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At least 919 records · Page 51

Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora

Abstract The oomycete Phytophthora palmivora infects the fruit of cacao trees ( Theobroma cacao ) causing black pod rot and reducing yields. Cacao genotypes vary in their resistance levels to P. palmivora , yet our understanding of how cacao fruit respond to the pathogen at the molecular level during disease establishment is limited. To address this issue, disease development and RNA-Seq studies were conducted on pods of seven cacao genotypes (ICS1, WFT, Gu133, Spa9, CCN51, Sca6 and Pound7) to better understand their reactions to the post-penetration stage of P. palmivora infection. The pod tissue- P. palmivora pathogen assay resulted in the genotypes being classified as susceptible (ICS1, WFT, Gu133 and Spa9) or resistant (CCN51, Sca6 and Pound7). The number of differentially expressed genes (DEGs) ranged from 1625 to 6957 depending on genotype. A custom gene correlation approach identified 34 correlation groups. De novo motif analysis was conducted on upstream promoter sequences of differentially expressed genes, identifying 76 novel motifs, 31 of which were over-represented in the upstream sequences of correlation groups and associated with gene ontology terms related to oxidative stress response, defense against fungal pathogens, general metabolism and cell function. Genes in one correlation group (Group 6) were strongly induced in all genotypes and enriched in genes annotated with defense-responsive terms. Expression pattern profiling revealed that genes in Group 6 were induced to higher levels in the resistant genotypes. An additional analysis allowed the identification of 17 candidate cis -regulatory modules likely to be involved in cacao defense against P. palmivora . This study is a comprehensive exploration of the cacao pod transcriptional response to P. palmivora spread after infection. We identified cacao genes, promoter motifs, and promoter motif combinations associated with post-penetration resistance to P. palmivora in cacao pods and provide this information as a resource to support future and ongoing efforts to breed P. palmivora -resistant cacao.

60 APPLIED LIFE SCIENCES↗

Microwave Flow Cytometric Detection and Differentiation of Escherichia coli

Label-free measurement and analysis of single bacterial cells are essential for food safety monitoring and microbial disease diagnosis. We report a microwave flow cytometric sensor with a microstrip sensing device with reduced channel height for bacterial cell measurement. Escherichia coli B and Escherichia coli K-12 were measured with the sensor at frequencies between 500 MHz and 8 GHz. The results show microwave properties of E. coli cells are frequency-dependent. A LightGBM model was developed to classify cell types at a high accuracy of 0.96 at 1 GHz. Thus, the sensor provides a promising label-free method to rapidly detect and differentiate bacterial cells. Nevertheless, the method needs to be further developed by comprehensively measuring different types of cells and demonstrating accurate cell classification with improved machine-learning techniques.

59 BASIC BIOLOGICAL SCIENCES↗

Boundary-element shape sensitivity analysis for thermal problems with nonlinear boundary conditions

Implicit differentiation of the discretized boundary integral equations governing the conduction of heat in solid objects subjected to nonlinear boundary conditions is shown to generate an accurate and economical approach for the computation of shape sensitivities for this class of problems. This approach involves the employment of analytical derivatives of boundary-element kernel functions with respect to shape design variables. A formulation is presented that can consistently account for both temperature-dependent convection and radiation boundary conditions. Several iterative strategies are presented for the solution of the resulting sets of nonlinear equations and the computational performances examined in detail. Multizone analysis and zone condensation strategies are demonstrated to provide substantive computational economies in this process for models with either localized nonlinear boundary conditions or regions of geometric insensitivity to design variables. A series of nonlinear example problems are presented that have closed-form solutions.

Kane, James H.↗

A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2

Most transcriptomic studies of SARS-CoV-2 infection have focused on differentially expressed genes, which do not necessarily reveal the genes mediating the transcriptomic changes. In contrast, exploiting curated biological network, our PathExt tool identifies central genes from the differentially active paths mediating global transcriptomic response. Here we apply PathExt to multiple cell line infection models of SARS-CoV-2 and other viruses, as well as to COVID-19 patient-derived PBMCs. The central genes mediating SARS-CoV-2 response in cell lines were uniquely enriched for ATP metabolic process, G1/S transition, leukocyte activation and migration. In contrast, PBMC response reveals dysregulated cell-cycle processes. In PBMC, the most frequently central genes are associated with COVID-19 severity. Importantly, relative to differential genes, PathExt-identified genes show greater concordance with several benchmark anti-COVID-19 target gene sets. We propose six novel anti-SARS-CoV-2 targets ADCY2, ADSL, OCRL, TIAM1, PBK, and BUB1, and potential drugs targeting these genes, such as Bemcentinib, Phthalocyanine, and Conivaptan.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-Omics Analysis of Mouse Retina Following Low Dose Radiation and/or Hindlimb Unloading

Rodent models have been used as analogs for studying the effects of spaceflight. NASA’s GeneLab provides access to omics datasets generated from spaceflight and ground-based experiments allowing for additional retrospective analysis. We used GeneLab’s GLDS-203, a dataset generated by researchers at Loma Linda University to study the impact of prolonged unloading and/or low-dose radiation on mouse retina. The purpose of this study was to understand the effect of gamma radiation and/or hindlimb unloading on mice retinas through a multi-omics analysis. In the experiment that generated the omics data, mice were irradiated with gamma-ray and/or subjected to hindlimb unloading for 21 days and multi-omics analysis was performed at 7 days, 1 month, or 4 months post exposure. In the current study, for each of the three timepoints, we compared epigenomic profiles for retinas from exposed mice against timepoint-matched controls. We identified a total of 5,271 differentially methylated loci (DML) and 321 differentially methylated regions (DMR; using a sliding window and step size of 500 bp) with methylation difference > 10% and q-value < 0.05 (sliding linear model corrected p-value) across the nine exposure groups. Highest correlation in methylation difference was seen for significant DMLs (q-value < 0.05) across different conditions at same post exposure timepoint (Figure 1).The location of DMLs and DMRs were characterized with respect to CpG islands and shores, putative promoters, gene body, and intergenic regions (Table 1). We analyzed RNA-seq counts and performed gene set enrichment analysis using differential expression results from comparing each exposure group to its timepoint-matched control group. Significant pathways (adjusted p-value <0.05) enriched in all three microgravity-only groups were related to morphogenesis of a branching epithelium, skeletal muscle cell differentiation, and response to fibroblast growth factor. Common processes across all timepoints in the radiation-only groups were retina homeostasis, synaptic vesicle exocytosis-endocytosis, and chemotaxis. In the combination groups, regulation of trans-synaptic signaling, and Rho protein signal transduction were enriched at all three timepoints. Processes related to purine nucleotide metabolism were enriched in all nine exposure groups, with activation at 1 month, and suppression at 7 days and 4 months. A total of 14 genes contained at least one DML and were differentially expressed at adjusted p-value < 0.05, including genes implicated in cataract development (Sipa1l3, Crybb3) and those involved in cytoskeletal organization (Plec, Flnb, Eef1a1). This analysis is part of a larger effort to understand the molecular mechanisms following spaceflight exposures that can help translate effects observed in animal models to human impacts.

Prachi Kothiyal↗

Energetic Copolymers From LLM-105 and Aliphatic Isocyanates

Energetic polymers typically feature fuel-rich backbones with pendant oxidizing explosophores, which are used to modify pressure and temperature characteristics in energetic formulations. However, these pendant explosophores generally increase sensitivity and decrease the thermal stability of the polymer in the condensed phase. Direct polymerization of insensitive high explosives (IHEs) bearing polymerizable functionalities, such as amines, provides a synthetic platform for deriving tunable energetic materials. Here, this work demonstrates the first direct polymerization of the IHE 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) with aliphatic isocyanate comonomers to yield an energetic copolyurea (PUa1) and an energetic copolyurea network (PUa2). 1 H and 13 C nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) confirm copolyurea synthesis. PUa1 exhibited branching reactions commonly found in polyurea syntheses, and these side reactions were suppressed in PUa2 through use of a polyfunctional isocyanate. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) demonstrate the energetic IHE based polyurea preserves the energetic decomposition of the parent monomer LLM-105 in PUa1 (1203 J g −1 ) and PUa2 (687 J g −1 ), albeit with reduced thermal stability with peak decomposition temperatures of 235°C and 233°C, respectively. This work presents a new approach for generating energetic polymers from IHE cores with tunable energetic, thermal, and structural characteristics.

Chemistry↗

Combustion in the ZrF 4 -Mg-Si and ZrF 4 -Al-Si systems for preparation of zirconium silicides

The exothermic reactions in the ZrF 4 –Mg-Si and ZrF 4 -Al-Si systems are investigated by a fast temperature recording (thermocouple) technique, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). A quenching method is used to arrest the combustion process and conduct a layer-by-layer analysis of the products by x-ray diffraction (XRD) and electron microscopy. Two seemingly similar reactive systems exhibited considerably different combustion characteristics, composition, and morphology. Based on these investigations, we propose and discuss phase formation mechanisms at the early stages for each system. Three different pathways involving the reaction of ZrF 4 with other reagents and the Mg 2 Si intermediate are identified to occur in the ZrF 4 –Mg-Si system. Contrary to the complex mechanism in the ZrF 4 –Mg-Si system, the early stage of the combustion process for the ZrF 4 -Al-Si system involves the interaction of ZrF 4 with Al-Si eutectic melt. The exothermic reaction between reduced solid Zr and Si melt is the primary heat-generating step for both systems in spite of substantial differences in the early stages of the reactions. The silicon content in the reactive mixtures governs the phase composition of products. The ZrSi 2 phase, with a high growth rate, forms first on the Zr particle surfaces and then grows by a reactive diffusion mechanism. The ZrSi 2+ Zr reaction produces silicon-lean phases (e.g., ZrSi) when the silicon supply is limited. The combustion temperature also has a considerable influence on the phase compositions of the products. High combustion temperature in the ZrF 4 +2Mg+Si mixture enables the formation of multiphase products (α-ZrSi and β-ZrSi), whereas the relatively lower temperatures in the 3ZrF 4 +4Al+3Si mixture yields a single-phase α-ZrSi. As a result, lower combustion temperatures also make the ZrF 4 -Al-Si system more advantageous for the preparation of zirconium silicides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Silicon alloying enhances fast heating rate combustion of aluminum particles

Alloys and composites of aluminum (Al) have shown promise in regulating and enhancing particle combustion for energy generation applications. Recent work on aluminum-silicon (Al-Si) spherical alloy particles has shown improved combustion at low heating rates through enhanced diffusion accompanying a lower melting temperature. This study extends reactivity analysis to higher heating rates, comparing oxidation of Al-Si with Al. Flame speeds of Al-Si powder mixed with molybdenum trioxide (MoO 3 ) powder (Al-Si+MoO 3 ) exhibited a faster transition to steady propagation relative to Al+MoO 3 . Bomb calorimetry experiments revealed up to 5.8% greater early temperature rise for Al-Si powder. Rapid steady propagation for Al-Si mixture and faster temperature rise for Al-Si particles were attributed to accelerated kinetics evidenced in thermal equilibrium analysis of the mixtures using a differential scanning calorimeter (DSC). Larger DSC exotherms in the early stages of oxidation (i.e., 480–720 °C) correlated with early heat release and promoted steady flame propagation for Al-Si+MoO 3 compared with Al+MoO 3 . Furthermore, in multiple heating rate DSC studies, Al-Si+MoO 3 ignited at a lower heating rate (i.e., 15 ⁰C/min) than Al+MoO 3 (i.e., 20 ⁰C/min). Both mixtures ignited at temperatures less than 625 °C which is above the melting temperature of Al-Si (574 °C) and below Al (659 °C). Thus, alloy particle fuels with enhanced diffusion-controlled kinetics promote steady flame propagation and show promise for energy generation applications. This is especially promising for technologies driven by enhanced condensed phase combustion such as some propellant additives or applications dependent on reliable burn rates such as pyrotechnic time delay formulations and primers.

36 MATERIALS SCIENCE↗

Automated identification of dominant physical processes

The identification of processes that locally and approximately dominate dynamical system behavior has enabled significant advances in understanding and modeling nonlinear differential dynamical systems. Conventional methods of dominant process identification involve piecemeal and ad hoc (non-rigorous, informal) scaling analyses to identify dominant balances of governing equation terms and to delineate the spatiotemporal boundaries (boundaries in space and/or time) of each dominant balance. For the first time, we present an objective global measure of the fit of dominant balances to observations, which is desirable for automation, and was previously undefined. Furthermore, we propose a formal definition of the dominant balance identification problem in the form of an optimization problem. Here, we show that the optimization can be performed by various machine learning algorithms, enabling the automatic identification of dominant balances. Our method is algorithm agnostic and it eliminates reliance upon expert knowledge to identify dominant balances which are not known beforehand.

42 ENGINEERING↗

Reticulated porous lanthanum strontium manganite structures for solar thermochemical hydrogen production

Porous ceramic foams are utilized in various fields and applications due to their advantageous properties such as high porosity, high specific surface area, and controlled permeability. Non-stoichiometric oxide foams are of particular interest for the solar thermochemical production of hydrogen in directly irradiated solar receivers due to their enhanced heat transfer capabilities and structural integrity. Here we report the fabrication of lanthanum strontium manganite replica foams and their solar thermochemical water splitting performance. Highly porous (>80%) foams were produced with controlled structure and tested in a high temperature water splitting furnace to demonstrate stability and overall performance. The temperature profile of the burnout and sintering of the foam structure were altered based on simultaneous differential scanning calorimetry and thermal gravimetry analysis. Two-step sintering was used both to retain micron-sized pores (D50 = 0.4 μm) on the foam's struts and to limit grain growth to a grain size of ~1 μm. The structural characteristics were confirmed by porosimetry and scanning electron microscopy. The foams were repeatedly cycled, producing approximately 200 μmol/g of H 2 per cycle. Water splitting performance was tested for 50 cycles and approximately 35 h at 1400 °C. No statistical difference in the effective hydrogen production per cycle was observed, which is promising for long-term redox cycle stability.

08 HYDROGEN↗

Recycled polyethylene and crumb rubber composites modified asphalt with improved aging resistance and thermal stability

Crumb rubbers (CR) and recycled Polyethylene (PE) are commonly used as modifiers to improve the asphalt properties. However, the addition of these modifiers individually may result in phase separation of PE and inadequate degradation of CR, which may not simultaneously satisfy the rheological and aging resistance of the binder blends. In this study, a type of CR/PE composites manufactured through melt extrusion procedures was adopted for the improvement of the modified binder blends. The modified binder blends after short-term (RTFO) and long-term (PAV) aging were collected for dynamic shear rheometer and bending beam rheometer tests. FTIR tests were also used to quantify the aging resistance, while differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were applied to evaluate the thermal behaviors of the binder blends. Optical microscopy tests were used to explore the modification mechanism and visualize the microstructures of original and PAV aged binder blends. Test results showed that CR/PE composites could significantly improve the aging resistance of the binder blends. The dispersed PE particles still interacted with each other and meanwhile worked with the diffused rubbery phase, which could form a similar TPEs network. The oxidation and high-temperature aging of such binder blends would strengthen the network that resisted the aging severity of the binder blends. Furthermore, it was also revealed that CR/PE modified asphalt could sustain more heat before a rapid degradation and the well-dispersed PE particles could interact with the diffused CR particles to form a network to resist aging.

02 PETROLEUM↗

Highly thermally stable copolymers of epoxy and trifunctional polybenzoxazine

Here, in this work, we report the copolymerization of a triamine-based benzoxazine and a commercial difunctional epoxy resin, and investigate their synergistic effect on improved thermal properties using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Results showed that a glass transition temperature increase of up to 268 °C was obtained for the copolymer with as low as 25 wt% epoxy. A higher thermal performance was also achieved with an onset degradation of nearly 400 °C and char yield of 39 wt% at 800 °C for the copolymer with 52 wt% epoxy. The behavior was compared to previously reported benzoxazine/epoxy combinations and was found to be advantageous. The curing behavior of different copolymer compositions was also investigated via DSC and a methodology for matching each peak with its corresponding reaction was developed. Results showed that the alternating favorability of the reactions was dependent on the benzoxazine/epoxy ratio. Overall, the prepared PBZ/epoxy copolymers displayed higher thermal stability than their individual components, indicating suitability for a number of potential extended uses including utility in higher temperature applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of natural carbon filler on thermo-oxidative degradation of thermoplastic-based composites

Here thermo-oxidative degradation of thermoplastic-based composites filled with two types of carbon filler including bituminous (Pittsburgh No.8, P8) and sub-bituminous (Powder River Basin, PRB) coals were investigated using differential scanning calorimetry (DSC) and thermogravimetric analysis. Oxidation induction time (OIT) and activation energy (AE) for coal plastic composites (CPCs), HDPE, and commercially available wood plastic composites (WPCs) were determined using isothermal and isoconversional kinetic methods. OIT values for CPC increased with coal content, indicating higher thermo-oxidative stability. AE values obtained using isothermal method were 52–116 kJ/mol for all CPC formulations, 32 kJ/mol for HDPE, and 33–114 kJ/mol for WPCs. AEs for CPCs obtained using isoconversional methods were not constant but rather dependent on the degree of degradation with CPC/ P8 coal possessing higher overall AE. Incorporating coal into HDPE increased thermo-oxidative stability of the resulting composite, indicating coal potentially acts as a natural primary and secondary antioxidant for polymer materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PD-L1 induces macrophage polarization toward the M2 phenotype via Erk/Akt/mTOR

Highlights: • PD-L1 treatment upregulates CD206 but not CD86 expression. • PD-L1-induced DEGs are related to the immune response, mitochondrial function, and metabolism. • Nivolumab, LY294002, U0126, and rapamycin inhibit the PD-L1-stimulated CD206 expression. • PD-L1 promotes M2 polarization via Erk/Akt/mTOR. PD-L1 (programmed death-ligand 1) is the ligand of PD-1 (programmed cell death protein 1) and regulates inhibitory immune responses. It is well known that PD-L1 suppresses T cell function via binding to PD-1. However, little is known about the role of the PD-1/PD-L1 axis in macrophage polarization. According to previous studies, the function of the PD-1/PD-L1 axis in macrophage polarization is controversial, and the underlying mechanism has not been fully elucidated. Thus, we treated THP-1-derived macrophages with human PD-L1 Fc to determine the role of the PD-1/PD-L1 axis in macrophage polarization. To further explore the mechanism, we performed RNA sequencing and used specific inhibitors to identify the implicated signalling pathways. In this study, we found that PD-L1 induces the upregulation of CD206 expression, which is inhibited by nivolumab, LY294002, U0126, and rapamycin. Evaluation of differentially expressed genes (DEGs) and bioinformatics analysis indicated that PD-L1 also induces the upregulation of the expression of genes that maintain mitochondrial function and mediate metabolic switching. In addition, we did not detect PD-L1-induced CD86 alterations, indicating that PD-L1 treatment has no significant influence on M1 polarization. Taken together, these results suggest that PD-L1 binds to PD-1 and promotes M2 polarization accompanied by mitochondrial function enhancement and metabolic reprogramming via Erk/Akt/mTOR. This study elucidates the role of PD-L1 in macrophage polarization and verifies the underlying mechanisms for the first time. Considering that aberrantly upregulated PD-L1 expression contributes to a wide variety of diseases, targeting PD-L1-mediated macrophage polarization is a prospective therapeutic strategy for both neoplastic and nonneoplastic diseases.

60 APPLIED LIFE SCIENCES↗

ThO 2 and Th 1– x U x O 2 Nanoscale Materials and Thin Films for Nuclear Science Applications

This study investigates the dynamics and mechanisms of solution combustion synthesis (SCS) for the preparation of nanoscale ThO 2 and Th 1–x U x O 2 materials, utilizing metal nitrates (Th(NO 3 ) 4 and UO 2 (NO 3 ) 2 ) and acetylacetone (C 5 H 8 O 2 ) as reactants dissolved in a 2-methoxyethanol (C 3 H 8 O 2 ) solvent. By combining thermodynamic calculations, dynamic time–temperature profile measurements with differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA), this research reveals how variations in acetylacetone concentration and uranium content influence the structural parameters of the synthesized oxides. The time–temperature measurements show that the heating rate and maximum combustion temperatures are sensitive to acetylacetone concentration. DSC-TGA results indicate shifts in exothermic peak temperatures as the uranium content changes. The complexation between thorium and acetylacetone emerges as a critical factor, impacting combustion parameters and the structural characteristics of the final products. The uniform distribution of Th and U in the Th 1–x U x O 2 solid solution and the formation of nanoscale particles with strained crystallites are considered essential for the low-temperature densification of these materials for nuclear fuel pellet applications. Additionally, high-quality ThO 2 and Th 1–x U x O 2 thin (100–150 nm) films are successfully synthesized via electrospray deposition of combustible solutions followed by a brief period of heat treatment. Furthermore, these films exhibit excellent structural and morphological uniformity, making them ideal candidates for nuclear measurements, irradiation damage studies, and investigations into the physical properties of both pure and mixed oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin

The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub 2 ) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub 2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub 2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub 2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

60 APPLIED LIFE SCIENCES↗

Metastable multimeric G-quadruplex 2′FY-RNA aptamers that selectively bind pyoverdines

Two 2′FY-RNA aptamers with distinct sequences were selected for specific binding to pyoverdine-Pf5 (PVD-Pf5), increasing chromophore fluorescence upon binding. They also recognized the peptide portion of pyoverdines, as shown by their differential specificity for related variants. Computational analysis and experimental data (NMM binding, CD spectra) identified G-quadruplex structures that were thermally metastable but reformed in the presence of PVD-Pf5. Further structural studies mainly with one aptamer revealed imino proton peaks in 1D H-NMR and pressure stability up to 2 kbar. Electrophoretic evidence identified dimeric G-quadruplexes formed by the 2′FY-RNA aptamers and their RNA equivalents. While cations were necessary for PVD-Pf5 binding, they were not required for G-quadruplex formation. Given the established role of G-quadruplexes as protein interaction sites, multimeric G-quadruplexes offer a potential framework for structure-based regulatory mechanisms in cellular RNAs. In addition to previously characterized multimeric G-quadruplexes, these aptamers contribute novel sequences that expand the repertoire of known multimeric G-quadruplexes.

2′FY-RNA↗