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At least 1,387 records · Page 77

Characterization of biological materials with soft X-ray scattering

The complex structure of biological assemblies is crucial for function yet challenging to discern given the chemical similarities between constituent components. Hard X-ray techniques, for example, rely on small density differences between domains that lead to modest scattering intensities. Resonant soft X-ray scattering (RSoXS) uses X-rays below 2 keV to access absorption edges of low-Z elements. In this way, RSoXS can enhance scattering contrast between domains of different chemical compositions or bonding motifs, thus providing structural information about specific chemical motifs. RSoXS is emerging as a technique applicable for biological systems, having been used to characterize protein structure in solution and polysaccharide organization in plant cell walls. Sample environment instrumentation, however, is challenging in the current state of the art, particularly with liquid samples. Here, this chapter contains a brief introduction to RSoXS and current beamline capabilities, and provides methods to prepare, store, and mount biological samples for RSoXS characterization. Furthermore, key details during RSoXS and X-ray absorption data acquisition are highlighted and some future opportunities in RSoXS instrumentation for biological systems are discussed.

47 OTHER INSTRUMENTATION↗

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonal orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configuration. Approaches for measuring the dichroic increment ratio with modern dichrometers are further discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Single molecule characterization of anomalous transport in a thin, anisotropic film

Here, the diffusion of small, charged molecules incorporated in an anisotropic polyelectrolyte multilayers (PEMs) was tracked in three dimensions by combining single-molecule fluorescence localization (to characterize lateral diffusion) with Förster resonance energy transfer (FRET) between diffusing molecules and the supporting surface (to measure diffusion in the surface-normal direction). Analysis of the surface-normal diffusion required model-based statistical analysis to account for the inherently noisy FRET signal. Combining these distinct single-molecule methods, which are inherently sensitive to different length scales, permitted simultaneous characterization of severely anisotropic diffusion, which was more than three orders of magnitude slower in the surface-normal direction. We hypothesize that the anomalously slow surface-normal diffusion was related to the periodic distribution of charge in the PEM, which created electrostatic barriers. The motion was strongly subdiffusive, with anomalous temporal scaling exponents in lateral and normal directions, suggesting a connection to the transient, random fractal conformation of polymer chains in the film’s matrix.

36 MATERIALS SCIENCE↗

X-ray characterization of the micromechanical response ahead of a propagating small fatigue crack in a Ni-based superalloy

The small fatigue crack (SFC) growth regime in polycrystalline alloys is complex due to the heterogeneity in the local micromechanical fields, which result in high variability in crack propagation directions and growth rates. Here in this study, we employ a suite of techniques, based on high-energy synchrotron-based X-ray experiments that allow us to track a nucleated crack, propagating through the bulk of a Ni-based superalloy specimen during cyclic loading. Absorption contrast tomography is used to resolve the intricate 3D crack morphology and spatial position of the crack front. Initial near-field high-energy X-ray diffraction microscopy (HEDM) is used for high-resolution characterization of the grain structure, elucidating grain orientations, shapes, and boundaries. Cyclic loading is periodically interrupted to conduct far-field HEDM to determine the centroid position, average orientation, and average lattice strain tensor for each grain within the volume of interest. Reciprocal space analysis is used to further examine the deformation state of grains that plasticize in the vicinity of the crack. Analysis of the local micromechanical state in the grains ahead of the crack front is used to rationalize the advancing small crack path and growth rate. Specifically, the most active slip system in a grain, determined by the maximum resolved shear stress, aligns with the crack growth direction; and the degree of microplasticity ahead of the crack tip helps to identify directions for potential occurrences of crack arrest or propagation. The findings suggest that both the slip system level stresses and microplasticity events within grains are necessary to get a complete description of the SFC progression. Further, this detailed dataset, produced by a suite of X-ray characterization techniques, can provide the necessary validation, at the appropriate length-scale, for SFC models.

36 MATERIALS SCIENCE↗

Three-dimensional atomic scale characterization of {11$\overline{2}$2} twin boundaries in titanium

The {11$\overline{2}$2}<11$\overline{23}$> compression twin can accommodate a considerable amount of strain under c-axis compression in Ti. However, unlike the tensile twin, the structure of the {10$\overline{1}$2}$\langle$$\overline{1}$011$\rangle$ compressive twins has not been completely characterized. In this study, we apply a combined technique of HR-TEM characterization, topological analysis, and atomistic simulations to explore the facets that bound the {11$\overline{2}$2}<11$\overline{23}$> twin in Ti. In addition to the currently known facets (CTB and B-Py), six new facets are observed and categorized for the first time from atomic-scale TEM observations along five crystallographic directions. The six new facets are (11$\overline{2}$0)//(11$\overline{2}$6), PrPr1, PyPy1, (2$\overline{11}$1)//($\overline{1}$2$\overline{1}$2), (1$\overline{1}$04)//(01$\overline{11}$), and (01$\overline{1}$0)//(2$\overline{11}$4). Results from the topological and computational analysis are in reasonable agreement with and support the HRTEM observations. Specifically, (1) the observed facets align with low-index interfaces in both twin and matrix domains, (2) the facets with lower surface energies are found to form extended interfaces, and (3) high-surface-energy facets are found at the twin tip region and explained by the fact that the energy of the combined facet and facet junction configuration is energetically preferred in the twin tip region. These results not only provide a comprehensive understanding of the 3D structure of the {11$\overline{2}$2}<11$\overline{23}$> compressive twins in Ti, but also validate the MD procedure and the Ti interatomic potential employed. This is extremely important for future study of the {11$\overline{2}$2} twin mobility and interactions with other defects, both features that remain extremely challenging to capture in experiments.

36 MATERIALS SCIENCE↗

Characterizing material transitions in large-scale Additive Manufacturing

Integrating Multiple Materials (MM) into large-scale Additive Manufacturing (AM) is a key for various industrial applications wishing to incorporate site-specific properties into geometrically complex designs that are difficult to manufacture with traditional techniques. Printing with multiple materials is typically accomplished by using layers as natural material boundaries, but having the capability to switch between materials within a single layer without pausing would further expand MM possibilities. This study used Cincinnati Incorporated’s Big Area Additive Manufacturing (BAAM) system to explore material transitions with a novel dual-hopper that enables in-situ material blending of a pelletized feedstock. Constructing MM and functionally graded material (FGM) structures requires depositing a specific material composition at a specific geometric location to achieve a desired performance. Furthermore, accurately implementing this with the BAAM’s blended extrusion system requires a thorough understanding of the transition between distinct material compositions. This study characterizes a step-change transition between neat acrylonitrile butadiene styrene (ABS) and carbon fiber-reinforced ABS. Three distinct techniques were compared for analyzing the fiber content, and the transition zone between materials was characterized as a function of transition direction. The transition process was consistent to within 0.7 wt% carbon fiber variation between different layers and prints. The transition between materials was found to be directionally dependent, with ABS to CF/ABS having a transition length of 3.5 m compared to 3.2 m for CF/ABS to ABS. Furthermore, the transition from Material A to Material B was found to be repeatable with a possible variance in transition length of 0.3 m.

36 MATERIALS SCIENCE↗

Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)

Selection of highly productive algal strains is crucial for establishing economically viable biomass and bioproduct cultivation systems. Characterization of algal genomes, including understanding strain-specific differences in genome content and architecture is a critical step in this process. Using genomic analyses, we demonstrate significant differences between three strains of Chlorella sorokiniana (strain 1228, UTEX 1230, and DOE1412). We found that unique, strain-specific genes comprise a substantial proportion of each genome, and genomic regions with >80% local nucleotide identity constitute <15% of each genome among the strains, indicating substantial strain specific evolution. Furthermore, cataloging of meiosis and other sex-related genes in C. sorokiniana strains suggests strategic breeding could be utilized to improve biomass and bioproduct yields if a sexual cycle can be characterized. Finally, preliminary investigation of epigenetic machinery suggests the presence of potentially unique transcriptional regulation in each strain. Our data demonstrate that these three C. sorokiniana strains represent significantly different genomic content. Based on these findings, we propose individualized assessment of each strain for potential performance in cultivation systems.

09 BIOMASS FUELS↗

Functional and phenotypic flow cytometry characterization of Picochlorum soloecismus

Multiple physiological traits essential for efficient cellular function are important when considering the selection and engineering of algal species for biofuel and bioproduct generation. Bioengineering methods have become more ubiquitous producing several novel algal lines with potentially enhanced traits. Complex metabolic interactions, however, require greater depth in characterizing cellular responses to delineate mechanistic understanding. Here, we have developed fluorescence-based high-throughput flow cytometry protocols to facilitate characterization of cell morphology, membrane permeability, metabolic activity, cell viability, intracellular pH, and reactive oxygen species in isolates derived from the species Picochlorum soloecismus. Flow cytometry parameters were optimized for each assay. This suite of molecular flow cytometry probes and procedures can be utilized for rapid screening of optimal phenotypes in microalgae under various environmental conditions as new technical strategies for improving algae strain productivity are established.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of the quantumness of unsteerable tripartite correlations

Quantumness for a bipartite unsteerable quantum correlation is operationally characterized by the notion of super-unsteerability. Super-unsteerability refers to the requirement of a larger dimension of the random variable that the steering party has to preshare with the party to be steered in the classical simulation protocol to generate an unsteerable correlation than the local Hilbert space dimension of the quantum states (reproducing the given unsteerable correlation) at the steering party’s side. In the present study, this concept of super-unsteerability is generalized by defining the notion of super-bi-unsteerability for tripartite correlations, which is unsteerable across a bipartite cut. Genuine super-bi-unsteerability is defined as the occurrence of super-bi-unsteerability across all possible bipartite cuts. Specific example of genuine super-bi-unsteerability for tripartite correlations has been presented. This study provides a tool to characterize the genuine quantumness of tripartite quantum correlations which are unsteerable across every bipartite cut.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Wave energy resource characterization employing joint distributions in frequency-direction-time domain

Joint and marginal distributions in the frequency, direction, and time domain are employed to demonstrate their value for wave energy resource characterization when full spectra are available. Insights gained through analysis of these distributions support wave energy converter concept design, operation and maintenance. Spatial trends in the wave energy resource and contributing wave energy systems along the continental shelf of the West Coast of the United States are investigated using the most recent two-dimensional wave spectra measurements at four buoys over an eleven year period (2008 to 2018). Resource hot spots and dominant resolved energy resource bands in the frequency-direction-time domain are delineated. Resource attributes, including frequency and directional spreading, and seasonal variability, are characterized using joint distributions and marginal distributions of wave power spectra. North Pacific westerly swells in the winter season, augmented by Aleutian low-pressure southwesterly swells, are the principal suppliers of the dominant resource and main drivers influencing resource attributes. In conclusion, the modification of these systems southward, especially the North Pacific westerly swells, explains the observed spatial resource trends. The dominant resource wave period shifts two seconds to higher wave periods, thirty degrees in the dominant direction band to a more northward orientation, and forward by one month.

16 TIDAL AND WAVE POWER↗

Characterization of Two Extraordinary AmLi Neutron Sources

Two legacy AmLi sources, MRC-101 and MRC-103, are routinely used for neutron detector characterization and testing campaigns that Pacific Northwest National Laboratory manages for the Defense Threat Reduction Agency within the U.S. Department of Defense. However, applicability of source measurement data has been substantially limited due to the lack of original manufacturer documentation and cross comparison to other sources. This paper summarizes results of the measurement campaign conducted to better quantify source radionuclide content, neutron energy spectrum and emission rate of the AmLi sources. The source characterization study consisted of three major consecutive measurement exercises. First, gamma spectrometry measurements using a high purity germanium detector were used to estimate the radionuclide content and potential impurities of the AmLi sources. Then neutron spectral measurements were taken to determine the unique neutron energy distribution. Finally, assessments of the total neutron yields of the sources were made with measurements in a neutron well counter. The neutron detection efficiency for these measurements was determined via detailed Monte Carlo modeling based on the neutron energy distribution measured with the rotating neutron spectrometer. The most exciting and unexpected finding of the study was a significant contamination of the source material with beryllium, contributing up to 17% to the total neutron emission rate and correspondingly changing the neutron energy spectrum. Also, the obtained lithium-only portion of the measured energy distribution of the sources was compared against several AmLi spectra previously reported by different researchers.

AWCC, AmLi, beryllium contamination, neutron spect↗

Cloning and functional characterization of a phenolic acid decarboxylase from the liverwort Conocephalum japonicum

Some commercially important vinyl derivatives are produced by the decarboxylation of phenolic acids. Enzymatically, this process can be achieved by phenolic acid decarboxylases (PADs), which are able to act on phenolic acid substrates such as ferulic and p-coumaric acid. Although many microbial PADs have been characterized, little is known regarding their plant homologs. Transcriptome sequencing in the liverworts has identified seven putative PADs, which share a measure of sequence identity with microbial PADs, but are typically much longer proteins. Here, a PAD-encoding gene was isolated from the liverwort species Conocephalum japonicum. The 1197 nt CjPAD cDNA sequence was predicted to be translated into a 398 residue protein. When the gene was heterologously expressed in Escherichia coli, its product exhibited a high level of PAD activity when provided with either p-coumaric or ferulic acid as substrate, along with the conversion of caffeic acid and sinapic acid to their corresponding decarboxylated products. Both N- and C-terminal truncation derivatives were non-functional. The transient expression in tobacco of a GFP/CjPAD fusion gene demonstrated that the CjPAD protein is expressed in the cytoplasm. It is first time a PAD was characterized from plants and the present investigation provided a candidate gene for catalyzing the formation of volatile phenols.

60 APPLIED LIFE SCIENCES↗

Expression and characterization of the Plasmodium translocon of the exported proteins component EXP2

The malaria parasite Plasmodium falciparum requires the Plasmodium translocon of exported proteins (PTEX) to proliferate in human red blood cells. During the blood stages of malaria, several hundred parasite-encoded proteins are exported from the parasite into the cytosol of red blood cells. PTEX is the translocon for protein export and comprises 5 proteins: EXP2, PTEX150, PTEX88, Hsp101 and TRX2. Among them, EXP2 is thought to constitute the transmembrane pore, whereas the other components seem to play a role in unfolding the luggage proteins or providing a driving force. However, detailed functional and structural characterizations of PTEX proteins have not been performed. In this study, we expressed and characterized the membrane-associated component EXP2. Because expression of EXP2 is lethal to E. coli, EXP2 was expressed as a fusion protein with GST, and the recombinant EXP2 was obtained by protease digestion. The recombinant EXP2 formed pores in bilayer lipid membranes. The inner diameter of the pore was estimated to be approximately 3.5 nm based on electron microscopy images and channel currents. From this size and the molecular mass as determined by size exclusion chromatography and blue native polyacrylamide gel electrophoresis, we determined that the pore comprises approximately 10–12 EXP2 subunits. However, there is a possibility that the pore structure is different in the PTEX complex. These results provide important insights in the protein transport mechanism of PTEX, which will aid in developing new drugs targeting PTEX.

60 APPLIED LIFE SCIENCES↗

Pharmacological characterization of synthetic serine palmitoyltransferase inhibitors by biochemical and cellular analyses

Highlights: • Tetrahydropyrazolopyridine derivatives were characterized as SPT inhibitors. • The SPT inhibitors exhibited dual inhibitory activities against SPT2 and SPT3. • A SPT inhibitor bound to the SPT2 or SPT3 subunit in SPT enzyme complexes. • One of the SPT inhibitors exhibited a significantly slow dissociation from SPT. • The SPT inhibitors suppressed ceramide content in a non-small-cell lung cancer cell line. Human serine palmitoyltransferase (SPT) is a PLP-dependent enzyme residing in the endoplasmic reticulum. It catalyzes the synthesis of 3-ketodihydrosphingosine (3-KDS) from the substrates palmitoyl-CoA and l-serine. It is a rate-limiting enzyme for sphingolipid synthesis in cells. In the present study, we characterized and pharmacologically profiled a series of tetrahydropyrazolopyridine derivatives that potently inhibit human SPT enzymatic activity, including two cell-active derivatives and one fluorescent-labelled derivative. These SPT inhibitors exhibited dual inhibitory activities against SPT2 and SPT3. We used a fluorescent-labelled probe to molecularly assess the inhibitory mechanism and revealed its binding to the SPT2 or SPT3 subunit in the small subunit (ss) SPTa/SPT1/SPT2/or ssSPTa/SPT1/SPT3 functional complexes. One of the SPT inhibitors exhibited a significantly slow dissociation from the SPT complex. We confirmed that our SPT inhibitors suppressed ceramide content in non-small-cell lung cancer cell line, HCC4006, by performing a target engagement analysis. The potency of ceramide reduction correlated to that observed in a recombinant SPT2 enzyme assay. We thus elucidated and provided a fundamental understanding of the molecular mode of action of SPT inhibitors and developed potent, cell-active SPT inhibitors that can be used to clarify the biological function of SPT.

60 APPLIED LIFE SCIENCES↗

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↗