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At least 595 records · Page 33

Enantioselectivity of Pentedrone and Methylone on Metabolic Profiling in 2D and 3D Human Hepatocyte-like Cells

Pentedrone and methylone can express stereoselectivity in toxicokinetic and toxicodynamic processes. Similarly, their chiral discrimination in metabolism, which was not yet evaluated, can result in different metabolic profiles and subsequent hepatotoxic effects. Therefore, the aim of this work was to assess, for the first time, both the hepatic cytotoxic and metabolic profile of pentedrone and methylone enantiomers using physiologically relevant in vitro models. The hepatotoxicity of these compounds was observed in a concentration-dependent manner in human stem-cell-derived hepatocyte-like cells (HLCs) cultured under 3D (3D-HLCs) and 2D (2D-HLCs) conditions. Enantioselectivity, on the other hand, was only shown for pentedrone (1 mM) in 3D-HLCs, being R-(−)-pentedrone the most cytotoxic. Furthermore, the metabolic profile was initially evaluated in human liver microsomes (HLM) and further demonstrated in 3D-HLCs and 2D-HLCs applying a gas chromatography coupled to a mass spectrometer (GC–MS) technique. Methylone and pentedrone showed distinct and preferential metabolic routes for their enantiomers, resulting in the production of differentiated metabolites; R-(+)-methylone and R-(−)-pentedrone are the most metabolized enantiomers. In conclusion, the results demonstrated enantioselectivity for pentedrone and methylone in the metabolic processes, with enantioselectivity in cytotoxicity for pentedrone.

Silva, Bárbara (ORCID:0000000173990197)↗

Nuclear charge densities in spherical and deformed nuclei: Toward precise calculations of charge radii

Precise measurements of atomic transitions affected by electron-nucleus hyperfine interactions offer sensitivity to explore basic properties of the atomic nucleus and study fundamental symmetries, including the search for new physics beyond the standard model of particle physics. Specifically, such measurements, augmented by atomic and nuclear calculations, will enable extraction of the higher-order radial moments of the charge-density distribution in spherical and deformed nuclei. The new data impose higher precision requirements on a theoretical description. The nuclear charge density is composed of the proton point distribution folded with the nucleonic charge distributions. The latter induce subtle relativistic corrections due to the coupling of nucleon magnetic moments with the nuclear spin-orbit density. Additional corrections come from the effect of center-of-mass projection. We assess the precision of nuclear charge density calculations by studying the behavior of relativistic and center-of-mass motion corrections to the second and fourth charge radial moments. Special attention has been paid to the magnetic spin-orbit density associated with the local variations of the spin-orbit current. The calculations for semimagic and open-shell nuclei are performed in the framework of self-consistent mean-field theory using quantified energy density functionals and density-dependent pairing forces. We used the general expression for the spin-orbit form factor that is valid for spherical and deformed nuclei. We studied the impact of various correction terms on the charge radii, fourth radial moments, diffraction radii, and surface thickness of spherical and deformed nuclei. The spin-orbit corrections to charge radial moments and surface thickness show strong shell fluctuations which can make an appreciable effect when aiming at high-precision predictions of isotopic shifts. The inclusion of relativistic and center-of-mass corrections impacts the quality of energy density functionals optimized to charge radii data. To establish reliable constraints on the existence of new forces from isotope shift measurements, precise calculations of nuclear charge densities of deformed nuclei are needed. The proper inclusion of the spin-orbit charge density and other correction terms is essential when aiming at extraction of subtle effects which become particularly visible in isotopic trends. It is also important when developing high-quality nuclear energy density functionals optimized using heterogeneous datasets involving absolute charge radii, differential charge radii, and charge form factor properties deduced from electron-scattering data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

Abstract Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific GRNs are limited in their ability to integrate scRNA-seq and scATAC-seq measurements and to model network dynamics on a cell lineage. To address this challenge, we have developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the GRN for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated and real datasets, we show that scMTNI is a broadly applicable framework for linear and branching lineages that accurately infers GRN dynamics and identifies key regulators of fate transitions for diverse processes such as cellular reprogramming and differentiation.

59 BASIC BIOLOGICAL SCIENCES↗

Taylor approximation variance reduction for approximation errors in PDE-constrained Bayesian inverse problems

In numerous applications, surrogate models are used as a replacement for accurate parameter-to-observable mappings when solving large-scale inverse problems governed by partial differential equations (PDEs). The surrogate model may be a computationally cheaper alternative to the accurate parameter-to-observable mappings and/or may ignore additional unknowns or sources of uncertainty. The Bayesian approximation error (BAE) approach provides a means to account for the induced uncertainties and approximation errors, i.e. the errors between the accurate parameter-to-observable mapping and the surrogate. The statistics of these errors are, however, in general unknown a priori, and are thus calculated using Monte Carlo sampling. Although the sampling is typically carried out offline, i.e. before considering the data, the process can still represent a computational bottleneck. In this work, we develop a scalable computational approach for reducing the costs associated with the sampling stage of the BAE approach. Specifically, we consider the Taylor expansion of the accurate and surrogate forward models with respect to the uncertain parameter fields either as a control variate for variance reduction or as a means to directly and efficiently approximate the mean and covariance of the approximation errors. We propose efficient methods for evaluating the expressions for the mean and covariance of the Taylor approximations based on linear(-ized) PDE solves. Furthermore, the proposed approach is independent of the dimension of the uncertain parameter, depending instead on the intrinsic dimension of the data, ensuring scalability to high-dimensional problems. The potential benefits of the proposed approach are demonstrated for two high-dimensional inverse problems governed by PDE examples, namely for the estimation of a distributed Robin boundary coefficient in a linear diffusion problem, and for a coefficient estimation problem governed by a nonlinear diffusion problem.

Bayesian approximation error↗

Renormalizing two-fermion operators in the SMEFT via supergeometry

We extend the geometric framework of field-space covariance for loop computations, thereby unifying the treatment of scalars, fermions, and gauge bosons in effective field theories. This allows us to derive a manifestly covariant formula for one-loop UV divergences that includes contributions from mixed boson-fermion graphs. The result is expressed in terms of geometric invariants of the field-space supermanifold. As a demonstration of this formula, we compute the renormalization group equations for two-fermion operators at the dimension-eight level in the Standard Model Effective Field Theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development

Most legumes can establish a symbiotic association with soil rhizobia that trigger the development of root nodules. These nodules host the rhizobia and allow them to fix nitrogen efficiently. The perception of bacterial lipo-chitooligosaccharides (LCOs) in the epidermis initiates a signaling cascade that allows rhizobial intracellular infection in the root and de-differentiation and activation of cell division that gives rise to the nodule. Thus, nodule organogenesis and rhizobial infection need to be coupled in space and time for successful nodulation. The plant hormone cytokinin (CK) contributes to the coordination of this process, acting as an essential positive regulator of nodule organogenesis. However, the temporal regulation of tissue-specific CK signaling and biosynthesis in response to LCOs or Sinorhizobium meliloti inoculation in Medicago truncatula remains poorly understood. In this study, using a fluorescence-based CK sensor (pTCSn::nls:tGFP), we performed a high-resolution tissue-specific temporal characterization of the sequential activation of CK response during root infection and nodule development in M. truncatula after inoculation with S. meliloti. Loss-of-function mutants of the CK-biosynthetic gene ISOPENTENYLTRANSFERASE 3 (IPT3) showed impairment of nodulation, suggesting that IPT3 is required for nodule development in M. truncatula. Simultaneous live imaging of pIPT3::nls:tdTOMATO and the CK sensor showed that IPT3 induction in the pericycle at the base of nodule primordium contributes to CK biosynthesis, which in turn promotes expression of positive regulators of nodule organogenesis in M. truncatula.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into regulatory T-cell and type-I interferon roles in determining abacavir-induced hypersensitivity or immune tolerance

Introduction Clinical use of several small molecule drugs may lead to severe T-cell-mediated idiosyncratic drug hypersensitivity reactions (iDHR) linked to HLA alleles, including abacavir (ABC) with HLA-B*57:01. Due to study limitations in humans, pathogenic networks in iDHR remain elusive. HLA transgenic murine models have been proposed to bridge knowledge gaps in tolerance and susceptibility to drugs. Methods Mice expressing HLA-B*57:01 and Foxp3-DTR/EGFP were generated to selectively deplete regulatory T-cells (Treg) with diphtheria toxin. ABC was administered for 8 days alone or together with cell- and cytokine-depleting antibodies. Cellular and transcriptomic responses were analyzed by RNA, flow cytometry and fluorescence methods. Results While CD8 + T-cell responses to ABC require HLA presentation, ABC also triggered mitochondrial stress in macrophagesin vitro, independently of HLA.In vivo, Treg were the primary mechanism of drug tolerance controlling HLA presentation and costimulation by antigen presenting cells. Treg ablation uncovered immune adverse events linked to activation and proliferation of both drug-specific and bystander CD8 + T-cells through CD28-mediated pathways with support from CD4 + non-Treg. Type-I interferon (IFN-I) and cellular-stress pathways influenced the fate of lymph node cells responding to ABC, implicating innate immune cells such as macrophages and plasmacytoid dendritic cells in the development of T-cell responses against the drug. IFN-I and IL-2 were necessary for CD8 + T-cell differentiation and ABC-induced adverse reactions. Conclusions This study unveils novel immune mechanisms driven by drug and host-related factors required forin vivoreactions and sheds light on potential biomarker and therapeutic targets for managing and preventing severe and life-threatening iDHR.

Immunology↗

VLBI Data Processing on Coronal Radio-sounding Experiments of Mars Express

The ESA’s Mars Express solar corona experiments were performed at two solar conjunctions in the years 2015 and 2017 by a number of radio telescopes in the European VLBI Network. This paper presents the methods to measure the frequency and phase fluctuations of the spacecraft radio signal, and the applications to study the characteristics of the plasma turbulence effects on the signal at a single station and at multiple stations via cross correlation. The power spectra of the frequency fluctuations observed between 4.9 and 76.3 R {sub s} have a power-law shape close to a Kolmogorov spectrum over the frequency interval ν {sub lo} < ν < ν {sub up}, where the nominal value of ν {sub lo} is set to 3 mHz and ν {sub up} is in the range of 0.03–0.15 Hz. The rms of the frequency fluctuations is presented as a function of the heliocentric distance. Furthermore, we analyze the variations of the electron column density fluctuations at solar offsets 4.9 R {sub s} and 9.9 R {sub s} and the cross-correlation products between the VLBI stations. The power density of the differential fluctuations between different stations decreases at ν < 0.01 Hz. Finally, the fast flow speeds of solar wind >700 km s{sup -1} are derived from the cross correlation of frequency fluctuations at ν < 0.01 Hz. The fast flow speeds of solar wind correspond to the high heliolatitude of the coronal region that the radio rays passed. The VLBI observations and analysis methods can be used to study the electron column density fluctuations and the turbulence at multiple spatial points in the inner solar wind by providing multiple lines of sight between the Earth and the spacecraft.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On-shell recursion and holomorphic HQET for heavy quark hadronic resonances

We develop a new theoretical framework for the treatment of heavy quark (HQ) resonances within heavy quark effective theory (HQET). This framework uses on-shell recursion techniques to express the resonant amplitude as a product of on-shell subamplitudes, which allows one to employ a form-factor representation of the hadronic matrix elements and to obtain an HQ expansion, but at the price of introducing complex momenta. We construct a generalized “holomorphic HQET” onto which such complex-momentum matrix elements can be matched, and we show that PT symmetry ensures the Isgur-Wise functions (and the perturbative corrections) become holomorphic functions of the complex recoil parameter with real coefficients. They are thus an analytic continuation of the standard HQET description. This framework admits a HQ hadron (strong decay) width expansion. At second order, we show it is compatible with data for the B12∗$$ {B}_{1(2)}^{\left(\ast \right)} $$ and D12∗$$ {D}_{1(2)}^{\left(\ast \right)} $$ HQ doublets. Taking the B¯→D1∗1−→Dπlν$$ \overline{B}\to \left({D}_1^{\ast}\left({1}^{-}\right)\to D\pi \right) l u $$ system as an example, we compute the holomorphic HQET expansion to first order, as well as the complex-momentum on-shell subamplitudes. A toy numerical study of the resulting differential rates demonstrates that this framework generates HQ resonance lineshapes with large tails, resembling those seen in data.

Manzari, Claudio Andrea↗

Clonality, local population structure, and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex

Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with approximately 300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. Here, we assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. 405 samples of the four species, representing 57 populations, were subjected to RADseq. Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Differences in fitness between genets was estimated as the numbers of ramets each genet comprised. Degree of clonality (numbers of genets/numbers of ramets [samples]) within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but 2-8 ramets were detected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St. Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets, and sexes were not detected. Within S. divinum, however, female gametophytes harbored 2-3 times the number oi of microbial taxa as males. These four Sphagnum species all exhibit a similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns where genets abut one another but do not extensively mix, because of limited ramet fragmentation, and the guerrilla patterns where extensive genet fragmentation and dispersal results in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

59 BASIC BIOLOGICAL SCIENCES↗

Model-Form Epistemic Uncertainty Quantification for Modeling with Differential Equations: Application to Epidemiology

Modeling real-world phenomena to any degree of accuracy is a challenge that the scientific research community has navigated since its foundation. Lack of information and limited computational and observational resources necessitate modeling assumptions which, when invalid, lead to model-form error (MFE). The work reported herein explored a novel method to represent model-form uncertainty (MFU) that combines Bayesian statistics with the emerging field of universal differential equations (UDEs). The fundamental principle behind UDEs is simple: use known equational forms that govern a dynamical system when you have them; then incorporate data-driven approaches – in this case neural networks (NNs) – embedded within the governing equations to learn the interacting terms that were underrepresented. Utilizing epidemiology as our motivating exemplar, this report will highlight the challenges of modeling novel infectious diseases while introducing ways to incorporate NN approximations to MFE. Prior to embarking on a Bayesian calibration, we first explored methods to augment the standard (non-Bayesian) UDE training procedure to account for uncertainty and increase robustness of training. In addition, it is often the case that uncertainty in observations is significant; this may be due to randomness or lack of precision in the measurement process. This uncertainty typically manifests as “noisy” observations which deviate from a true underlying signal. To account for such variability, the NN approximation to MFE is endowed with a probabilistic representation and is updated using available observational data in a Bayesian framework. By representing the MFU explicitly and deploying an embedded, data-driven model, this approach enables an agile, expressive, and interpretable method for representing MFU. In this report we will provide evidence that Bayesian UDEs show promise as a novel framework for any science-based, data-driven MFU representation; while emphasizing that significant advances must be made in the calibration of Bayesian NNs to ensure a robust calibration procedure.

97 MATHEMATICS AND COMPUTING↗

Deciphering Reaction Mechanisms of Molecular Proton Reduction Catalysts with Cyclic Voltammetry: Kinetic vs Thermodynamic Control

The kinetics and thermodynamics of elementary reaction steps involved in the catalytic reduction of protons to hydrogen define the reaction landscape for catalysis. The mechanisms can differ in the order of the elementary proton transfer, electron transfer, and bond-forming steps and can be further differentiated by the sites at which protons and electrons localize. Access to fully elucidated mechanistic, kinetic, and thermochemical details of molecular catalysts is crucial to facilitate the development of new catalysts that operate with optimal efficiency, selectivity, and durability. The mechanism by which a catalyst operates, as well as the kinetics and thermodynamics associated with the individual steps, can often be accessed through electroanalytical studies. Here, this Account details the application of cyclic voltammetry to interrogate reaction mechanisms and quantify the kinetics and thermodynamics of elementary reaction steps for a series of molecular catalysts that mediate electrochemical proton reduction. I distinguish the limiting scenarios wherein a catalyst operates under kinetic control vs thermodynamic control, with a focus on detecting how cyclic voltammetry features shift with proton source strength and concentration, as well as scan rate. For systems that operate under kinetic control, catalytic currents are observed at, or slightly positive toward, the formal potential for the redox process that triggers catalysis. Under thermodynamic control, catalytic responses shift as a function of the proton source pKa and effective pH of the solution. After drawing this distinction, we introduce the appropriate voltammetry experiments and accompanying analytical expressions for extracting key metrics from the data. To illustrate analytical strategies to quantify elementary reaction steps of catalysts operating under kinetic control, I describe our studies of proton reduction catalysts Co(dmgBF 2 ) 2 (CH 3 CN) 2 (dmgBF 2 = difluoroboryl-dimethylglyoxime) and [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ (P 2 Ph N 2 Ph = 1,5-phenyl-3,7-phenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, peak shift analysis, foot-of-the-wave analysis, and plateau current analysis are applied to data sets wherein voltammetric response are recorded as a function of catalyst concentration, proton source concentration, proton source strength, and scan rate to quantify rate constants for elementary proton transfer and bond-forming steps in a catalytic cycle. Further, the case study of [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ illustrates how complementary spectroscopic methods can bolster the mechanistic assignment. Collectively, these two studies showcase how detailed mechanistic studies inform on rate-limiting elementary steps in catalysis and other key processes underpinning catalysis. Second, I present analytical strategies to interrogate catalysts operating under thermodynamic control, centered on the case study of [Ni II (P 2 Ph N 2 Bn ) 2 ] 2+ (P 2 Ph N 2 Bn = 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, the application of nonaqueous Pourbaix theory to extract thermodynamic information is introduced, and the construction of a coupled Pourbaix diagram is detailed. This study identifies ligand-based protonation as the key process that places catalysis under thermodynamic control and influences the reaction mechanism. Together, the work detailed in this Account showcases the utility of electroanalytical methods to disentangle complex reaction mechanisms and extract key thermochemical and kinetic parameters for elementary steps of catalysis. Through detailed presentation of the key analytical expressions that underpin these analyses, this Account seeks to facilitate the adoption of cyclic voltammetry by the community to fully extract kinetic, thermochemical, and mechanistic information on electrochemical small-molecule activation.

catalysts↗

Impact of three-body forces on elastic nucleon-nucleus scattering observables

In a previous series of papers we investigated the domain of applicability of chiral potentials to the construction of a microscopic optical potential (OP) for elastic nucleon-nucleus scattering. The OP was derived at the first order of the spectator expansion of the Watson multiple scattering theory and its final expression was a folding integral between the nucleon-nucleon ( N N ) t matrix and the nuclear density of the target. In the calculations N N and three-nucleon ( 3 N ) chiral interactions were used for the target density and only the N N interaction for the N N t matrix. The purpose of this study is to achieve another step towards the calculation of a more consistent OP introducing the 3 N force also in the dynamic part of the OP. The full treatment of the 3 N interaction is beyond our present capabilities. Thus, here it is approximated with a density dependent N N interaction obtained after the averaging over the Fermi sphere. In practice, in our model the 3 N force acts as a medium correction of the bare N N interaction used to calculate the t matrix. Even if the 3 N force is treated in an approximate way, this method naturally extends our previous model of the OP and allows a direct comparison of our present and previous results. We consider as case studies the elastic scattering of nucleons off C 12 and O 16 . We present results for the differential cross section and the spin observables for different values of the projectile energy. From the comparison with the experimental data and with the results of our previous model we assess the importance of the 3 N interaction in the dynamic part of the OP. Conclusions: Our analysis indicates that the contribution of the 3 N force in the t matrix is small for the differential cross section and it is sizable for the spin observables, in particular, for the analyzing power. We find that the two-pion exchange term is the major contributor to the 3 N force. A chiral expansion order-by-order analysis of the scattering observables confirms the convergence of our results at the next-to-next-to-next-to-leading-order, as already established in our previous work.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Evolution of a σ–(c-di-GMP)–anti-σ switch

Filamentous actinobacteria of the genus Streptomyces have a complex lifecycle involving the differentiation of reproductive aerial hyphae into spores. We recently showed c-di-GMP controls this transition by arming a unique anti-σ, RsiG, to bind the sporulation-specific σ, WhiG. The Streptomyces venezuelae RsiG–(c-di-GMP) 2 –WhiG structure revealed that a monomeric RsiG binds c-di-GMP via two E(X) 3 S(X) 2 R(X) 3 Q(X) 3 D repeat motifs, one on each helix of an antiparallel coiled-coil. Here we show that RsiG homologs are found scattered throughout the Actinobacteria. Strikingly, RsiGs from unicellular bacteria descending from the most basal branch of the Actinobacteria are small proteins containing only one c-di-GMP binding motif, yet still bind their WhiG partners. Our structure of a Rubrobacter radiotolerans (RsiG) 2 –(c-di-GMP) 2 –WhiG complex revealed that these single-motif RsiGs are able to form an antiparallel coiled-coil through homodimerization, thereby allowing them to bind c-di-GMP similar to the monomeric twin-motif RsiGs. Further data show that in the unicellular actinobacterium R. radiotolerans , the (RsiG) 2 –(c-di-GMP) 2 –WhiG regulatory switch controls type IV pilus expression. Phylogenetic analysis indicates the single-motif RsiGs likely represent the ancestral state and an internal gene-duplication event gave rise to the twin-motif RsiGs inherited elsewhere in the Actinobacteria. Thus, these studies show how the anti-σ RsiG has evolved through an intragenic duplication event from a small protein carrying a single c-di-GMP binding motif, which functions as a homodimer, to a larger protein carrying two c-di-GMP binding motifs, which functions as a monomer. Consistent with this, our structures reveal potential selective advantages of the monomeric twin-motif anti-σ factors.

59 BASIC BIOLOGICAL SCIENCES↗

The calculation of light element impurity (α, n) yield curves in a PuO 2 matrix and associated specific yield coefficients: Influence of the reaction cross sections

Most of the Pu separated from irradiated commercial nuclear fuel is stored as PuO 2 . The primary quantitative nondestructive measurement technique used to verify the amount of Pu in storage containers is passive neutron correlation counting. An important physical property of the oxide material is the ratio, α, of the rate of (α, n) neutrons produced inside the item to the rate of neutrons produced by spontaneous fission. This ratio influences the precision of the correlated counting method and affects the interpretation of the data because of how it changes both the primary total neutron production rate and the rate of induced fission events taking place inside the item. In addition to the main O(α, n) contribution, additional contributions come from α-particle interactions with light element impurities that are inevitably present. In this work, we calculate specific (α, n) yield coefficients, expressed in units of neutrons per second per gram of α-emitting nuclide per part per million by mass of the specified impurity element distributed in a pure PuO 2 matrix, for some key α-emitting actinides commonly present in reprocessed Pu ( 238–242 Pu+ 241 Am). These coefficients are directly applicable to nuclear safeguards verification work in which the α ratio is often calculated from the Pu-isotopic composition and chemical information obtained by other means. Further, they also provide a convenient up-to-date reference set against which values generated by other methods can be compared. Results are presented for impurities with atomic number from 3 to 17 inclusive, plus K and Fe. In most cases, these coefficients are not expected to change by more than 5%–10% at any time in the future. However, as new data become available, changes as large as 20% may be needed for some targets (e.g., F). The present yield calculations are limited by the general shortage of quality experimental total (α, n) reaction cross section data, which, together with unexplained variation between determinations, means that an objective and coherent evaluation is not possible. The situation is even less satisfactory for the partial differential cross section needed to calculate neutron spectra.

(𝛼, n) reactions↗

Simple, efficient and open-source CRISPR/Cas9 strategy for multi-site genome editing in Populus tremula × alba

Although the CRISPR/Cas9 system has been successfully used for crop breeding, its application remains limited in forest trees. Here, we describe an efficient gene editing strategy for hybrid poplar, (Populus tremula × alba INRA clone 717-1B4) based on the Golden Gate MoClo cloning. To test the system efficiency for generating single gene mutants, two single guide RNAs (sgRNAs) were designed and incorporated into the MoClo Tool Kit level 2 binary vector with the Cas9 expression cassette to mutate the SHORT ROOT (SHR) gene. Moreover, we also tested its efficiency for introducing mutations in two genes simultaneously by expressing one sgRNA targeting a single site of the YUC4 gene and the other sgRNA targeting the PLT1 gene. For a robust evaluation of the approach, we repeated the strategy to target the LBD12 and LBD4 genes simultaneously, using an independent construct. We generated hairy roots by Agrobacterium rhizogenes-mediated leaf transformation. Sequencing results confirmed the CRISPR/Cas9-mediated mutation in the targeted sites of PtaSHR. Biallelic and homozygous knockout mutations were detected. A deletion spanning both target sites and small insertions/deletions were the most common mutations. Out of the 22 SHR alleles sequenced, 21 were mutated. The phenotype’s characterization showed that transgenic roots with biallelic mutations for the SHR gene lacked a defined endodermal single cell layer, suggesting a conserved gene function similar to its homolog in Arabidopsis Arabidopsis thaliana (L.) Heynh. Sequencing results also revealed the high efficiency of the system for generating double mutants. Biallelic mutations for both genes in the yuc4/plt1 and lbd12/lbd4 roots were detected in three (yuc4/plt1) and two (lbd12/lbd4) out of four transgenic roots evaluated. A small deletion or a single nucleotide insertion at the single target site was the most common mutations. This CRISPR/Cas9 strategy arises as a rapid, simple and standardized gene-editing tool to evaluate the gene role in essential developmental programs such as radial cell differentiation of poplar roots.

59 BASIC BIOLOGICAL SCIENCES↗

A Mathematical Model of Breast Tumor Progression Based on Immune Infiltration

Breast cancer is the most prominent type of cancer among women. Understanding the microenvironment of breast cancer and the interactions between cells and cytokines will lead to better treatment approaches for patients. In this study, we developed a data-driven mathematical model to investigate the dynamics of key cells and cytokines involved in breast cancer development. We used gene expression profiles of tumors to estimate the relative abundance of each immune cell and group patients based on their immune patterns. Dynamical results show the complex interplay between cells and molecules, and sensitivity analysis emphasizes the direct effects of macrophages and adipocytes on cancer cell growth. In addition, we observed the dual effect of IFN-γ on cancer proliferation, either through direct inhibition of cancer cells or by increasing the cytotoxicity of CD8+ T-cells.

60 APPLIED LIFE SCIENCES↗

Mini-Micropulse Lidar data from TAMU TRACER campaign in the Houston TX region from July to September 2022

During TRACER, the Texas A&M Rapid Onsite Atmospheric Measurements Van (ROAM-V) was deployed to capture airmasses behind (maritime) and ahead (continental) of the passage of the sea-breeze front through Houston. On select sampling days, ROAM-V sampled in the morning/mid-day on the coast and then transited to a second inland site for the afternoon/evening. The suite of instruments deployed on ROAM-V included a Condensation Particle Counter (CPC; GRIMM Model 5.403 CPC), Scanning Mobility Particle Sizer (SMPS; TSI 3750 detector, TSI 3082 classifier, TSI 3088 neutralizer, TSI 3081A Differential Mobility Analyzer), Cloud Condensation Nuclei counter (Droplet Measurement Technologies CCN Counter), micro pulse lidar (Droplet Measurement Technologies Micro Pulse LiDAR (mini-MPL)), and a Davis Rotating Uniform size-cut Monitor (DRUM; DRUMAir 4-DRUM). Before sampling at each location, the latitude and longitude were recorded using the GPS on the phone application “My Altitude”. The mini-MPL deployed with ROAM-V is a 532 nm elastic and polarization lidar. The mini-MPL outputs normalized relative backscatter (NRB) derived from raw signal after after-pulse, overlap, and dead-time correction calibration. The depolarization ratio is calculated from the co-polarized and cross-polarized NRB (Flynna et al., 2007). The NRB and depolarization ratio data are resampled from the original data at 1-minute intervals. The vertical resolution of the mini-MPL data is 15 meters. The mini-MPL data can be used to determine the boundary layer, cloud top, and cloud bottom height and can be used to retrieve aerosol type and concentration profile. This data was collected for ARM Field Campaign AFC07055 and supported by DOE ASR grant DE-SC0021047. For any further questions, please feel free to contact the instrument PI, Sarah D. Brooks, sbrooks@tamu.edu . Flynna, C. J., Mendozaa, A., Zhengb, Y., & Mathurb, S. (2007). Novel polarization-sensitive micropulse lidar measurement technique. Optics express, 15(6), 2785-2790.

54 ENVIRONMENTAL SCIENCES↗