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At least 1,567 records · Page 87

Identification and functional characterization of three type III polyketide synthases from Aquilaria sinensis calli

Type III polyketide synthases (PKSs) play an important role in biosynthesis of various plant secondary metabolites and plant adaptation to environmental stresses. Aquilaria sinensis (A. sinensis) is the main plant species for production of agarwood, little is known about its PKS family. In this study, AsCHS1 and two new type III PKSs, AsPKS1 and AsPKS2, were isolated and characterized in A. sinensis calli. The comparative sequence and phylogenetic analysis indicated that AsPKS1 and AsPKS2 belonged to non-CHS group different from AsCHS1. The recombinant AsPKS1 and AsPKS2 produced the lactone-type products, suggesting their different enzyme activities from AsCHS1. Three PKS genes had a tissues-specific pattern in A. sinensis. Moreover, we examined the expression profiles of three PKS genes in calli under different abiotic stresses and hormone treatments. AsCHS1 transcript was most significantly induced by salt stress, AsPKS1 abundance was most remarkably enhanced by CdCl{sub 2} treatment, while AsPKS2 expression was most significantly induced by mannitol treatment. Furthermore, AsCHS1, AsPKS1 and AsPKS2 expression was enhanced upon gibberellins (GA3), methyl jasmonate (MeJA), or salicylic acid (SA) treatment, while three PKS genes displayed low transcript levels at the early stage under abscisic acid (ABA) treatment. In addition, three GFP:PKSs fusion proteins were localized in the cytoplasm and cell wall in Nicotiana benthamiana cells. These results indicated the multifunctional role of three type III PKSs in polyketide biosynthesis, plant resistance to abiotic stresses and signal transduction. - Highlights: • Two new PKS genes (AsPKS1 and AsPKS2) were isolated and characterized from A. sinensis. • The recombinant AsPKS1 and AsPKS2 catalyzed lactone-type products in vitro. • AsCHS1, AsPKS1 and AsPKS2 were involved in plant responses to abiotic stresses and hormone stimuli. • Our results also indicated that AsCHS1, AsPKS1 and AsPKS2 were predominantly localized in the cytoplasm and cell wall.

60 APPLIED LIFE SCIENCES↗

Biophysical characterization of actin bundles generated by the Chlamydia trachomatis Tarp effector

Highlights: • The F-actin binding domain of Tarp is sufficient to bundle filamentous actin. • Actin bundles formed by Tarp are more flexible than that of α-actinin and fascin. • Tarp mediated actin bundling is independent of actin nucleation. Chlamydia trachomatis entry into host cells is mediated by pathogen-directed remodeling of the actin cytoskeleton. The chlamydial type III secreted effector, translocated actin recruiting phosphoprotein (Tarp), has been implicated in the recruitment of actin to the site of internalization. Tarp harbors G-actin binding and proline rich domains required for Tarp-mediated actin nucleation as well as unique F-actin binding domains implicated in the formation of actin bundles. Little is known about the mechanical properties of actin bundles generated by Tarp or the mechanism by which Tarp mediates actin bundle formation. In order to characterize the actin bundles and elucidate the role of different Tarp domains in the bundling process, purified Tarp effectors and Tarp truncation mutants were analyzed using Total Internal Reflection Fluorescence (TIRF) microscopy. Our data indicate that Tarp mediated actin bundling is independent of actin nucleation and the F-actin binding domains are sufficient to bundle actin filaments. Additionally, Tarp-mediated actin bundles demonstrate distinct bending stiffness compared to those crosslinked by the well characterized actin bundling proteins fascin and alpha-actinin, suggesting Tarp may employ a novel actin bundling strategy. The capacity of the Tarp effector to generate novel actin bundles likely contributes to chlamydia's efficient mechanism of entry into human cells.

60 APPLIED LIFE SCIENCES↗

Molecular characterization of single-chain antibody variable fragments (scFv) specific to Pep27 from Streptococcus pneumoniae

Highlights: • Two antibody fragments specific to pneumococcal autolysis factor Pep27 are selected. • The antibody fragments show sub-micromolar affinity with good selectivity. • Molecular docking supports epitope on Pep27 identified by alanine scanning. Pep27 from Streptococcus pneumoniae is reported to initiate pneumococcal autolysis, thereby constituting a major virulence factor. Although a few antisera recognizing Pep27 have been reported, no monoclonal, well-characterized antibody for Pep27 has been developed. Here we screened two single-chain antibody variable fragments (scFv) using a phage display from a large human synthetic scFv library to select clones E2 and F9. Dissociation constants (K{sub d}) of E2 and F9 were 1.1 μM and 0.50 μM, respectively. E2 and F9 did not cross-react with other pneumococcal and unrelated proteins. The epitopes of Pep27 were localized to residues 24, 26 and 27 by alanine scanning. Molecular docking analysis supported the experimentally investigated epitope. The E2 and F9 clones specifically detected Pep27 in an environment mimicking in vivo conditions, demonstrated in human serum. The scFv clones characterized here represent molecular tools for the detection of pneumococcal diseases with potential for further improvement in affinity.

60 APPLIED LIFE SCIENCES↗

Identification and characterization of the zinc finger protein SjZF in Schistosoma japonicum

Highlights: • The zinc finger protein SjZF in S. japonicum was identified and characterized. • SjZF was mainly located in the intestinal tract of adult worms and the vitelline glands of females. • The rSjZF induced significant protection against S. japonicum infection in mouse. Schistosomiasis represents one of the most prevalent parasitic infections affecting over 249 million people worldwide. The pathological damage is mainly caused by the eggs laid by female schistosomes. Zinc finger proteins (ZFPs) usually play critical roles in many biological functions. In this study, we cloned, identified and characterized the zinc finger protein SjZF of Schistosoma japonicum. SjZF ortholog proteins were also identified in S. mansoni, S. haematobium, Opisthorchis viverrini and O. sinensis. Fluorescence localization showed that SjZF was particularly expressed in the worm gut of both genders and the vitelline glands of females. In vitro RNAi assay indicated that decreased expression of SjZF could affect the survival rate of adult worms. The immune protection assay indicated that rSjZF did partially protect mice with 54.8% reduction in the worm burden and 34.1% reduction in the liver eggs. Taken in concert, our preliminary results suggest that SjZF may be a potential vaccine candidate for schistosomiasis and may further provide evidence for a possible role of SjZF in the development of schistosomes.

60 APPLIED LIFE SCIENCES↗

Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1

Highlights: • The crystal structure of PaAlr was solved. • Sequences and structures were compared among species with two alanine racemases. • d-Lysine was observed in active site, but not covanlently linked, which is somehow similar but different from PaDadX. • Optimal reaction conditions were characterized. Alanine racemase is a pyridoxal-5′-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.

60 APPLIED LIFE SCIENCES↗

Characterization of a novel ω-transaminase from a Triassic salt mine metagenome

Highlights: • Metagenome derived from hypersaline environment, formed during Triassic Period. • Novel and active ω-transaminase enzyme synthesized from environmental DNA. • Molecular modeling and docking simulations reveal equivalents to mesophilic enzymes. • Characterization shows different profile to previous halophilic transaminases. Chiral amines are valuable building blocks for the pharmaceutical industry, and are increasingly synthesized by transaminase-mediated (TAm) synthesis. Currently available TAms, primarily isolated from the genomes of cultured mesophilic bacteria, often suffer from a number of drawbacks, including poor substrate range and an inability to tolerate the harsh conditions often demanded by industrial processes. These characteristics have, in part, driven the search for novel biocatalysts from both metagenomic sources and extreme environments. Herein, we report the isolation and characterization of an ω-TAm from a metagenome of a Triassic salt mine in Kilroot, N. Ireland, an extremely hypersaline environment formed circa 220–250 mya. The gene sequence was identified based on homology with existing bacterial TAms, synthesized within a pET28a(+) plasmid and expressed in E. coli BL21 DE3 cells. The resultant 49 kDa protein accepted (S)-methylbenzylamine (MBA) as amino donor and had a specific activity of 0.54 U/mg using α-ketoglutarate (ΑKG) as substrate. Molecular modeling and substrate docking indicated the presence of key residues, conserved in a number of other TAms. Despite the hypersaline environment from which it was isolated, the enzyme displayed low halotolerance, highlighting that not all biocatalysts will demonstrate the extreme characteristics associated with their source environment. This study does however reinforce the viability of mining metagenomic datasets as a means of discovering novel and functional biocatalysts, and adds to a currently scant list of such examples in the field of TAms.

60 APPLIED LIFE SCIENCES↗

Near-infrared spectroscopy as a green analytical tool for sustainable biomass characterization for biofuels and bioproducts: An overview

Biomass, a widely used renewable energy source, requires characterization to optimize biofuel and bioproduct processes, customize feedstocks, and ensure economic and environmental sustainability. Conventional wet-chemistry methods for biomass analysis are slow, expensive, and require significant reagents and skilled personnel. In contrast, near-infrared (NIR) spectroscopy, a faster, cost-effective, and reagent-free green technology, enables non-destructive biomass analysis with minimal sample preparation. This study provides an overview of the fundamentals of NIR spectroscopy and explores its recent applications for analyzing various biomass properties important to the biofuel and bioproduct industry. The study also critically evaluates the challenges and opportunities of using NIR spectroscopy for biomass analysis. This review aims to guide future research for rapid and high throughput characterization of biomass in the biomass industry, supporting the United Nations’ sustainable development goal (SDG) 7: producing affordable and sustainable energy.

Biofuels↗

Generation and characterization of carbon fiber microstructure in atomistic simulations

A clear understanding of carbon fiber (CF) microstructure is necessary for the development of high strength CFs. Here, we present an atomistic approach for generating and characterizing realistic mi- crostructures of CFs. Large-scale reactive molecular dynamics simulations are used to generate a set of distinct CF microstructures. Comprehensive characterization of the simulated microstructures is enabled by the development of a suite of computational structural analysis tools capable of evaluation of hy- bridization states of carbon atoms, populations and orientations of individual carbon rings, degree of graphitization, and pore size distribution. The calculation of X-ray diffraction profiles provides a direct link between the structural features of simulated samples and experimental data available for CFs. The CF generation algorithm is shown to produce microstructures with experimental densities and with structural characteristics matching those of PAN-based CFs. The key structural features affecting the properties of CFs, such as the relative fractions of graphitic, turbostratic and amorphous micro- constituents, degree of alignment, pore size distributions, and chemical cross-linking can be effectively controlled in simulations, thus enabling efficient exploration of structureeproperties relationships in CFs. The capabilities of the developed approach are illustrated by performing computational analysis of the mechanical deformation and fracture of CFs under axial tensile loading.

36 MATERIALS SCIENCE↗

Proteogenomic Characterization of Endometrial Carcinoma

We undertook a comprehensive proteogenomic characterization of 95 endometrial carcinomas, of which 83 were endometrioid tumors and 12 were serous tumors. This analysis revealed new consequences of perturbations to the p53 and Wnt/ß-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new insights into proteomic markers of clinical and genomic tumor subgroups, some of which are in known druggable pathways. We performed a broad genome-wide acetylation survey, one of the first of its kind, yielding insights into regulatory mechanisms of histone acetylation. We also characterized the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, further our understanding of the molecular mechanisms underlying endometrial carcinoma, and identify new avenues for investigating potential therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of a sustainable sulfur polymer concrete using activated fillers

Sulfur polymer concrete (SPC) is a thermoplastic composite concrete consisting of chemically modified sulfur polymer and aggregates. This study focused on the characterization of a new SPC that has been developed as a sustainable construction material. It is made from industrial by-product sulfur that is modified with activated fillers of fly ash, petroleum refinery residual oil, and sand. Unlike conventional sulfur polymer cements made using dicyclopentadiene as a chemical modifier, the use of inexpensive industrial by-products enables the new SPC to cost-effectively produce sustainable, low-carbon, thermoplastic binder that can compete with conventional hydraulic cement concretes. A series of characterization analyses was conducted including thermal analysis, X-ray diffraction, and spatially-resolved Xray absorption spectroscopy to confirm the polymerization of sulfur induced from the presence of the oil. In addition, mechanical testing, internal pore structure analysis, and scanning electron microscope studies evaluate the performance of this new SPC as a sustainable construction material with a reduced environmental impact.

54 ENVIRONMENTAL SCIENCES↗

Mechanical Characterization of Low Modulus Polymer-Modified Calcium-Silicate-Hydrate (C-S-H) Binder

Calcium-silicate-hydrate (C-S-H) represents a key microstructural phase that governs the mechanical properties of concrete at a large scale. Defects in the C-S-H phase are also responsible for the poor ductility and low tensile strength of concrete. Manipulating the microstructure of C-S-H can lead to new cementitious materials with improved structural performance. This paper presents an experimental investigation aiming to characterize a new synthetic polymer-modified synthetic calcium-silicate-hydrate (C-S-H)/styrene-butadiene rubber (SBR) binder. The new C-S-H/SBR binder is produced by calcining calcium carbonate and mixing this with fumed silica (SiO 2 ), deionized water and SBR. Mechanical, physical, chemical and microstructural characterization was conducted to measure the properties of new hardened C-S-H binder. Results from the experimental investigation demonstrate the ability to engineer a new C-S-H binder with low elastic modulus and improved toughness and bond strength by controlling the SBR content and method of C-S-H synthesis. The new binder suggests the possible development of a new family of low-modulus silica-polymer binders that might fit many engineering applications such as cementing oil and gas wells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization of alkali silica reaction gels using Raman spectroscopy

The ability of Raman spectroscopy to characterize amorphous materials makes this technique ideal to study alkali silica reaction (ASR) gels. The structure of several synthetic ASR gels was thoroughly characterized using Raman Spectroscopy. The results were validated with additional techniques such as Fourier transmission infrared spectroscopy, X-ray powder diffraction and thermogravimetric analysis. The Raman spectra were found to have two broad bands in the 800 to 1200 cm{sup −1} range and the 400 to 700 cm{sup −1} range indicating the amorphous nature of the gel. Important information regarding the silicate polymerization was deduced from both of these spectral regions. An increase in alkali content of the gels caused a depolymerization in the silicate framework which manifested in the Raman spectra as a gradual shift of predominant peaks in both regions. The trends in silicate depolymerization were in agreement with results from a NMR spectroscopy study on similar synthetic ASR gels.

36 MATERIALS SCIENCE↗

Laser diagnostics to characterize the in-flame growth of platinum nanoparticles manufactured by the reactive spray deposition technology

Reactive Spray Deposition Technology (RSDT) is an atmospheric pressure, flame-based advanced manufacturing method used to fabricate Membrane Electrode Assemblies (MEAs) for proton exchange fuel cells and water electrolyzers. RSDT combines the flame synthesis of catalyst nanoparticles and their deposition onto the membrane in one step. The properties of the synthesized nanoparticles, such as their Size Distribution Function (SDF), determine the manufactured electrodes’ performance, which can be evaluated when the deposition is complete via ex-situ characterization of the products. Efforts to improve RSDT for manufacturing state-of-the-art MEAs can be significantly enhanced with integrated laser diagnostics that enable in situ measurement of the synthesized catalyst nanoparticles. This paper reports the implementation of laser diagnostics in an RSDT facility and evaluates their potential to assist the manufacturing process. Laser Light Scattering (LS) and Laser-Induced Incandescence (LII) measurements are performed in the oxygen-rich zone of the flame at various distances from the flame fuel jet nozzle downstream of its luminous region. The measurements quantitatively track the evolution in size and volume fraction of platinum-based nanoparticles in two flames that yield different catalytic properties in the manufactured electrodes. The profiles of the measured nanoparticles’ volume fraction along the flame axis can be estimated a priori so that the average nanoparticle sizes can be measured in quasi-real time via LS. Nanoparticles experience an extremely slow growth rate while being convected at distances from 150 nm to 300 nm from the fuel nozzle. Complementary characterizations of the synthesized nanoparticles are performed ex-situ via High-Angle Annular Darkfield Scanning Transmission Electron Microscopy (HAADF-STEM) image analyses of samples collected on grids at a fixed distance from the fuel jet nozzle. Comparing the results from laser and microscopy techniques not only cross-validates the findings but also provides the parameters to infer the bimodal SDF in-situ and yields evidence that the coagulation efficiency of the synthesized nanoparticles has extremely low values in the investigated zone of the flames.

Rayleigh Light Scattering (LS)↗

The role of energy transfer and competing bimolecular reactions in characterizing the unimolecular dissociations of allylic radicals

Resonantly stabilized radicals (RSR's) such as allylic radicals typically have bond energies exceeding 45 kcal/mol and are therefore reasonably long-lived up to quite high temperatures. Consequently, kinetics of the unimolecular dissociations and bimolecular reactions of these long-lived RSR's assume significance in high temperature chemically reacting systems such as in flames. Our recent analyses (J. Cho et al., Proc. Comb. Inst., 2022) of the uncertainty propagated by the energy transfer parameters for 1-methylallyl (1MA) dissociation to the laminar flame speed, indicates an intricate coupling between the kinetics of 1MA dissociation (chain propagation) and its reaction with H-atoms (chain-termination). Here, this work extends such analyses to other C 3 – C 5 allylic radicals: allyl, 2-methylallyl, 1,1-dimethylallyl, 1,2-dimethylallyl, and 1,3-dimethylallyl. Theoretical kinetics for the C 3 – C 4 allylic radicals were taken from prior literature studies (J.A. Miller et al., J. Phys. Chem., 2008; J. Cho et al., Proc. Comb. Inst., 2022; R.S. Tranter et al., Proc. Comb. Inst., 2017). Potential energy surfaces were newly computed for the dissociations of the larger C5 allylic radicals and the reactions of these radicals with H-atoms. These PES's were then used to calculate rate constants for the relevant unimolecular and bimolecular reactions. Energy transfer has a crucial role to play in these pressure-dependent reactions and therefore the present kinetics calculations relied on a-priori predictions of collisional energy transfer parameters to best characterize the branching between chain propagating unimolecular dissociations of these allylic radicals and chain terminating bimolecular reactions of these RSR's with H-atoms. Prompt dissociations are now established to be a universal feature of free radical dissociations. Here we have also characterized the propensity for prompt dissociations in these more-stable allylic RSR's and their role in combustion simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Examining infrared thermography based approaches to rapid fatigue characterization of additively manufactured compression molded short fiber thermoplastic composites

A novel additive manufacturing (AM) methodology combined with a compression molding (CM) process has been developed to optimize the microstructure of short fiber thermoplastic composites (SFTs)with higher fiber alignment and lower porosity, yielding superior stiffness, strength, and structural integrity. Here, the current work examines the efficacy of the ‘passive’ infrared thermography (IRT) techniques for rapid fatigue characterization of SFTs that use the surface temperature evolution during cyclic loading due to self-heating as a fatigue indicator. A comparison of fatigue limits obtained from traditional stress-life (SN) (≈53.1%σ uts ) and IRT (≈54.1%σ uts ) shows a close match. However, the SN curve required 18 specimens and two weeks of continuous cyclic testing, while IRT used three specimens with 5 hours of testing. Thus, the IRT approach provides an accelerated testing framework for rapidly estimating the fatigue limit. Additionally, existing phenomenological approaches to IRT fatigue characterization have been examined.

42 ENGINEERING↗

Microstructural characterization and assessment of mechanical properties of concrete based on combined elemental analysis techniques and Fast-Fourier transform-based simulations

This paper presents a pixel-based modeling approach of concrete which combines an experimental characterization of concrete and the Fast-Fourier transform simulations. High-resolution phase maps created from experimental characterization by micro X-ray fluorescence, energy dispersive X-ray analysis, and X-ray diffraction contain 9 different phases, including 22.17 vol.% of hydrated cement paste, 54.21 vol.% of minerals, and 23.62 vol.% of interfaces. These phases provide the input for determining the effective elastic properties, coupled with Fast-Fourier transform-based simulation. The simulation results show that the effective range of Young’s modulus of concrete is comparable with the range of experimental values ~ 37 ± 4 GPa with the assumption of realistic properties of interfaces.

36 MATERIALS SCIENCE↗

Characterization data of an (AlFeNiTiVZr) 1-x Cr x multi-principal element alloy continuous composition spread library

The data provided in this article is related to the research article entitled “Phase stabilization and oxidation of a continuous composition spread multi-principal element (AlFeNiTiVZr) 1-x Cr x alloy”. This data article describes the high-throughput synthesis and characterization processes of an (AlFeNiTiVZr) 1-x Cr x alloy system. Continuous composition spread (CCS) thin-film libraries were synthesized by co-depositing an AlFeNiTiVZr metal alloy target and Cr target via magnetron sputtering. Post-processing was performed on the sample libraries with a vacuum anneal at 873 K and an air anneal at 873 K. Compositional data was determined via WDS in order to verify parameters provided by an in-house sputter model. Crystallographic data was captured via synchrotron diffraction and diffractograms were compared as a function of the change in Cr concentration. These measurements were taken in order to observe phase behavior after oxidation throughout the composition library. Furthermore, vibrational spectrographic data is provided of the oxidized library to show surface speciation along the composition gradient of the alloy system. The structural and oxidative behavior of the (AlFeNiTiVZr) 1-x Cr x alloy can be analysed using the data provided in this article. Additionally, this characterization dataset can be utilized in machine learning algorithms for determining important features and parameters for future hypothesis generation of functional multi-principal element alloys (MPEAs).

36 MATERIALS SCIENCE↗

Characterizing Long COVID: Deep Phenotype of a Complex Condition

Background: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or "long COVID"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies. Methods: The Human Phenotype Ontology (HPO) is a widely used standard for exchange and analysis of phenotypic abnormalities in human disease but has not yet been applied to the analysis of COVID-19. Funding: We identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to HPO terms. We present layperson synonyms and definitions that can be used to link patient self-report questionnaires to standard medical terminology. Long COVID clinical manifestations are not assessed consistently across studies, and most manifestations have been reported with a wide range of synonyms by different authors. Across at least 10 cohorts, authors reported 31 unique clinical features corresponding to HPO terms; the most commonly reported feature was Fatigue (median 45.1%) and the least commonly reported was Nausea (median 3.9%), but the reported percentages varied widely between studies. Interpretation: Translating long COVID manifestations into computable HPO terms will improve analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared/pooled more effectively. Furthermore, mapping lay terminology to HPO will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, thereby improving the stratification, diagnosis, and treatment of long COVID.

60 APPLIED LIFE SCIENCES↗