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Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore

Various proteoforms may be generated from a single gene due to primary structure alterations (PSAs) such as genetic variations, alternative splicing, and post-translational modifications (PTMs). Top-down mass spectrometry is capable of analyzing intact proteins and identifying patterns of multiple PSAs, making it the method of choice for studying complex proteoforms. In top-down proteomics, proteoform identification is often performed by searching tandem mass spectra against a protein sequence database that contains only one reference protein sequence for each gene or transcript variant in a proteome. Because of the incompleteness of the protein database, an identified proteoform may contain unknown PSAs compared with the reference sequence. Proteoform characterization is to identify and localize PSAs in a proteoform. Although many software tools have been proposed for proteoform identification by top-down mass spectrometry, the characterization of proteoforms in identified proteoform-spectrum matches still relies mainly on manual annotation. We propose to use the Modification Identification Score (MIScore), which is based on Bayesian models, to automatically identify and localize PTMs in proteoforms. Experiments showed that the MIScore is accurate in identifying and localizing one or two modifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design and Measurement of a Low-Noise 64-Channels Front-End Readout ASIC for CdZnTe Detectors

Cadmium zinc telluride (CdZnTe) detectors, as one of the principal detectors for the next-generation X-ray and γ-ray imagers, have high energy resolution and supporting electrode patterning in the radiation environment at room-temperature. In the present, a number of internationally renowned research institutions and universities are actively using these detector systems to carry out researches of energy spectrum analysis, medical imaging, materials characterization, high-energy physics, nuclear plant monitoring, and astrophysics. As the most important part of the readout system for the CdZnTe detector, the front-end readout application specific integrated circuit (ASIC) would have an important impact on the performances of the whole detector system. In order to ensure the small signal to noise ratio (SNR) and sufficient range of the output signal, it is necessary to design a front-end readout ASIC with very low noise and very high dynamic range. In addition, radiation hardness should be considered when the detectors are utilized in the space applications and high energy physics experiments. In this paper, we present measurements and performances of a novel multi-channel radiation-hardness low-noise front-end readout ASIC for CdZnTe detectors. The readout circuits in each channel consist of charge sensitive amplifier, leakage current compensation circuit (LCC), CR-RC shaper, S-K filter, inverse proportional amplifier, peak detect and hold circuit (PDH), discriminator and trigger logic, time sequence control circuit and driving buffer. All of 64 readout channels' outputs enter corresponding inputs of a 64 channel multiplexer. The output of the mux goes directly out of the chip via the output buffer. The 64-channel readout ASIC is implemented using the TSMC 0.35 μm mixed-signal CMOS technology. The die size of the prototype chip is 2.7 mm x 8 mm. At room temperature, the equivalent noise level of a typical channel reaches 66 e{sup -} (rms) at zero farad for a power consumption of 8 mW per channel. The linearity error is lower than 1% and the overall gain of the readout channel is 165 V/pC. The crosstalk between the channels is less than 3%. By connecting the readout ASIC to a CdZnTe detector, we obtained a γ-ray spectrum, the energy resolution is 5.1% at the 59.5-keV line of {sup 241}Am source. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

High Resolution Mapping of Bactericidal Monoclonal Antibody Binding Epitopes on Staphylococcus aureus Antigen MntC

The Staphylococcus aureus manganese transporter protein MntC is under investigation as a component of a prophylactic S.aureus vaccine. Passive immunization with monoclonal antibodies mAB 305-78-7 and mAB 305-101-8 produced using MntC was shown to significantly reduce S. aureus burden in an infant rat model of infection. Earlier interference mapping suggested that a total of 23 monoclonal antibodies generated against MntC could be subdivided into three interference groups, representing three independent immunogenic regions. In the current work binding epitopes for selected representatives of each of these interference groups (mAB 305-72-5 – group 1, mAB 305-78-7 – group 2, and mAB 305-101-8 – group 3) were mapped using Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS). All of the identified epitopes are discontinuous, with binding surface formed by structural elements that are separated within the primary sequence of the protein but adjacent in the context of the three-dimensional structure. The approach was validated by co-crystallizing the Fab fragment of one of the antibodies (mAB 305-78-7) with MntC and solving the three-dimensional structure of the complex. X-ray results themselves and localization of the mAB 305-78-7 epitope were further validated using antibody binding experiments with MntC variants containing substitutions of key amino acid residues. These results provided insight into the antigenic properties of MntC and how these properties may play a role in protecting the hostagainst S. aureus infection by preventing the capture and transport of Mn 2+ , a key element that the pathogen uses to evade host immunity.

59 BASIC BIOLOGICAL SCIENCES↗

A NEW CLASS OF NASCENT ECLIPSING BINARIES WITH EXTREME MASS RATIOS

Early B-type main-sequence (MS) stars (M {sub 1} ≈ 5-16 M {sub ☉}) with closely orbiting low-mass stellar companions (q = M {sub 2}/M {sub 1} < 0.25) can evolve to produce Type Ia supernovae, low-mass X-ray binaries, and millisecond pulsars. However, the formation mechanism and intrinsic frequency of such close extreme mass-ratio binaries have been debated, especially considering none have hitherto been detected. Utilizing observations of the Large Magellanic Cloud galaxy conducted by the Optical Gravitational Lensing Experiment, we have discovered a new class of eclipsing binaries in which a luminous B-type MS star irradiates a closely orbiting low-mass pre-MS companion that has not yet fully formed. The primordial pre-MS companions have large radii and discernibly reflect much of the light they intercept from the B-type MS primaries (ΔI {sub refl} ≈ 0.02-0.14 mag). For the 18 definitive MS + pre-MS eclipsing binaries in our sample with good model fits to the observed light-curves, we measure short orbital periods P = 3.0-8.5 days, young ages τ ≈ 0.6-8 Myr, and small secondary masses M {sub 2} ≈ 0.8-2.4 M {sub ☉} (q ≈ 0.07-0.36). The majority of these nascent eclipsing binaries are still associated with stellar nurseries, e.g., the system with the deepest eclipse ΔI {sub 1} = 2.8 mag and youngest age τ = 0.6 ± 0.4 Myr is embedded in the bright H II region 30 Doradus. After correcting for selection effects, we find that (2.0 ± 0.6)% of B-type MS stars have companions with short orbital periods P = 3.0-8.5 days and extreme mass ratios q ≈ 0.06-0.25. This is ≈10 times greater than that observed for solar-type MS primaries. We discuss how these new eclipsing binaries provide invaluable insights, diagnostics, and challenges for the formation and evolution of stars, binaries, and H II regions.

79 ASTRONOMY AND ASTROPHYSICS↗

A Tail Structure Associated with a Protoplanetary Disk around SU Aurigae

We present Atacama Large Millimeter/submillimeter Array observations of the CO (J = 2 − 1) line emission from a protoplanetary disk around T-Tauri star SU Aurigae (hereafter SU Aur). Previous observations in optical and near-infrared wavelengths find a unique structure in SU Aur. One of the highlights of the observational results is that an extended tail-like structure is associated with the disk, indicating mass transfer from or into the disk. Here we report the discovery of the counterpart of the tail-like structure in CO gas extending more than 1000 au long. Based on geometric and kinematic perspectives, both of the disk and the tail-like structure components physically connect to each other. Several theoretical studies predicted the observed tail-like structure via the following possible scenarios: (1) a gaseous stream from the molecular cloud remnant, (2) collision with a (sub)stellar intruder or a gaseous blob from the ambient cloud, and (3) ejection of a planetary or brown dwarf mass object due to gravitational instability via multibody gravitational interaction. Since the tail-like structures associated with the SU Aur disk are a new example following RW Aurigae, some disks may experience the internal or external interaction and drastically lose mass during disk evolution.

79 ASTRONOMY AND ASTROPHYSICS↗

Influence of Carbon and Microbial Community Priming on the Attenuation of Uranium in a Contaminated Floodplain Aquifer

The capacity for subsurface sediments to sequester metal contaminants, such as uranium (U), and retain them after bioremediation efforts are completed is critical to site stewardship. Sediments enriched in natural organic matter are capable of sequestering significant quantities of U, but may also serve as sources to the aquifer, contributing to plume persistence. Two types of sediments were compared to better understand the mechanisms contributing to the sequestration and release of U in the presence of organic matter. Artificially bioreduced sediments were retrieved from a field experimental plot previously stimulated with acetate while naturally bioreduced sediments were collected from a location enriched in organic matter but never subject to acetate amendment. Batch incubations demonstrated that the artificially bioreduced sediments were primed to rapidly remove uranium from the groundwater whereas naturally bioreduced sediments initially released a sizeable portion of sediment U before U(VI)-removal commenced. Column experiments confirmed that U release persisted for 65 pore volumes in naturally bioreduced sediments, demonstrating the sink-source behavior of this sediment. Acetate addition to artificially bioreduced sediments shifted the microbial community from one dominated by sulfate-reducing bacteria within Desulfobacteraceae to the iron-reducing family Geobacteraceae and Firmicutes during U(VI) reduction. In contrast, initial Geobacteraceae communities innaturally reduced sediments were replaced by clone sequences with similarity to opportunistic Pseudomonas spp. during U release, while U(VI) removal occurred concurrent with enrichment of Firmicutes. These investigations stress the importance of characterizing zones with heterogeneous carbon pools at U contaminated sites prior to the determination of a remedial strategy.

Artificially reduced Rifle sediments↗

High-quality draft genome sequence of Gracilimonas tropica CL-CB462 T (DSM 19535 T ), isolated from a Synechococcus culture

Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535 T , was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535 T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project. Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. Finally, the strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535 T did not form spore.

59 BASIC BIOLOGICAL SCIENCES↗

Roles for epigenetics in wood formation and stress response intrees–from basic biology to forest management

Annual model and crop species have been the subject of most epigenetic studies for plants. In contrast to annuals, forest trees persist on natural landscapes and experience environmental variation within and across seasons, years, and decades or even centuries. Most forest trees species are undomesticated and typically grown on variable landscapes with no irrigation or application of agricultural chemicals. Forest trees must thus rely on their inherent ability to alter growth and physiology to mitigate the effects of changing abiotic and biotic stressors. Like other plants, trees have mechanisms encoded in their genomic DNA sequence that can respond directly to stress events such as drought or heat. Hypothetically, it would be highly advantageous to join these mechanisms with a dynamic “memory” of past exposure to stress. It is now well established that annual model and crop plants can establish epigenetic-based memory of stress events that support more rapid and robust response to stress in the future. Here, evidence is discussed for epigenetic regulation and “memory” in two fundamental biological processes in trees, wood formation and abiotic stress response. Wood formation is an ideal trait for epigenetic research in trees, as wood formation is highly responsive to environmental conditions and includes multiple rapid developmental changes as cells adopt distinct fates within complex tissues. This is followed by a discussion of research needs that would provide the foundation for new epigenetic applications for forestry.

Groover, Andrew↗

CHARACTERIZING THE POPULATION OF BRIGHT INFRARED SOURCES IN THE SMALL MAGELLANIC CLOUD

We have used the Infrared Spectrograph (IRS) on the Spitzer Space Telescope to observe stars in the Small Magellanic Cloud (SMC) selected from the Point Source Catalog of the Midcourse Space Experiment (MSX). We concentrate on the dust properties of the oxygen-rich evolved stars. The dust composition has smaller contributions from alumina compared to the Galaxy. This difference may arise from the lower metallicity in the SMC, but it could be a selection effect, as the SMC sample includes more stars that are brighter and thus more massive. The distribution of the SMC stars along the silicate sequence looks more like the Galactic sample of red supergiants than asymptotic giant branch stars (AGBs). While many of the SMC stars are definitively on the AGB, several also show evidence of hot bottom burning. Three of the supergiants show PAH emission at 11.3 μ m. Two other sources show mixed chemistry, with both carbon-rich and oxygen-rich spectral features. One, MSX SMC 134, may be the first confirmed silicate/carbon star in the SMC. The other, MSX SMC 049, is a candidate post-AGB star. MSX SMC 145, previously considered a candidate OH/IR star, is actually an AGB star with a background galaxy at z = 0.16 along the same line of sight. We consider the overall characteristics of all the MSX sources, the most infrared-bright objects in the SMC, in light of the higher sensitivity and resolution of Spitzer , and compare them with the object types expected from the original selection criteria. This population represents what will be seen in more distant galaxies by the upcoming James Webb Space Telescope ( JWST ). Color–color diagrams generated from the IRS spectra and the mid-infrared filters on JWST show how one can separate evolved stars from young stellar objects (YSOs) and distinguish among different classes of YSOs.

79 ASTRONOMY AND ASTROPHYSICS↗

Wood Decomposition: Understanding Processes Regulating Carbon Transfer to Soil Carbon Pools Using FACE Wood at Multiple Scales

Dead wood comprises approximately 20% of forest biomass. While it is widely recognized for its role in ecosystem functions relative to habitat and nutrient cycling, there are considerable uncertainties associated with its role in the forest carbon (C) cycle. The principal uncertainty is whether dead wood contributes to the soil C pool. With little supporting evidence, the presumption is that C in wood is respired back to the atmosphere through decomposition processes. The inability to attribute forest soil C to its source components has been a barrier to addressing this important forest carbon cycle question. The U.S. Dept. of Energy’s Free Air CO 2 Enrichment (FACE) experiment produced wood that has a distinct δ 13 C signature that can be used to trace its fate through organic matter decomposition processes. Using two hardwood species (aspen, birch) from the Rhinelander FACE site and pine from the Duke FACE site, the FACE Wood Decomposition Experiment (FWDE) was established in 2011 to provide the foundation for addressing wood decomposition and its associated processes at the continental scale. Plots were installed on nine experimental forests representing a range in bioclimatic forest conditions within the continental U.S. Each identical plot has logs of the three species incubating on the soil surface and pine logs suspended in the air, representing standing dead wood. Abiotic conditions are monitored continuously, and soil and forest conditions characterized. Logs on the sites have been measured every two years to assess decay. This project was initiated in 2016 with specific objectives to: (a) determine whether dead wood C contributes to the soil C pool, (b) assess the fungal community composition mediating the decay, (c) assess the interactions of termites with microbial decay, and (d) develop a mechanistic model to simulate wood decomposition. The principal field sampling was conducted in 2017; correspondingly, the results reported here represent six years of decomposition. Wood decomposition varied from 13 to 75 % loss across the bioclimatic gradient. Sites in the southeastern U.S. coastal plain and piedmont had fastest decomposition rates for each of the species. In contrast sites in the Rocky Mountains had the slowest decay rates, which were associated with cold temperatures. Standing deadwood decomposes at a much slower rate than logs on the soil surface; a response due to differences in wood moisture content. Wood carbon was measured in the mineral soil across each of the sites; accordingly, this is the first study to affirm that a portion of the wood C does become part of the soil C pool. Averaged across the FWDE sites, approximately 1.4% of the soil C in the upper 10 cm of the mineral soil directly beneath the log was derived from the deadwood; within 50 cm of the log, wood C accounted for an average of 2.1%. These results demonstrate that the contribution of deadwood to the soil C pool is a soil volume surrounding the log; and it’s likely a larger volume than what we sampled. We also hypothesized that there would be more wood C in the mineral soil when termites were present. However, that hypothesis wasn’t supported by measurements on the Santee Experimental Forest termite exclusion (SEF-TX) plots under FACE logs that incubated for 6 years. Across all the sites, the majority of the wood C was transferred to the atmosphere. Approximately 7,000 fungal species were sequenced. The fungal communities were different among each of the sites suggesting local colonization; interestingly, within sites the three species also exhibited differences in fungal community composition. White rot was the dominant fungal form in pine and hardwood, which yields less lignin in the wood residue. Brown rot occurred in approximately 20% of the pine and aspen logs, and it did not occur in birch logs. The occurrence of brown rot was only weakly correlated to site factors. We conducted two additional experiments to assess the effects of termites on wood decomposition and the associated interactions with the fungal community. Pine and birch logs were incubated on the Santee Experimental Forest termite exclusion plots in upland and riparian settings. There was no difference in decay between areas where termites were able colonize and plots where they had been excluded. Highly variable foraging by termites was a primary contributor the result. Correspondingly, fungal communities did not vary on logs incubated among the two treatments, but they did reflect site and species differences. The second experiment was conducted on each of the nine FWDE sites where pine and birch wood blocks were incubated for two years with and without a wrapping designed to exclude termites and other arthropods. The effects of termites on wood decomposition could be confirmed on two of the four sites known to have subterranean termites. On the two southeastern sites, termites contributed approximately 8% to mass loss in pine blocks over two years. A major factor clouding the role of termites in wood decomposition is the inability to assess the time, duration, and intensity of the foraging with the logs. Another uncertainty is related to whether a piece of wood will be foraged. A process-based wood decomposition model was developed representing biological processes mediated by fungi, bacteria, termites, beetles, as well as physical and chemical processes. The Coarse Wood Decomposition Model (CWDM) was parameterized based on a thorough review of the literature and it was validated using data from the FWDE. In the initial setup, the model considers softwoods and hardwoods groups, as opposed to individual species. Sensitivity analyses incorporating climate data from 89 locations in North America demonstrated that CWDM was stable from the tropics to the boreal zone. Model calibration and validation showed it to perform very well. The CWDM is poised for additional testing with subsequent FWDE data as well as other data sets, and it is available for incorporation into forest biogeochemical models or DOEs Earth System Modeling framework.

54 ENVIRONMENTAL SCIENCES↗

Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad Repeat

The N-heptad repeat (NHR) of the HIV-1 gp41 prehairpin intermediate (PHI) is an attractive potential vaccine target with high sequence conservation across diverse strains. However, despite the potency of NHR-targeting peptides and clinical efficacy of the NHR-targeting entry inhibitor enfuvirtide, no potently neutralizing NHR-directed monoclonal antibodies (mAbs) nor antisera have been identified or elicited to date. The lack of potent NHR-binding mAbs both dampens enthusiasm for vaccine development efforts at this target and presents a barrier to performing passive immunization experiments with NHR-targeting antibodies. To address this challenge, we previously developed an improved variant of the NHR-directed mAb D5, called D5_AR, which is capable of neutralizing diverse tier-2 viruses. Building on that work, here we present the 2.7Å-crystal structure of D5_AR bound to NHR mimetic peptide IQN17. We then utilize protein language models and supervised machine learning to generate small (n < 100) libraries of D5_AR variants that are subsequently screened for improved neutralization potency. We identify a variant with 5-fold improved neutralization potency, D5_FI, which is the most potent NHR-directed monoclonal antibody characterized to date and exhibits broad neutralization of tier-2 and −3 pseudoviruses as well as replicating R5 and X4 challenge strains. Additionally, our work highlights the ability of protein language models to efficiently identify improved mAb variants from relatively small libraries.

Biopolymers↗

Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia

The decomposition of dead plant biomass contributes to the carbon cycle and is one of the key processes in temperate forests. While fungi in litter decomposition drive the chemical changes occurring in litter, the bacterial community appears to be important as well, especially later in the decomposition process when its abundance increases. In this paper, we describe the bacterial community composition in live Quercus petraea leaves and during the subsequent two years of litter decomposition. Members of the classes Alpha-, Beta- and Gammaproteobacteria and the phyla Actinobacteria, Bacteroidetes and Acidobacteria were dominant throughout the experiment. Bacteria present in the oak phyllosphere were rapidly replaced by other taxa after leaf senescence. There were dynamic successive changes in community composition, in which the early-stage (months 2-4), mid-stage (months 6-8) and late-stage (months 10-24) decomposer communities could be distinguished, and the diversity increased with time. Bacteria associated with dead fungal mycelium were important during initial decomposition, with sequence relative abundances of up to 40% of the total bacterial community in months 2 and 4 when the highest fungal biomass was observed. Cellulose-decomposing bacteria were less frequent, with abundance ranging from 4% to 15%. The bacterial community dynamics reflects changes in the availability of possible resources either of the plant or microbial origin.

54 ENVIRONMENTAL SCIENCES↗

Subsurface catalysis-mediated selectivity of dehydrogenation reaction

Progress in heterogeneous catalysis is often hampered by the difficulties of constructing active architectures and understanding reaction mechanisms at the molecular level due to the structural complexity of practical catalysts, in particular for multicomponent catalysts. Although surface science experiments and theoretical simulations help understand the detailed reaction mechanisms over model systems, the direct study of the nature of nanoparticle catalysts remains a grand challenge. This paper describes a facile construction of well-defined Pt-skin catalysts modified by different 3d transition metal (3dTM) atoms in subsurface regions. However, on the catalyst containing both surface and subsurface 3dTMs, the selectivity of propane dehydrogenation decreases in the sequences of Pt ~ PtFe > PtCo > PtNi due to the easier C–C cracking on exposed Co and Ni sites. After the exposed 3dTMs were removed completely, the C 3 H 6 selectivity was found to increase markedly in the row Pt < PtNi@Pt < PtCo@Pt < PtFe@Pt, which is in line with the calculated trend of d-band center shifting. The established relationship between reactivity and d-band center shifting illustrates the role of subsurface catalysis in dehydrogenation reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards an informative mutant phenotype for every bacterial gene

Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, in Z. mobilis , most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.

59 BASIC BIOLOGICAL SCIENCES↗

In-beam $$\gamma $$-ray spectroscopy of $$^{94}$$Ag

Abstract A recoil-beta-tagging experiment has been performed to study the excited $$T=0$$ T = 0 and $$T=1$$ T = 1 states in the odd–odd $$N=Z$$ N = Z nucleus $$^{94}$$ 94 Ag, populated via the $$^{40}$$ 40 Ca( $$^{58}$$ 58 Ni,1p3n) $$^{94}$$ 94 Ag reaction. The experiment was conducted using the MARA recoil separator and JUROGAM3 array at the Accelerator Laboratory of the University of Jyväskylä. Through correlating fast, high-energy beta decays at the MARA focal plane with prompt $$\gamma $$ γ rays emitted at the reaction target, a number of transitions between excited states in $$^{94}$$ 94 Ag have been identified. The timing characteristics of these transitions confirm that they fall within decay sequences that feed the short-lived $$T=1$$ T = 1 ground state of $$^{94}$$ 94 Ag. The transitions are proposed to proceed within and between the sets of states with $$T=0$$ T = 0 and $$T=1$$ T = 1 . Possible correspondence between some of these transitions from analog states in $$^{94}$$ 94 Pd has been discussed, and shell-model calculations including multipole and monopole electromagnetic effects have been presented, in order to enable predictions of the decay patterns between the $$T=0$$ T = 0 and $$T=1$$ T = 1 states and to allow a theoretical set of Coulomb energy differences to be calculated for the $$A = 94$$ A = 94 $$T=1$$ T = 1 analog states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Hypomyelinating leukodystrophy-associated missense mutation in HSPD1 blunts mitochondrial dynamics

Myelin-forming glial cells undergo dynamic morphological changes in order to produce mature myelin sheaths with multiple layers. In the central nervous system (CNS), oligodendrocytes differentiate to insulate neuronal axons with myelin sheaths. Myelin sheaths play a key role in homeostasis of the nervous system, but their related disorders lead not only to dismyelination and repeated demyelination but also to severe neuropathies. Hereditary hypomyelinating leukodystrophies (HLDs) are a group of such diseases affecting oligodendrocytes and are often caused by missense mutations of the respective responsible genes. Despite increasing identification of gene mutations through advanced nucleotide sequencing technology, studies on the relationships between gene mutations and their effects on cellular and subcellular aberrance have not followed at the same rapid pace. In this study, we report that an HLD4-associated (Asp-29-to-Gly) mutant of mitochondrial heat shock 60-kDa protein 1 (HSPD1) causes short-length morphologies and increases the numbers of mitochondria due to their aberrant fission and fusion cycles. In experiments using a fluorescent dye probe, this mutation decreases the mitochondrial membrane potential. Also, mitochondria accumulate in perinuclear regions. HLD4-associated HSPD1 mutant blunts mitochondrial dynamics, probably resulting in oligodendrocyte malfunction. This study constitutes a first finding concerning the relationship between disease-associated HSPD1 mutation and mitochondrial dynamics, which may be similar to the relationship between another disease-associated HSPD1 mutation (MitCHAP-60 disease) and aberrant mitochondrial dynamics. - Highlights: • The HLD4 mutant of HSPD1 decreases mitochondrial fission frequency. • The HLD4 mutant decreases mitochondrial fusion frequency. • Mitochondria harboring the HLD4 mutant exhibit slow motility. • The HLD4 mutant of HSPD1 decreases mitochondrial membrane potential. • HLD4-related diseases may be due to decreased mitochondrial dynamics.

60 APPLIED LIFE SCIENCES↗

Frhodo: A program for simulating chemical kinetic measurements and optimizing kinetic mechanisms

Chemical kinetic simulations are frequently used to extract kinetic and mechanistic information from experimental data by fitting simulations to the data. For simple systems of consecutive single channel reactions this is a relatively straightforward task. However, as the complexity of the system increases and particularly for systems involving competitive multi-channel reactions manually optimizing a mechanism to obtain the best fits to a range of experimental data quickly becomes a time-intensive and challenging process, especially when rate coefficients have pressure and temperature dependencies. There is considerable potential for exploiting automated optimization methods to rapidly screen reaction mechanisms and optimize the fit by adjusting rate coefficients within well-defined constraints. A new chemical kinetics simulation program, Frhodo, has been developed for this purpose. The program allows either manual simulation of individual experiments or fully automated optimization against a range of experimental data by adjusting user selected reactions within user defined constraints. Frhodo incorporates machine learning-based optimization routines that work by either minimizing standardized residuals or through Bayesian parameter estimation. Frhodo's optimization capabilities are demonstrated by reexamining two previously studied systems of relevance to combustion. Dissociation of diacetyl followed by recombination of methyl radicals is an example of a sequence of single channel, consecutive reactions. Pyrolysis of 2-methyl furan exemplifies multi-channel, unimolecular reactions that are often encountered and have temperature and pressure dependencies in the rate coefficients of the channels and branching ratios between them. For both systems the optimization routines resulted in solutions similar to the original studies. Finally, comments are made on the strengths and limitations of the approach.

0D simulation↗

Pressure-induced isostructural phase transition and charge transfer in superconducting FeSe

Here, we present extensive investigations of the crystallographic phase diagram and electronic properties of the Fe-based superconductor FeSe under extreme conditions (high pressure (HP) and low temperature (LT)) by synchrotron X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS). An isostructural phase transition (Tetragonal (T) →high-pressure Tetragonal (T')) is discovered in FeSe at ~2.8 GPa based on the axial ratio c/a with finer pressure step as observed in Fe-As-based superconductor such as EuFe 2 As 2 . We also find a pressure-induced T' → MnP-type phase transition at 7.6 GPa in FeSe, which is consistent with the documented pressure-induced high-spin → low-spin transition (~6–7 GPa). These results reveal the pressure-induced structural phase transition sequence in FeSe at room temperature to be T → T' → T'+MnP-type at pressures of 0–10.6 GPa, enriching the crystallographic phase diagram. The HPLT XRD data also indicate that a sluggish structural phase transition ( Cmma → Pnma ) begins at 7.5 GPa, and these two phases coexist up to 26.5 GPa. The HP X-ray absorption near-edge spectroscopy (XANES) measurement shows that E o of Se experiences a pressure-induced shift to high energy, evidencing strongly charge transfer between Fe and Se under high pressure. Our results shed lights on the correlation between crystallographic/electronic structure and superconductivity in this material.

36 MATERIALS SCIENCE↗