US Department of Energy Office of Nuclear Energy High Burnup Spent Fuel Data Project, Oak Ridge National Laboratory has performed 4pt-bend tests on a series of 17x17 PWR fuel rods that were discharged with rod average burnups between 50 and 60 GWd/MTU. The rods include four different kinds of fuel cladding: standard Zircaloy-4 (Zirc-4), low-tin (LT) Zirc-4, ZIRLO, and M5. Six rods of each type (combining Zirc-4 and LT Zirc-4 as one type) were tested to failure at room temperature and 200 oC. Three of each type experienced a full-length heat treatment cycle from RT to 400 oC to RT with an 8 hr soak at 400 oC to simulate the expected limiting vacuum drying condition, which potentially induces hydride reorientation and causes some annealing of irradiation damage in the cladding. Overall, the fuel rods show significant capacity to deflect in bending and exhibit non-linear deformation before failing. The calculated failure strains range from 1.5% to 3.8%. The simulated vacuum drying heat treatment had the largest effect on fuel rods with ZIRLO and M5 cladding. In both cases the heat treatment caused increases in the plastic strain at failure, suggesting some annealing of irradiation damage is occurring. The finite element modeling of the 4pt bending test assume the pellet is a collection of pellet wedge pieces. The results for the Zircaloy-4 rods suggest that the pellets are bonded to the cladding and friction controls the relative motion of the pellet wedge pieces.
Cantonwine, Paul↗
Evaluating multi-slice ptychography tomography for X-ray imaging
X-ray ptychography typically relies on single-slice reconstruction approaches that assume minimal beam propagation through the specimen. However, this approximation breaks down for thick samples or when using high numerical aperture optics, leading to reconstruction artifacts due to multiple scattering. Multi-slice ptychographic tomography (MSPT) addresses this limitation by explicitly modeling beam propagation through the specimen while reducing angular sampling requirements for tomography, but its performance depends critically on reconstruction parameters and experimental conditions. Here, we systematically evaluate MSPT using numerical simulations and experimental X-ray datasets to understand how factors such as object thickness, optical parameters, and initialization strategies affect reconstruction accuracy. We demonstrate that informed object initialization significantly improves depth resolution and enables accurate projection extension, reducing the angular sampling requirements for tomographic reconstruction. Experimental demonstration confirms that MSPT produces reconstructions with reduced artifacts, establishing it as a robust approach for nanoscale imaging at modern synchrotron facilities.
Luktuke, Amey [Argonne National Laboratory (ANL), ↗
Fidelity-preserving enhancement of ptychography with foundational text-to-image models
Ptychographic phase retrieval enables high-resolution imaging of complex samples but often suffers from artifacts such as grid pathology and multislice crosstalk, which degrade reconstructed images. We propose a plug-and-play (PnP) framework that integrates physics model-based phase retrieval with text-guided image editing using foundational diffusion models. By employing the alternating direction method of multipliers, our approach ensures consensus between data fidelity and artifact removal subproblems, maintaining physical consistency while enhancing image quality. Artifact removal is achieved using a text-guided diffusion image editing method (LEDITS++) with a pre-trained foundational diffusion model, allowing users to specify artifacts for removal in natural language. Demonstrations on simulated and experimental datasets show significant improvements in artifact suppression and structural fidelity, validated by metrics such as peak signal-to-noise ratio and diffraction pattern consistency. This work highlights the combination of text-guided generative models and model-based phase retrieval algorithms as a transferable and fidelity-preserving method for high-quality diffraction imaging.
image editing↗
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management
3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.
59 BASIC BIOLOGICAL SCIENCES↗
Real-time structural motif searching in proteins using an inverted index strategy
Biochemical and biological functions of proteins are the product of both the overall fold of the polypeptide chain, and, typically, structural motifs made up of smaller numbers of amino acids constituting a catalytic center or a binding site that may be remote from one another in amino acid sequence. Detection of such structural motifs can provide valuable insights into the function(s) of previously uncharacterized proteins. Technically, this remains an extremely challenging problem because of the size of the Protein Data Bank (PDB) archive. Existing methods depend on a clustering by sequence similarity and can be computationally slow. We have developed a new approach that uses an inverted index strategy capable of analyzing >170,000 PDB structures with unmatched speed. The efficiency of the inverted index method depends critically on identifying the small number of structures containing the query motif and ignoring most of the structures that are irrelevant. Our approach (implemented at motif.rcsb.org ) enables real-time retrieval and superposition of structural motifs, either extracted from a reference structure or uploaded by the user. Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids.
59 BASIC BIOLOGICAL SCIENCES↗
A Trans -Acting Protein Effect Causes Severe Eye Malformation in the Mp Mouse
Mp is an irradiation-induced mouse mutation associated with microphthalmia, micropinna and hind limb syndactyly. We show that Mp is caused by a 660 kb balanced inversion on chromosome 18 producing reciprocal 3-prime gene fusion events involving Fbn2 and Isoc1. The Isoc1-Fbn2 fusion gene (Isoc1 Mp ) mRNA has a frameshift and early stop codon resulting in nonsense mediated decay. Homozygous deletions of Isoc1 do not support a significant developmental role for this gene. The Fbn2-Isoc1 fusion gene (Fbn2 Mp ) predicted protein consists of the N-terminal Fibrillin-2 (amino acids 1–2646, exons 1– 62) lacking the C-terminal furin-cleavage site with a short out-of-frame extension encoded by the final exon of Isoc1. The Mp limb phenotype is consistent with that reported in Fbn2 null embryos. However, severe eye malformations, a defining feature of Mp, are not seen in Fbn2 null animals. Fibrillin-2 Mp forms large fibrillar structures within the rough endoplasmic reticulum (rER) associated with an unfolded protein response and quantitative mass spectrometry shows a generalised defect in protein secretion in conditioned media from mutant cells. In the embryonic eye Fbn2 is expressed within the peripheral ciliary margin (CM). Mp embryos show reduced canonical Wnt-signalling in the CM – known to be essential for ciliary body development - and show subsequent aplasia of CM-derived structures. We propose that the Mp ‘‘worse-than-null’’ eye phenotype plausibly results from a failure in normal trafficking of proteins that are co-expressed with Fbn2 within the CM. The prediction of similar trans-acting protein effects will be an important challenge in the medical interpretation of human mutations from whole exome sequencing.
59 BASIC BIOLOGICAL SCIENCES↗
Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)
Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (~40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. In conclusion, the Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.
59 BASIC BIOLOGICAL SCIENCES↗
The Initiation of GTP Hydrolysis by the G-Domain of FeoB: Insights from a Transition-State Complex Structure
Abstract not provided
Ash, Miriam-Rose↗
Behavioral and Physiological Changes during Benthic-Pelagic Transition in the Harmful Alga, Heterosigma akashiwo : Potential for Rapid Bloom Formation
Many species of harmful algae transition between a motile, vegetative stage in the water column and a non-motile, resting stage in the sediments. Physiological and behavioral traits expressed during benthic-pelagic transition potentially regulate the timing, location and persistence of blooms. The roles of key physiological and behavioral traits involved in resting cell emergence and bloom formation were examined in two geographically distinct strains of the harmful alga, Heterosigma akashiwo. Physiological measures of cell viability, division and population growth, and cell fatty acid content were made using flow cytometry and gas chromatography – mass spectrometry techniques as cells transitioned between the benthic resting stage and the vegetative pelagic stage. Video-based tracking was used to quantify cell-level swimming behaviors. Data show increased temperature and light triggered rapid emergence from the resting stage and initiated cell swimming. Algal strains varied in important physiological and behavioral traits, including survivorship during life-stage transitions, population growth rates and swimming velocities. Collectively, these traits function as “population growth strategies” that can influence bloom formation. Many resting cells regained the up-swimming capacity necessary to cross an environmentally relevant halocline and the ability to aggregate in near-surface waters within hours after vegetative growth supporting conditions were restored. Using a heuristic model, we illustrate how strain-specific population growth strategies can govern the timescales over which H. akashiwo blooms form. Our findings highlight the need for identification and quantification of strain-specific physiological and behavioral traits to improve mechanistic understanding of bloom formation and successful bloom prediction.
59 BASIC BIOLOGICAL SCIENCES↗
Citing a Data Repository: A Case Study of the Protein Data Bank
The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB’s large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.
59 BASIC BIOLOGICAL SCIENCES↗
Differential Regulation of Duplicate Light-Dependent Protochlorophyllide Oxidoreductases in the Diatom Phaeodactylum tricornutum
Not Available
60 APPLIED LIFE SCIENCES↗
A High-Resolution Crystal Structure of a Psychrohalophilic α–Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface
Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO 2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s.
36 MATERIALS SCIENCE↗
Investigation of protein quaternary structure via stoichiometry and symmetry information
The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators.
59 BASIC BIOLOGICAL SCIENCES↗
Molecular basis of P[II] major human rotavirus VP8* domain recognition of histo-blood group antigens
Initial cell attachment of rotavirus (RV) to specific cell surface glycan receptors, which is the essential first step in RV infection, is mediated by the VP8* domain of the spike protein VP4. Recently, human histo-blood group antigens (HBGAs) have been identified as receptors or attachment factors for human RV strains. RV strains in the P[4] and P[8] genotypes of the P[II] genogroup share common recognition of the Lewis b (Le b ) and H type 1 antigens, however, the molecular basis of receptor recognition by the major human P[8] RVs remains unknown due to lack of experimental structural information. Here, we used nuclear magnetic resonance (NMR) spectroscopy-based titration experiments and NMR-derived high ambiguity driven docking (HADDOCK) methods to elucidate the molecular basis for P[8] VP8* recognition of the Leb (LNDFH I) and type 1 HBGAs. We also used X-ray crystallography to determine the molecular details underlying P[6] recognition of H type 1 HBGAs. Unlike P[6]/P[19] VP8*s that recognize H type 1 HBGAs in a binding surface composed of an α-helix and a β-sheet, referred as the “βα binding site”, the P[8] and P[4] VP8*s bind Le b HBGAs in a previously undescribed pocket formed by the edges of two β-sheets, referred to as the “ββ binding site”. Importantly, the P[8] and P[4] VP8*s retain binding capability to non-Le b type 1 HBGAs using the βα binding site. The presence of two distinct binding sites for Le b and non-Le b HBGA glycans in the P[8] and P[4] VP8* domains suggests host-pathogen co-evolution under structural and functional adaptation of RV pathogens to host glycan polymorphisms. Assessment and understanding of the precise impact of this co-evolutionary process in determining RV host ranges and cross-species RV transmission should facilitate improved RV vaccine development and prediction of future RV strain emergence and epidemics.
59 BASIC BIOLOGICAL SCIENCES↗
Structural Inventory of Great Basin Geothermal Systems and Definition of Favorable Structural Settings
Structural controls of 426 geothermal systems in the Great Basin region including western Nevada, central Nevada, northwestern Nevada, northeastern Nevada, east-central Nevada, eastern California, southern Oregon, and western Utah were analyzed with literature research, air photos, Google Earth imagery, and/or field reviews. Of the systems analyzed, we were able to determine the structural settings of more than 240 sites. The structural catalogue is stored in a master spreadsheet included in this submission. Data components include structural setting, primary fault orientation, presence or absence of Quaternary faulting, reservoir lithology, geothermometry, presence or absence of recent magmatism, and distinguishing blind systems from those that have surface expressions. Systems were cataloged into the following eight major groups, based on the dominant pattern of faulting: - Major normal fault segments (i.e., near displacement maxima). - Fault bends. - Fault terminations or tips. - Step-overs or relay ramps in normal faults. - Fault intersections. - Accommodation zones (i.e., belts of intermeshing oppositely dipping normal faults), - Displacement transfer zones whereby strike-slip faults terminate in arrays of normal faults. - Transtensional pull-aparts. These settings form a hierarchal pattern with respect to fault complexity. - Major normal faults and fault bends are the simplest. - Fault terminations are typically more complex than mid-segments, as faults commonly break up into multiple strands or horsetail near their ends. - A fault intersection is generally more complex, as it generally contains both multiple fault strands and can include discrete dilational quadrants. - A step-over consists of two overlapping fault terminations and thus involves additional complexity, especially where the relay ramp is breached by multiple fault splays between the main overlapping faults and thus contains multiple fault intersections. - Accommodation zones involve further complexity, as they contain multiple fault terminations and fault intersections.
15 GEOTHERMAL ENERGY↗
First Tracer Test After Circulation in Desert Peak 27-15
Following the successful stimulation of Desert Peak target EGS well 27-15, a circulation test was initiated by injecting a conservative tracer (1,5-nds) in combination with a reactive tracer (7-amino-1,3-naphthalene disulfonate). The closest production well 74-21 was monitored over the subsequent several months.
15 GEOTHERMAL ENERGY↗