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At least 73 records · Page 4

Structure-function analysis of the FCRL5–IgG1 Fc complex reveals an unappreciated pathway for B cell modulation by Fc-attenuated IgG

The Fc region of therapeutic IgG antibodies is often engineered to remove or “silence” Fc effector functions, but it remains unclear whether these mutations eliminate all Fc-mediated effector activity. Human Fc receptor-like 5 (FCRL5/FcRH5) is a low-affinity IgG Fc receptor expressed on B cells and is an actively pursued antibody target in multiple myeloma. Here, we show that common Fc function-silencing mutations do not impair FCRL5-mediated activity and therefore attenuate, rather than eliminate, Fc effector function. The crystal structure of the FCRL5-IgG1 Fc complex, solved at 3.4 Å resolution, revealed that FCRL5 binds IgG1 Fc in a 1:1 complex through a binding mode distinct from that of classical Fcγ receptors, explaining why mutations that attenuate Fc effector function spare FCRL5 binding. Fc-engineered antibodies that selectively engage FCRL5 inhibited B cell receptor-induced Ca 2+ flux in FCRL5-expressing B cells. These findings demonstrate that Fc-attenuated therapeutic IgG retains the ability to engage FCRL5, identifying an unappreciated pathway for B cell modulation.

Herpers, Bart M. [Department of Biomedical Enginee↗

Structure-function analysis of microRNA 3'-end trimming by Nibbler

Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr’s N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in Drosophila S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of A. aegypti and Drosophila melanogaster Nbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr’s EXO domain exhibits Mn2+-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'-O-methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of Time Window and Spectral Measurement Options on Empirical Green’s Function Analysis Using DAS Array and Seismic Stations

The recorded seismic waveform is a convolution of event source term, path term, and station term. Removing high-frequency attenuation due to path effect is a challenging problem. Empirical Green’s function (EGF) method uses nearly collocated small earthquakes to correct the path and station terms for larger events recorded at the same station. However, this method is subject to variability due to many factors. Here, we focus on three events that were well recorded by the seismic network and a rapid response distributed acoustic sensing (DAS) array. Using a suite of high-quality EGF events, we assess the influence of time window, spectral measurement options, and types of data on the spectral ratio and relative source time function (RSTF) results. Increased number of tapers (from 2 to 16) tends to increase the measured corner frequency and reduce the source complexity. Extended long time window (e.g., 30 s) tends to produce larger variability of corner frequency. The multitaper algorithm that simultaneously optimizes both target and EGF spectra produces the most stable corner-frequency measurements. The stacked spectral ratio and RSTF from the DAS array are more stable than two nearby seismic stations, and are comparable to stacked results from the seismic network, suggesting that DAS array has strong potential in source characterization.

58 GEOSCIENCES↗

Python wrapper library and analysis functions for Geotab Altitude API [SWR-24-77]

This software library serves as a Python wrapper for Geotab's Altitude API. It streamlines querying of the API, converts loosely structured API outputs into a standardized tabular data format, and enables analysis of the resulting data tables. It also includes example notebooks showing how to use the library.

Bruchon, Matthew↗

Transfer function analysis of the autonomic response to respiratory activity during random interval breathing

We report a new method for the noninvasive characterization of the frequency response of the autonomic nervous system (ANS) in mediating fluctuations in heart rate (HR). The approach entails computation of the transfer function magnitude and phase between instantaneous lung volume and HR. Broad band fluctuations in lung volume were initiated when subjects breathed on cue to a sequence of beeps spaced randomly in time. We studied 10 subjects in both supine and standing positions. The transfer function, averaged among all the subjects, showed systematic differences between the two postures, reflecting the differing frequency responses of the sympathetic and parasympathetic divisions of the ANS.

Non-NASA Center↗

Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis

Background: Investigators using metagenomic sequencing to study microbiomes often trim and decontaminate reads without knowing their effect on downstream analyses. Objective: This study was designed to evaluate the impacts JGI trimming and decontamination procedures have on assembly and binning metrics, placement of MAGs into species trees, and functional profiles of MAGs extracted from complex rhizosphere metagenomes, as well as how more aggressive trimming impacts these binning metrics. Methods: Twenty-three Miscanthus x giganteus rhizosphere metagenomes were subjected to different combinations and thresholds of force, kmer, and quality trimming and decontamination using BBDuk. Reads were assembled and binned in KBase. Phylogenomic and statistical analyses were applied to evaluate the effects of trimming and decontamination on downstream analyses. Results: We found that JGI trimmed and decontaminated reads had significant impacts on assembly and binning metrics compared to raw reads, including significantly higher total contig counts, more contigs greater than 10k bp in length, and larger total lengths of raw assemblies compared to QC assemblies, and 2.0% lower average contamination of QC MAGs compared to raw MAGs. We also found that differences in the placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. Furthermore, aggressive trimming (Q20) was found to significantly reduce MAG counts. Conclusion: Trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing?” However, mild trimming and decontamination of metagenomic reads with high-quality scores are recommended for removing sample processing and sequencing artifacts.

Whitham, Jason M.↗

Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans

Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of double-strand breaks in the mutant cells, triggering death of vulnerable brain cells—a potential cause of neurodegeneration in AOA4 patients.

59 BASIC BIOLOGICAL SCIENCES↗

Application of functional analysis to perturbation theory of differential equations

The deviation of the solution of the differential equation y' = f(t, y), y(O) = y sub O from the solution of the perturbed system z' = f(t, z) + g(t, z), z(O) = z sub O was investigated for the case where f and g are continuous functions on I x R sup n into R sup n, where I = (o, a) or I = (o, infinity). These functions are assumed to satisfy the Lipschitz condition in the variable z. The space Lip(I) of all such functions with suitable norms forms a Banach space. By introducing a suitable norm in the space of continuous functions C(I), introducing the problem can be reduced to an equivalent problem in terminology of operators in such spaces. A theorem on existence and uniqueness of the solution is presented by means of Banach space technique. Norm estimates on the rate of growth of such solutions are found. As a consequence, estimates of deviation of a solution due to perturbation are obtained. Continuity of the solution on the initial data and on the perturbation is established. A nonlinear perturbation of the harmonic oscillator is considered a perturbation of equations of the restricted three body problem linearized at libration point.

Bogdan, V. M.↗

Research study on stabilization and control: Modern sampled-data control theory. Continuous and discrete describing function analysis of the LST system

The dynamics of the Large Space Telescope (LST) control system were studied in order to arrive at a simplified model for computer simulation without loss of accuracy. The frictional nonlinearity of the Control Moment Gyroscope (CMG) Control Loop was analyzed in a model to obtain data for the following: (1) a continuous describing function for the gimbal friction nonlinearity; (2) a describing function of the CMG nonlinearity using an analytical torque equation; and (3) the discrete describing function and function plots for CMG functional linearity. Preliminary computer simulations are shown for the simplified LST system, first without, and then with analytical torque expressions. Transfer functions of the sampled-data LST system are also described. A final computer simulation is presented which uses elements of the simplified sampled-data LST system with analytical CMG frictional torque expressions.

Kuo, B. C.↗

Functional analysis of the methylerythritol phosphate pathway terminal enzymes IspG and IspH from Zymomonas mobilis

ABSTRACT Isoprenoids are a diverse family of compounds that are synthesized from two isomeric compounds, isopentenyl diphosphate and dimethylallyl diphosphate. In most bacteria, isoprenoids are produced from the essential methylerythritol phosphate (MEP) pathway. The terminal enzymes of the MEP pathway IspG and IspH are [4Fe-4S] cluster proteins, and in Zymomonas mobilis, the substrates of IspG and IspH accumulate in cells in response to O 2 , suggesting possible lability of their [4Fe-4S] clusters. Here, we show using complementation assays in Escherichia coli that even under anaerobic conditions, Z. mobilis IspG and IspH are not as functional as their E. coli counterparts, requiring higher levels of expression to rescue viability. A deficit of the sulfur utilization factor (SUF) Fe-S cluster biogenesis pathway did not explain the reduced function of Z. mobilis IspG and IspH since no improvement in viability was observed in E. coli expressing the Z. mobilis SUF pathway or having increased expression of the E. coli SUF pathway. Complementation of single and double mutants with various combinations of Z. mobilis and E. coli IspG and IspH indicated that optimal growth required the pairing of IspG and IspH from the same species. Furthermore, Z. mobilis IspH conferred an O 2 -sensitive growth defect to E. coli that could be partially rescued by co-expression of Z. mobilis IspG. In vitro analysis showed O 2 sensitivity of the [4Fe-4S] cluster of both Z. mobilis IspG and IspH. Altogether, our data indicate an important role of the cognate protein IspG in Z. mobilis IspH function under both aerobic and anaerobic conditions. IMPORTANCE Isoprenoids are one of the largest classes of natural products, exhibiting diversity in structure and function. They also include compounds that are essential for cellular life across the biological world. In bacteria, isoprenoids are derived from two precursors, isopentenyl diphosphate and dimethylallyl diphosphate, synthesized primarily by the methylerythritol phosphate pathway. The aerotolerant Z. mobilis has the potential for methylerythritol phosphate pathway engineering by diverting some of the glucose that is typically efficiently converted into ethanol to produce isoprenoid precursors to make bioproducts and biofuels. Our data revealed the surprising finding that Z. mobilis IspG and IspH need to be co-optimized to improve flux via the methyl erythritol phosphate pathway in part to evade the oxygen sensitivity of IspH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Two-Flux Green's Function Analysis for Transient Spectral Radiation in a Composite

An analysis is developed for obtaining transient temperatures in a two-layer semitransparent composite with spectrally dependent properties. Each external boundary of the composite is subjected to radiation and convection. The two-flux radiative transfer equations are solved by deriving a Green's function. This yields the local radiative heat source needed to numerically solve the transient energy equation. An advantage of the two-flux method is that isotropic scattering is included without added complexity. The layer refractive indices are larger than one. This produces internal reflections at the boundaries and the internal interface; the reflections are assumed diffuse. Spectral results using the Green's function method are verified by comparing with numerical solutions using the exact radiative transfer equations. Transient temperature distributions are given to illustrate the effect of radiative heating on one side of a composite with external convective cooling. The protection of a material from incident radiation is illustrated by adding scattering to the layer adjacent to the radiative source.

Siegel, Robert↗

Transfer function analysis of dynamic cerebral autoregulation in humans

To test the hypothesis that spontaneous changes in cerebral blood flow are primarily induced by changes in arterial pressure and that cerebral autoregulation is a frequency-dependent phenomenon, we measured mean arterial pressure in the finger and mean blood flow velocity in the middle cerebral artery (VMCA) during supine rest and acute hypotension induced by thigh cuff deflation in 10 healthy subjects. Transfer function gain, phase, and coherence function between changes in arterial pressure and VMCA were estimated using the Welch method. The impulse response function, calculated as the inverse Fourier transform of this transfer function, enabled the calculation of transient changes in VMCA during acute hypotension, which was compared with the directly measured change in VMCA during thigh cuff deflation. Beat-to-beat changes in VMCA occurred simultaneously with changes in arterial pressure, and the autospectrum of VMCA showed characteristics similar to arterial pressure. Transfer gain increased substantially with increasing frequency from 0.07 to 0.20 Hz in association with a gradual decrease in phase. The coherence function was > 0.5 in the frequency range of 0.07-0.30 Hz and < 0.5 at < 0.07 Hz. Furthermore, the predicted change in VMCA was similar to the measured VMCA during thigh cuff deflation. These data suggest that spontaneous changes in VMCA that occur at the frequency range of 0.07-0.30 Hz are related strongly to changes in arterial pressure and, furthermore, that short-term regulation of cerebral blood flow in response to changes in arterial pressure can be modeled by a transfer function with the quality of a high-pass filter in the frequency range of 0.07-0.30 Hz.

NASA Discipline Cardiopulmonary↗

Correlation Function Analysis of Fiber Networks: Implications for Thermal Conductivity

The heat transport in highly porous fiber structures is investigated. The fibers are supposed to be thin, but long, so that the number of the inter-fiber connections along each fiber is large. We show that the effective conductivity of such structures can be found from the correlation length of the two-point correlation function of the local conductivities. Estimation of the parameters, determining the conductivity, from the 2D images of the structures is analyzed.

Martinez-Garcia, Jorge↗

Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination

Abstract The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate Salix in tissue culture, previous studies investigating the mechanisms regulating sex in the genus Salix have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow Salix purpurea . Six candidate master regulator genes for sex determination were heterologously expressed in Arabidopsis, followed by floral proteome analysis. In addition, 11 transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP‐Seq in both male and female S. purpurea DNA. The results of this study provide further evidence to support models for the roles of ARR17 and GATA15 as master regulator genes of sex determination in S. purpurea , contributing to a regulatory system that is notably different from that of its sister genus Populus . Evidence was also obtained for the roles of two transcription factors, an AP2 / ERF family gene and a homeodomain‐like transcription factor, in downstream regulation of sex dimorphism.

60 APPLIED LIFE SCIENCES↗

Transfer function analysis of thermospheric perturbations

Applying perturbation theory, a spectral model in terms of vectors spherical harmonics (Legendre polynomials) is used to describe the short term thermospheric perturbations originating in the auroral regions. The source may be Joule heating, particle precipitation or ExB ion drift-momentum coupling. A multiconstituent atmosphere is considered, allowing for the collisional momentum exchange between species including Ar, O2, N2, O, He and H. The coupled equations of energy, mass and momentum conservation are solved simultaneously for the major species N2 and O. Applying homogeneous boundary conditions, the integration is carred out from the Earth's surface up to 700 km. In the analysis, the spherical harmonics are treated as eigenfunctions, assuming that the Earth's rotation (and prevailing circulation) do not significantly affect perturbations with periods which are typically much less than one day. Under these simplifying assumptions, and given a particular source distribution in the vertical, a two dimensional transfer function is constructed to describe the three dimensional response of the atmosphere. In the order of increasing horizontal wave numbers (order of polynomials), this transfer function reveals five components. To compile the transfer function, the numerical computations are very time consuming (about 100 hours on a VAX for one particular vertical source distribution). However, given the transfer function, the atmospheric response in space and time (using Fourier integral representation) can be constructed with a few seconds of a central processing unit. This model is applied in a case study of wind and temperature measurements on the Dynamics Explorer B, which show features characteristic of a ringlike excitation source in the auroral oval. The data can be interpreted as gravity waves which are focused (and amplified) in the polar region and then are reflected to propagate toward lower latitudes.

Mayr, H. G.↗

Towards Fully Secure 5G Ultra-Low Latency Communications: A Cost-Security Functions Analysis

Future components to enhance the basic, native security of 5G networks are either complex mechanisms whose impact in the requiring 5G communications are not considered, or lightweight solutions adapted to ultra-reliable low-latency communications (URLLC) but whose security properties remain under discussion. Although different 5G network slices may have different requirements, in general, both visions seem to fall short at provisioning secure URLLC in the future. In this work we address this challenge, by introducing cost-security functions as a method to evaluate the performance and adequacy of most developed and employed non-native enhanced security mechanisms in 5G networks. We categorize those new security components into different groups according to their purpose and deployment scope. We propose to analyze them in the context of existing 5G architectures using two different approaches. First, using model checking techniques, we will evaluate the probability of an attacker to be successful against each security solution. Second, using analytical models, we will analyze the impact of these security mechanisms in terms of delay, throughput consumption, and reliability. Finally, we will combine both approaches using stochastic cost-security functions and the PRISM model checker to create a global picture. Our results are first evidence of how a 5G network that covers and strengthened all security areas through enhanced, dedicated non-native mechanisms could only guarantee secure URLLC with a probability of ~55%.

5G networks↗

Structure of Sulfuric Acid Solutions Using Pair Distribution Function Analysis

Solvation and mesoscale ordering of sulfuric acid and other strong acid solutions leads to suppressed freezing points and strong rheological changes with varying concentration. While the solid-state structures are well-understood, studies focused on the evolving solvation structure in the solution phase have probed a limited concentration range (~1–6 M). This study applies a total scattering approach in both the wide-angle X-ray scattering (WAXS) and pair distribution function (PDF) regimes to elucidate the evolving solvation structure over its full range of acid concentration (0–18 M). The emergence of a prepeak in the WAXS regime at intermediate concentrations indicates a transition from noninteracting sulfate molecules in the dilute limit to sterically limited sulfates at concentrations near its deep eutectic point. Fits to the PDF data quantify this trend, showing a transition from octahedrally hydrated sulfates up to 6–7 M concentrations, followed by gradual dehydration, and eventually reaching a solution structure similar to that of water-in-salt electrolyte systems at high acid concentrations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗