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At least 271 records · Page 15

Expression of the Acyl-Coenzyme A: Cholesterol Acyltransferase GFP Fusion Protein in Sf21 Insect Cells

The enzyme acyl-coenzyme A:cholesterol acyltransferase (ACAT) is an important contributor to the pathological expression of plaque leading to artherosclerosis n a major health problem. Adequate knowledge of the structure of this protein will enable pharmaceutical companies to design drugs specific to the enzyme. ACAT is a membrane protein located in the endoplasmic reticulum.t The protein has never been purified to homogeneity.T.Y. Chang's laboratory at Dartmouth College provided a 4-kb cDNA clone (K1) coding for a structural gene of the protein. We have modified the gene sequence and inserted the cDNA into the BioGreen His Baculovirus transfer vector. This was successfully expressed in Sf2l insect cells as a GFP-labeled ACAT protein. The advantage to this ACAT-GFP fusion protein (abbreviated GCAT) is that one can easily monitor its expression as a function of GFP excitation at 395 nm and emission at 509 nm. Moreover, the fusion protein GCAT can be detected on Western blots with the use of commercially available GFP antibodies. Antibodies against ACAT are not readily available. The presence of the 6xHis tag in the transfer vector facilitates purification of the recombinant protein since 6xHis fusion proteins bind with high affinity to Ni-NTA agarose. Obtaining highly pure protein in large quantities is essential for subsequent crystallization. The purified GCAT fusion protein can readily be cleaved into distinct GFP and ACAT proteins in the presence of thrombin. Thrombin digests the 6xHis tag linking the two protein sequences. Preliminary experiments have indicated that both GCAT and ACAT are expressed as functional proteins. The ultimate aim is to obtain large quantities of the ACAT protein in pure and functional form appropriate for protein crystal growth. Determining protein structure is the key to the design and development of effective drugs. X-ray analysis requires large homogeneous crystals that are difficult to obtain in the gravity environment of earth. Protein crystals grown in microgravity are often larger and have fewer defects than those grown on earth. The analysis of higher quality space-grown crystals will assist in structure-based drug design. We have successfully grown GCAT-infected Sf21 cells in both adhesion and suspension cultures. Expression levels of GCAT in cell lines such as Sf9 and High Five appear to be reduced. We intend to replicate GCAT expression in all three cell lines using the NASA rotating wall bioreactor which effectively duplicates a microgravity environment. The bioreactor itself could be launched to study the expression of the GFP and GCAT proteins in the actual microgravity environment achieved in orbit.

Mahtani, H. K.↗

Global droughts connected by linkages between drought hubs

Abstract Quantifying the spatial and interconnected structure of regional to continental scale droughts is one of the unsolved global hydrology problems, which is important for understanding the looming risk of mega-scale droughts and the resulting water and food scarcity and their cascading impact on the worldwide economy. Using a Complex Network analysis, this study explores the topological characteristics of global drought events based on the self-calibrated Palmer Drought Severity Index. Event Synchronization is used to measure the strength of association between the onset of droughts at different spatial locations within the time lag of 1-3 months. The network coefficients derived from the synchronization network indicate a highly heterogeneous connectivity structure underlying global drought events. Drought hotspot regions such as Southern Europe, Northeast Brazil, Australia, and Northwest USA behave as drought hubs that synchronize regionally and with other hubs at inter-continental or even inter-hemispheric scale. This observed affinity among drought hubs is equivalent to the ‘rich-club phenomenon’ in Network Theory, where ‘rich’ nodes (here, drought hubs) are tightly interconnected to form a club, implicating the possibility of simultaneous large-scale droughts over multiple continents.

54 ENVIRONMENTAL SCIENCES↗

A systems analysis of the erythropoietic responses to weightlessness. Volume 2: Description of the model of erythropoiesis regulation. Part A: Model for regulation of erythropoiesis. Part B: Detailed description of the model for regulation of erythropoiesis

A mathematical model of the erythropoiesis on total red blood cell mass is presented. The loss of red cell mass has been a consistent finding during space flight. Computer simulation of this phenomenon required a model that could account for oxygen transport, red cell production, and red cell destruction. The elements incorporated into the feedback regulation loop of the model are based on the accepted concept that erythrocyte production is governed by the balance between oxygen supply and demand in the body. The mechanisms and pathways of the control circuit include oxygenation of hemoglobin and oxygenation of tissues by blood transport and diffusional processes. Other features of the model include a variable oxygen-hemoglobin affinity, and time delays which represent time for erythropoietin (erythrocyte-stimulating hormone) distribution in plasma, and time for maturation of the erythrocytes in bone marrow.

Leonard, J. I.↗

ZrN coating as diffusion barrier in U(Mo) dispersion fuel systems

The control of the interaction between the U(Mo) fuel phase and the Al matrix is one of the challenges of dispersion fuel plate development for research reactors. Given the specific properties of this interaction layer, larger amounts of it in the meat could lead to a reduction of the plate mechanical integrity and thermal conductivity, eventually leading to pillowing. The SELENIUM project showed that by depositing a ZrN coating on the surface of the U(Mo) fuel particles, the amount of formed U(Mo)-Al interaction layer is limited but still present. Microstructural analysis performed on the as fabricated coating and fresh fuel plates containing ZrN coated U(Mo) dispersed in an Al matrix, revealed that the coating gets damaged during plate production. The post irradiation examinations (PIE) of the ZrN coated U(Mo) fuel plates, from the SELENIUM and SEMPER FIDELIS experiments, show how the U(Mo)-Al interaction layer is formed -only at those locations where the coating is missing or damaged -and the evolution of coating microstructure during irradiation. Finally, as a remedy, to further reduce the amount of interaction layer formed, the use of an Al-Si matrix was proposed based on the higher affinity of Si for U compared to the affinity of Al for U. PIE of a fuel plate consisting of ZrN coated U(Mo) dispersed in an Al-Si matrix irradiated in the SEMPER FIDELIS experiment, clearly demonstrates the benefit of adding Si to the matrix.

36 MATERIALS SCIENCE↗

Influence of Aqueous Phase Acidity on Ln(III) Coordination by N , N , N ', N '-Tetraoctyldiglycolamide

Here, this study highlights the importance of combining distribution ratio measurements with multiple spectroscopic techniques to provide a more comprehensive understanding of organic phase Ln coordination chemistry. Solvent extraction investigations with N,N,N',N'-tetraoctyldiglycolamide (TODGA) in n-heptane reveal the sensitivity of Ln complexation to the HNO 3 concentration. Distribution ratio measurements in tandem with UV–Vis demonstrated that increasing the concentration of HNO3 above 0.5 M with a constant NO 3 – of 1 M increases the number of coordinating TODGA molecules, from a 1:2 to a 1:3 Ln:TODGA complex. At each concentration of HNO 3 considered herein (from 0.01 to 1 M), Eu lifetime analysis demonstrated no evidence of H 2 O coordination. Results from Fourier transform infrared investigations suggest the presence of inner-sphere NO 3 – under low concentrations of HNO 3 when the 1:2 Ln:TODGA complex is present. Increasing the HNO 3 concentration above 0.5 M increases the propensity for outer-sphere interactions by removing the coordinated NO 3 – and saturating the Ln coordination sphere with three TODGA molecules, resulting in the well-established cationic, trischelate homoleptic [Ln(TODGA) 3 ] 3+ complex. This work demonstrates the importance in considering the NO 3 – source for solvent extraction systems. In particular, for systems with an affinity for outer-sphere interactions with molar concentrations of HNO 3 , changing the NO 3 – source can change the inner-sphere coordination of the Ln complex, which, in turn, affects the separation efficacy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Label-free single-vesicle based surface enhanced Raman spectroscopy: A robust approach for investigating the biomolecular composition of small extracellular vesicles

Small extracellular vesicles (sEVs) are cell-released vesicles ranging from 30-150nm in size. They have garnered increasing attention because of their potential for both the diagnosis and treatment of disease. The diversity of sEVs derives from their biological composition and cargo content. Currently, the isolation of sEV subpopulations is primarily based on bio-physical and affinity-based approaches. Since a standardized definition for sEV subpopulations is yet to be fully established, it is important to further investigate the correlation between the biomolecular composition of sEVs and their physical properties. In this study, we employed a platform combining single-vesicle surface-enhanced Raman spectroscopy (SERS) and machine learning to examine individual sEVs isolated by size-exclusion chromatography (SEC). The biomolecular composition of each vesicle examined was reflected by its corresponding SERS spectral features (biomolecular “fingerprints”), with their roots in the composition of their collective Raman-active bonds. Origins of the SERS spectral features were validated through a comparative analysis between SERS and mass spectrometry (MS). SERS fingerprinting of individual vesicles was effective in overcoming the challenges posed by EV population averaging, allowing for the possibility of analyzing the variations in biomolecular composition between the vesicles of similar and/or different sizes. Using this approach, we uncovered that each of the size-based fractions of sEVs contained particles with predominantly similar SERS spectral features. Indeed, more than 84% of the vesicles residing within a particular group were clearly distinguishable from that of the other EV sub-populations, despite some spectral variations within each sub-population. Our results suggest the possibility that size-based EV fractionation methods produce samples where similarly eluted sEVs are correlated with their respective biochemical contents, as reflected by their SERS spectra. Our findings therefore highlight the possibility that the biogenesis and respective biological functionalities of the various sEV fractions may be inherently different.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Arabidopsis fad4 mutant analysis provides insights into thermo sensing within plant plasma membrane

Increasing evidence suggests that the plasma membrane is the initial site for temperature sensing. In searching for the contributions of membrane lipids to stress-induced cytosolic calcium, we found that FATTY ACID DESATURASE 4 (FAD4) knockout mutant exhibited an elevated acute cytosolic calcium spike in response to heat shock or oxidative stress, but not cold shock. fad4 mutant plants are more tolerant to heat stress but less tolerant to cold or high light stress. Lipidomic profiling demonstrated that overall phosphatidylglycerol (PG) levels, specifically, PG (36:7) levels, were reduced in the plasma membrane of fad4 mutants. Based on liposome binding assays, calcium channel proteins annexin2 and annexin4 showed higher association with fad4 plasma membranes compared to wild type (WT) control. Fat Western analyses indicated that anionic lipids, including phosphatidylserine (PS), phosphatidic acid (PA), and PG, bind to annexin1, 2, 3, and 4 with variable affinity, with PS binding the most tightly and PG the least. These results support the hypothesis that the plasma membrane is the initial site of thermo sensing in Arabidopsis.

annexins↗

Humic Acid Complexation of Th, Hf and Zr in Ligand Competition Experiments: Metal Loading and Ph Effects

The mobility of metals in soils and subsurface aquifers is strongly affected by sorption and complexation with dissolved organic matter, oxyhydroxides, clay minerals, and inorganic ligands. Humic substances (HS) are organic macromolecules with functional groups that have a strong affinity for binding metals, such as actinides. Thorium, often studied as an analog for tetravalent actinides, has also been shown to strongly associate with dissolved and colloidal HS in natural waters. The effects of HS on the mobilization dynamics of actinides are of particular interest in risk assessment of nuclear waste repositories. Here, we present conditional equilibrium binding constants (Kc, MHA) of thorium, hafnium, and zirconium-humic acid complexes from ligand competition experiments using capillary electrophoresis coupled with ICP-MS (CE- ICP-MS). Equilibrium dialysis ligand exchange (EDLE) experiments using size exclusion via a 1000 Damembrane were also performed to validate the CE-ICP-MS analysis. Experiments were performed at pH 3.5-7 with solutions containing one tetravalent metal (Th, Hf, or Zr), Elliot soil humic acid (EHA) or Pahokee peat humic acid (PHA), and EDTA. CE-ICP-MS and EDLE experiments yielded nearly identical binding constants for the metal- humic acid complexes, indicating that both methods are appropriate for examining metal speciation at conditions lower than neutral pH. We find that tetravalent metals form strong complexes with humic acids, with Kc, MHA several orders of magnitude above REE-humic complexes. Experiments were conducted at a range of dissolved HA concentrations to examine the effect of [HA]/[Th] molar ratio on Kc, MHA. At low metal loading conditions (i.e. elevated [HA]/[Th] ratios) the ThHA binding constant reached values that were not affected by the relative abundance of humic acid and thorium. The importance of [HA]/[Th] molar ratios on constraining the equilibrium of MHA complexation is apparent when our estimated Kc, MHA values attained at very low metal loading conditions are compared to existing literature data. Overall, experimental data suggest that the tetravalent transition metal/-actinide-humic acid complexation is important over a wide range of pH values, including mildly acidic conditions, and thus, these complexes should be included in speciation models.

humic acid↗

Pro5 is not essential for the formation of ‘Ni-hook’ in nickel superoxide dismutase

The N-terminus of nickel-dependent superoxide dismutase (NiSOD) forms a structural motif known as the "Ni-hook," where the peptide wraps around the metal to bring cysteine-2 and cysteine-6 into spatial proximity, allowing these residues to coordinate in a cis-geometry. A highly conserved proline-5 residue in the Ni-hook adopts a cis-conformation that is widely considered important for its formation. Herein, we investigate this role by point mutation of Pro5 to alanine. The results obtained show that the variant exhibits wild-type-like redox catalysis and features a Ni(III) center very similar to that found in enzyme. Structural analysis using x-ray absorption spectroscopy of the nickel sites in as-isolated P5A-NiSOD reveals changes in the variant and are consistent with a six-coordinate Ni site with (N/O) 4 S 2 coordination. These changes are attributed to changes in the Ni(II) site structure. Nickel-binding studies using isothermal titration calorimetry reveal two binding events with K d = 25(20) nM, and 250(60) nM. These events are attributed to i) Ni(II) binding to a preformed Ni-hook containing cis-Pro5 and ii) the combination of trans- to cis- isomerization upon Ni(II) binding, respectively. Finally, the higher-affinity binding event is absent in P5A-NiSOD, an observation attributed to the low abundance of the cis-Ala5 isomer in the apo-protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Chlorocobaltate-Enabled Selective Separation of CoCl 2 from Mixed Chloride and Nitrate Salts of Mn, Co, and Ni

Described here is the effect of anionic metalates─chlorocobaltate and nitratocobaltate─on the heat-driven separation of the critical element cobalt from potentially competing transition metal salts. Resins bearing the hexadentate glycolamide receptor L (PS-L) exhibit sorption capacities, Q = 1.33 mmol/g for CoCl 2 and Q = 0.66 mmol/g for Co(NO 3 ) 2 , as inferred from sorption isotherm studies. This trend runs counter to the typical Hofmeister series for anion selectivity. Ion chromatographic analysis of a mixed CoCl 2 /Co(NO 3 ) 2 solution revealed an increase in chloride content from 55 mol % to 90 mol % after a single thermally driven catch-and-release cycle. This chloride-selective behavior was recapitulated in a mixed-metal cation, mixed-anion system containing the chloride and nitrate salts of Mn(II), Co(II), and Ni(II) at near-equimolar concentrations. PS-L also displayed enhanced selectivity for Co using this mixed stock solution as observed by ICP-OES. In contrast, for a nitrate-only solution containing Mn(II), Co(II), and Ni(II), PS-L showed increased affinity for Mn, with its proportion rising from 36.6 mol % to 58.1% after a single catch-and-release cycle. Density functional theory calculations support the suggestion that the enhanced uptake of Co(II) in chloride-rich media arises from the high thermodynamic stability of [CoCl 4 ] 2– , which facilitates its outer-sphere coordination to cationic resin-bound cobalt species. Single crystal X-ray crystallographic analyzes of L•MCl 2 (M = Mn, Co, Ni) and L•M(NO 3 ) 2 (M = Mn, Co) confirmed metal complexation by L in the solid state and the concomitant formation of metalate counteranions. Here, the present study highlights a relatively simple approach for separating cobalt from its transition metal congeners.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of the DNA binding properties of polyomavirus capsid protein

The DNA binding properties of the polyomavirus structural proteins VP1, VP2, and VP3 were studied by Southwestern analysis. The major viral structural protein VP1 and host-contributed histone proteins of polyomavirus virions were shown to exhibit DNA binding activity, but the minor capsid proteins VP2 and VP3 failed to bind DNA. The N-terminal first five amino acids (Ala-1 to Lys-5) were identified as the VP1 DNA binding domain by genetic and biochemical approaches. Wild-type VP1 expressed in Escherichia coli (RK1448) exhibited DNA binding activity, but the N-terminal truncated VP1 mutants (lacking Ala-1 to Lys-5 and Ala-1 to Cys-11) failed to bind DNA. The synthetic peptide (Ala-1 to Cys-11) was also shown to have an affinity for DNA binding. Site-directed mutagenesis of the VP1 gene showed that the point mutations at Pro-2, Lys-3, and Arg-4 on the VP1 molecule did not affect DNA binding properties but that the point mutation at Lys-5 drastically reduced DNA binding affinity. The N-terminal (Ala-1 to Lys-5) region of VP1 was found to be essential and specific for DNA binding, while the DNA appears to be non-sequence specific. The DNA binding domain and the nuclear localization signal are located in the same N-terminal region.

NASA Discipline Cell Biology↗

Crystal structure of MutYX: a novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-oxoguanine recognition sphere

Abstract The [4Fe–4S] cluster is an important cofactor of the base excision repair (BER) adenine DNA glycosylase MutY to prevent mutations associated with 8-oxoguanine (OG). Several MutYs lacking the [4Fe–4S] cofactor have been identified. Phylogenetic analysis shows that clusterless MutYs are distributed in two clades suggesting cofactor loss has occurred in multiple independent evolutionary events. Herein, we determined the first crystal structure of a clusterless MutY complexed with DNA. On the basis of the dramatic structural divergence from canonical MutYs, we refer to this as representative of a clusterless MutY subgroup “MutYX.” Interestingly, MutYX compensates for the missing [4Fe–4S] cofactor to maintain positioning of catalytic residues by expanding a pre-existing α-helix and acquisition of a new α-helix. Surprisingly, MutYX also acquired a new C-terminal domain that uniquely recognizes OG using residues Gln201 and Arg209. Adenine glycosylase assays and binding affinity measurements indicate that Arg209 is the primary residue responsible for OG:A lesion specificity, while Gln201 assists by bridging OG and Arg209. Surprisingly, replacement of Arg209 and Gln201 with Ala increased activity toward G:A mismatches. The MutYX structure serves as an example of devolution, capturing structural features required to retain function in the absence of a metal cofactor considered indispensable.

Trasviña-Arenas, Carlos H [University of Californi↗

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses

We currently understand the carbon cycle in methanogenic environments as trophic interactions revolving around interspecies H 2 transfer between organotrophs and methanogens. However, many H 2 -generating processes are thermodynamically sensitive to H 2 accumulation and can be inhibited by high H 2 concentrations produced by other metabolisms. To uncover how anaerobes combat this H 2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology – methanogenic bioreactors. Through analysis of 15 anaerobic digesters, we recover 1343 high-quality metagenome-assembled genomes (MAGs) and corresponding gene expression profiles for diverse uncultured lineages spanning 66 phyla and reconstruct their individual metabolic capacities. We discover that diverse uncultured organotrophic populations can drive H 2 -sensitive degradation through (i) metabolic coupling with concurrent H 2 -tolerant catabolism, (ii) unprecedented shifts from H 2 generation to CO 2 -reducing formate transfer and cytochrome/pili-mediated direct interspecies electron transfer for avoiding thermodynamic conflict, and (iii) integration of low-concentration O 2 as an ancillary thermodynamics-enhancing electron sink. Archaeal populations in situ support the above processes through novel metabolisms distinct from conventional methanogenesis – high-affinity H 2 oxidation driven by methyl-reducing methanogenesis and concomitant uptake of formate, electrons, and acetate from HS metabolism by Methanothrix. In total, synthesis of omics analyses and eco-thermodynamics reveals overlooked metabolic behavior and interactions of uncultured organisms that address a central issue in methanogenic carbon cycling, thermodynamic conflict among diverse concurrent metabolic processes.

59 BASIC BIOLOGICAL SCIENCES↗

UNESE Data Analysis-Disko Elm Gas Transport Characteristics (NA-22 Quarterly Report)

Recently published papers have demonstrated the impact of sorption mechanisms on gas transport in the subsurface following an underground nuclear explosion. To include sorption processes in the multi-physics models of noble gas production and transport, researchers have conducted experiments of gas sorption in geologic materials and calibrated a linear (Henry’s law) sorption model for all gases in various geologic materials. As a part of Task #4, we requested the experimental data from Sandia Laboratories and derived a dual-mode (Henry’s absorption and Langmuir adsorption) sorption model. The derived model better describes the nonlinear sorption mechanism with much higher fitness with the experimental data. When gas concentrations are relatively low (in the conditions of field experiments or underground nuclear explosions) compared to those used sorption experiments, the nonlinear sorption model can be approximated as a linear sorption model. The equivalent Henry’s constant, which equals the product of Langmuir capacity and affinity, is systematically higher than the literature values. Further analyses and comparison of sorption models are planned in FY2020 Q4 and the sorption model will be coupled in models of nonisothermal multiphase transport for studying noble gas detectability.

58 GEOSCIENCES↗

A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain

Abstract SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5′-TCGGAT-3′) of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

Biochemistry & Molecular Biology↗

Using Ultrasound Image Augmentation and Ensemble Predictions to Prevent Machine-Learning Model Overfitting

Deep learning predictive models have the potential to simplify and automate medical imaging diagnostics by lowering the skill threshold for image interpretation. However, this requires predictive models that are generalized to handle subject variability as seen clinically. Here, we highlight methods to improve test accuracy of an image classifier model for shrapnel identification using tissue phantom image sets. Using a previously developed image classifier neural network—termed ShrapML—blind test accuracy was less than 70% and was variable depending on the training/test data setup, as determined by a leave one subject out (LOSO) holdout methodology. Introduction of affine transformations for image augmentation or MixUp methodologies to generate additional training sets improved model performance and overall accuracy improved to 75%. Further improvements were made by aggregating predictions across five LOSO holdouts. This was done by bagging confidences or predictions from all LOSOs or the top-3 LOSO confidence models for each image prediction. Top-3 LOSO confidence bagging performed best, with test accuracy improved to greater than 85% accuracy for two different blind tissue phantoms. This was confirmed by gradient-weighted class activation mapping to highlight that the image classifier was tracking shrapnel in the image sets. Overall, data augmentation and ensemble prediction approaches were suitable for creating more generalized predictive models for ultrasound image analysis, a critical step for real-time diagnostic deployment.

60 APPLIED LIFE SCIENCES↗

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

We report analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗