Plant-Based Biosensors for Detecting CRISPR-Mediated Genome Engineering
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59 BASIC BIOLOGICAL SCIENCES↗
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An Intein-Mediated Split–nCas9 System for Base Editing in Plants
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Oxic–anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors
Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic–anoxic cycling increased the mobilization of organic C, increased nitrate (NO 3 – ) removal rates, and attenuated production of nitrous oxide (N 2 O). Here, in this work, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO 3 – removal and attenuated N 2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic–anoxic transition was strongly correlated with the N 2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.
59 BASIC BIOLOGICAL SCIENCES↗
Recent Developments in Revealing the Impact of Complex Metal Oxide Reconstruction on Catalysis
Surface reconstruction of complex metal oxides refers to the alterations of the topmost catalyst surface, relative to the bulk structure, following exposure to pretreatment or reaction conditions during heterogeneous catalysis. (1) This structural and electronic transformation may involve (1) changes of the exposed crystallographic facets, (2) changes in chemical composition, such as the enrichment of specific elements, and, (3) morphological variations, including surface roughness and defects (Scheme 1). Beyond relaxation, surface reconstruction here also encompasses disruptions to the periodicity of the sublayers and changes to its stoichiometry. This change significantly influences the chemical properties of the catalyst surface, such as redox sites, (2) acid/base pairs, hydroxyl groups, (3) and surface defects. Surface reconstruction occurs due to the thermodynamic drive to lower the surface energy of the catalyst under the surrounding environment (e.g., temperature, chemical potential of species present). In addition to the treatment or reaction conditions, the extent of reconstruction also depends on the elements in the metal oxide structure. For instance, annealing ABO 3 perovskites (SrTiO 3 , BaTiO 3 , and BaZrO 3 ) at high temperatures (500 °C) in O 2 has a very different impact on the A/B ratio at the surface (ranging from 0.9 to 2.5), depending on the identity of A and B. (4) Metal oxide surface reconstruction under an electric field and exposure to acidic and alkaline media has recently gained increased attention in electrocatalysis, such as in the oxygen evolution reaction (OER); (5,6) however, in this Viewpoint we focus on the impact of surface reconstruction on thermal catalysis, a critical enduring research theme with ongoing challenges. Here, we start showcasing approaches to characterize surface reconstruction at the topmost surface layer, such as low-energy ion scattering (LEIS), discussing advantages and limitations. Next, we connect characterization of surface reconstruction to site-specific kinetic analysis, enabled via steady-state isotopic transient kinetic analysis (SSITKA), and we express our viewpoint on building structure–performance relationships by deeply understanding reconstructed surfaces. Later, we comment on the potential of tuning surface reconstruction to enhance catalytic performance. Finally, we explore the interplay between surface reconstruction and the “intelligent behavior”.
alcohol conversion↗
Post-puff SOL broadening on MAST-U under high-recycling conditions: evidence consistent with cross-field transport changes
Transient broadening of the scrape-off layer (SOL) density profile can modify main-chamber first-wall particle fluxes and divertor loading, yet its control parameters remain debated between divertor-regime transitions, neutral dynamics and changes in cross-field transport. We investigate fueling-driven SOL density-profile evolution and post-fueling relaxation on MAST-Upgrade (MAST-U) in ohmic L-mode, using two otherwise similar double-null Conventional Divertor discharges (I p = 450 kA, B T = 0.33 T) with identical 50 ms low-field side gas puffs; the only intentional difference is the puff start time. Upstream Thomson scattering shows that both discharges develop a transient far-SOL density profile modification, expressed as an increased SOL-width metric λ n e and a far-SOL enhancement consistent with a shoulder-like signature. In the earlier-puff case, the SOL-width metric remains elevated after puff termination and the post-puff decay time scales are systematically longer across the analysed radii. Outer-target Langmuir probes indicate high-recycling conditions during the analysed window (few-eV T e with radially peaked j sat,∥ and q ∥ profiles, without signatures of deep detachment). The outer-divertor collisionality proxy Λ div is elevated in both cases and does not discriminate between the different post-puff persistence. The target-integrated ion flux proxy ∫ J sat dA evolves nearly identically in both discharges when aligned to the puff start. Taken together, these observations suggest that the late/post-puff upstream SOL evolution is not set by parallel exhaust to the outer targetalone and is more consistent with upstream cross-field redistribution, with a possible role for plasma–neutral coupling and fueling geometry.
MAST-U↗
The endocannabinoid system in bovine tissues: characterization of transcript abundance in the growing Holstein steer
Abstract Background The endocannabinoid system (ECS) is highly integrated with seemingly all physiological and pathophysiological processes in the body. There is increasing interest in utilizing bioactive plant compounds, for promoting health and improving production in livestock. Given the established interaction between phytochemicals and the ECS, there are many opportunities for identification and development of therapies to address a range of diseases and disorders. However, the ECS has not been thoroughly characterized in cattle, especially in the gastrointestinal tract. The objective of this study was to characterize the distribution and transcriptional abundance of genes associated with the endocannabinoid system in bovine tissues. Methods Tissues including brain, spleen, thyroid, lung, liver, kidney, mesenteric vein, tongue, sublingual mucosa, rumen, omasum, duodenum, jejunum, ileum and colon were collected from 10-mo old Holstein steers (n = 6). Total RNA was extracted and gene expression was measured using absolute quantification real time qPCR. Gene expression of endocannabinoid receptorsCNR1andCNR2, synthesis enzymesDAGLA,DAGLBandNAPEPLD, degradation enzymesMGLLandFAAH, and transient receptor potential vanilloidsTRPV3andTRPV6was measured. Data were analyzed in R using a Kruskal-Wallis followed by a Wilcoxon rank-sum test. Results are reported as the median copy number/20 ng of equivalent cDNA (CN) with interquartile range (IQR). Results The greatest expression ofCNR1andCNR2was in the brain and spleen, respectively. Expression of either receptor was not detected in any gastrointestinal tissues, however there was a tendency (P = 0.095) forCNR2to be expressed above background in rumen. Expression of endocannabinoid synthesis and degradation enzymes varied greatly across tissues. Brain tissue had the greatestDAGLAexpression at 641 CN (IQR 52;P ≤ 0.05).DAGLBwas detected in all tissues, with brain and spleen having the greatest expression (P ≤ 0.05). Expression ofNAPEPLDin the gastrointestinal tract was lowest in tongue and sublingual mucosal. There was no difference in expression ofNAPEPLDbetween hindgut tissues, however these tissues collectively had 592% greater expression than rumen and omasum (P ≤ 0.05). WhileMGLLwas found to be expressed in all tissues, expression ofFAAHwas only above the limit of detection in brain, liver, kidney, jejunum and ileum.TRPV3was expressed above background in tongue, rumen, omasum and colon. Although not different from each other, thyroid and duodenum had the greatest expression ofTRPV6, with 285 (IQR 164) and 563 (IQR 467) CN compared to all other tissues (P < 0.05). Conclusions These data demonstrate the complex distribution and variation of the ECS in bovine tissues. Expression patterns suggest that regulatory functions of this system are tissue dependent, providing initial insight into potential target tissues for manipulation of the ECS.
Veterinary Sciences↗
Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid
Agrobacterium is not only a costly plant pathogen but is also an essential tool for plant transformation. Though Agrobacterium-mediated transformation (AMT) has been heavily studied, its polygenic nature and complex transcriptional regulation make identification of the genetic basis of transformational efficiency difficult through traditional genetic and bioinformatic approaches. Here, we use a bottom-up synthetic approach to systematically engineer the tumor-inducing plasmid (pTi), wherein the majority of virulence machinery is encoded. Using a validated toolkit to control Agrobacterium gene expression in planta, we perform a quantitative dissection of AMT to investigate the contributions of critical vir-genes at different expression levels. We construct a synthetic pTi capable of transient plant and stable fungal transformation and characterize bottlenecks and solutions for complex polygenic synthetic pTi designs. Our reductionist approach demonstrates how bottom-up engineering can be used to dissect and elucidate the genetic underpinnings of complex biological traits, laying the foundation for future engineering to establish full synthetic control over the critical process of AMT.
Agrobacterium-mediated transformation↗
Viral‐mediated delivery of morphogenic regulators enables leaf transformation in Sorghum bicolor (L.)
Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom (Bbm), Wuschel2 (Wus2), Wuschel-like homeobox protein 2a (Wox2a) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.
59 BASIC BIOLOGICAL SCIENCES↗
Flux-based three-dimensional electrodynamic modeling approach to superconducting circuits and materials
Modeling the behavior of superconducting electronic circuits containing Josephson junctions is crucial for the design of superconducting information processors and devices. In this paper, we introduce DEC-QED, a computational approach for modeling the electrodynamics of superconducting electronic circuits containing Josephson junctions in arbitrary three-dimensional electromagnetic environments. DEC-QED captures the nonlinear response and induced currents in BCS superconductors and accurately captures phenomena such as the Meissner effect, flux quantization, and Josephson effects. Using a spatial coarse-graining formulation based on discrete exterior calculus (DEC), DEC-QED can accurately simulate transient and long-time dynamics in superconductors. Finally, the expression of the entire electrodynamic problem in terms of the gauge-invariant flux field and charges makes the resulting classical field theory suitable for second quantization.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Crystal Structure and Characterization of Human Heavy-Chain Only Antibodies Reveals a Novel, Stable Dimeric Structure Similar to Monoclonal Antibodies
We report the novel crystal structure and characterization of symmetrical, homodimeric humanized heavy-chain-only antibodies or dimers (HC2s). HC2s were found to be significantly coexpressed and secreted along with mAbs from transient CHO HC/LC cotransfection, resulting in an unacceptable mAb developability attribute. Expression of full-length HC2s in the absence of LC followed by purification resulted in HC2s with high purity and thermal stability similar to conventional mAbs. The V H and C H 1 portion of the heavy chain (or Fd) was also efficiently expressed and yielded a stable, covalent, and reducible dimer (Fd2). Mutagenesis of all heavy chain cysteines involved in disulfide bond formation revealed that Fd2 intermolecular disulfide formation was similar to Fabs and elucidated requirements for Fd2 folding and expression. For one HC2, we solved the crystal structure of the Fd2 domain to 2.9 Å, revealing a highly symmetrical homodimer that is structurally similar to Fabs and is mediated by conserved (C H 1) and variable (V H ) contacts with all CDRs positioned outward for target binding. Interfacial dimer contacts revealed by the crystal structure were mutated for two HC2s and were found to dramatically affect HC2 formation while maintaining mAb bioactivity, offering a potential means to modulate novel HC2 formation through engineering. These findings indicate that human heavy-chain dimers can be secreted efficiently in the absence of light chains, may show good physicochemical properties and stability, are structurally similar to Fabs, offer insights into their mechanism of formation, and may be amenable as a novel therapeutic modality.
60 APPLIED LIFE SCIENCES↗
Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods
Symbiotic relationships between heterotrophic and phototrophic partners are common in microbial eukaryotes. Among Arcellinida (Amoebozoa) several species are associated with microalgae of the genus Chlorella (Archaeplastida). So far, these symbioses were assumed to be stable and mutualistic, yet details of the interactions are limited. Here, we analyzed 22 single-cell transcriptomes and 36 partially-sequenced genomes of the Arcellinida morphospecies Hyalosphenia papilio, which contains Chlorella algae, to shed light on the amoeba-algae association. By characterizing the genetic diversity of associated Chlorella, we detected two distinct clades that can be linked to host genetic diversity, yet at the same time show a biogeographic signal across sampling sites. Fluorescence and transmission electron microscopy showed the presence of intact algae cells within the amoeba cell. Yet analysis of transcriptome data suggested that the algal nuclei are inactive, implying that instead of a stable, mutualistic relationship, the algae may be temporarily exploited for photosynthetic activity before being digested. Furthermore, differences in gene expression of H. papilio and Hyalosphenia elegans demonstrated increased expression of genes related to oxidative stress. Together, our analyses increase knowledge of this host-symbiont association and reveal 1) higher diversity of associated algae than previously characterized, 2) a transient association between H. papilio and Chlorella with unclear benefits for the algae, 3) algal-induced gene expression changes in the host.
59 BASIC BIOLOGICAL SCIENCES↗
Neonatal Zika virus infection causes transient perineuronal net degradation
Perineuronal nets (PNNs) form a specialized extracellular matrix that predominantly surrounds parvalbumin (PV)-expressing GABAergic inhibitory interneurons and help regulate neuronal activity. Their formation early in the postnatal period is regulated by neuronal signaling and glial activation raising concerns that part of the long-term effects ascribed to perinatal viral infections could be mediated by altered PNN formation. Previously, we developed a model of neonatal Zika virus (ZIKV) infection where mice have lifelong neurological sequelae that includes motor disfunction and reduced anxiety coupled with a persistent low-grade expression in proinflammatory markers despite resolving the acute infection. Here, we demonstrate that ZIKV infection to P1 neonatal mice results in a reduction of PNN formation during the acute disease with significant reduction in Wisteria floribunda agglutinin (WFA) staining at the peak of infection [15 days post infection (dpi)] that persisted after the symptoms resolved (30 dpi). At 60 dpi, when there is residual inflammation in the CNS, the number of WFA + cells and the level of WFA staining as well as levels of aggrecan and brevican in the brains of convalescent mice were not different from those in uninfected controls, however, there was increased frequency of PNNs with an immature phenotype. Over time the impact of the perinatal infection became less evident and there were no clear differences in PNN morphology between the groups at 1 year post infection. Of note, the reduction in PNNs during acute ZIKV infection was not associated with decreased mRNA levels of aggrecan or brevican, but increased levels of degraded aggrecan and brevican indicating increased PNN degradation. These changes were associated with increased expression of matrix metalloproteinase 12 (MMP12) and MMP19, but not MMP9, a disintegrin and metalloproteinase with thrombospondin motifs 4 (ADAMTS4) or ADAMTS5. Together our findings indicate that infection at the time of PNN development interferes with PNN formation, but the nets can reform once the infection and inflammation subside.
60 APPLIED LIFE SCIENCES↗
Analytical model for laser-induced transient grating measurements of thermal diffusivity in non-opaque materials
The thermal transport and elastic properties of materials are often measured using the laser-induced transient grating spectroscopy (TGS) technique. The analysis of the TGS signal usually involves fitting well-known expressions, derived assuming the limiting cases of opaque or transparent materials, to the measured data. In this paper, the system of thermoelastic equations is analytically solved for an isotropic homogeneous material assuming finite laser penetration depth, which is an important consideration when the penetration depth is on the order of the acoustic wavelength. The need to use such a solution is discussed and compared to the expression for opaque material. The solution is benchmarked against TGS signal measured on single-crystal silicon with {100} surface orientation and is found to significantly improve the accuracy of the calculated thermal diffusivity as compared to using the expression for opaque material.
36 MATERIALS SCIENCE↗
Method for quantification of porcine type I interferon activity using luminescence, by direct and indirect means
Abstract Background Type I interferons are widely used in research applications and as biotherapeutics. Current assays used to measure interferon concentrations, such as plaque reduction assays and ELISA, are expensive, technically challenging, and may take days to provide results. We sought to develop a robust and rapid assay to determine interferon concentrations produced from transiently transfected cell cultures. Method Indirect quantification of recombinant interferon was evaluated using a novel bi-cistronic construct encoding the Foot-and-mouth disease virus 2A translational interrupter sequence to yield equimolar expression of Gaussia princeps luciferase and porcine interferon α. Direct quantification was evaluated by expression of a novel fusion protein comprised of Gaussia princeps luciferase and porcine type I interferon. Plasmids encoding constructs are transiently transfected into cell cultures and supernatant harvested for testing of luminescence, ELISA determined concentration, and anti-viral activity against vesicular stomatitis virus. Results Bi-cistronic constructs, utilized for indirect quantification, demonstrate both luciferase activity and anti-viral activity. Fusion proteins, utilized for direct quantification, retained secretion and luminescence however only the interferon α fusion protein had antiviral activity comparable to wildtype porcine interferon α. A strong linear correlation was observed between dilution and luminescence for all compounds over a dynamic range of concentrations. Conclusion The correlation of antiviral and luciferase activities demonstrated the utility of this approach, both direct and indirect, to rapidly determine recombinant interferon concentrations. Concentration can be determined over a more dynamic concentration range than available ELISA based assays using this methodology.
59 BASIC BIOLOGICAL SCIENCES↗
Observability of negative capacitance of a ferroelectric film: Theoretical predictions
Here, we theoretically explore mechanisms that can potentially give rise to the steady-state and transient negative capacitance in a uniaxial ferroelectric film stabilized by a dielectric layer. The analytical expressions for the steady-state capacitance of a single-domain and polydomain states are derived within the Landau-Ginzburg-Devonshire approach and used to study the state stability vs the domain splitting as a function of dielectric layer thickness. Analytical expressions for the critical thickness of the dielectric layer, polarization amplitude, equilibrium domain period, and susceptibility are obtained and corroborated by finite element modeling. Furthermore we explore the possible effects of nonlinear screening by two types of screening charges at the ferroelectric-dielectric interface and show that if at least one of the screening charges is very slow, the total polarization dynamics can exhibit complex time- and voltage-dependent behaviors that can be interpreted as an observable negative capacitance. In this setting, the transient negative capacitance effect is accompanied by almost zero dielectric susceptibility in a wide voltage range and low frequencies. These results may help to elucidate the observation of the transient negative capacitance in thin ferroelectric films, and identify materials systems that can give rise to the behavior.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Incorporating concentration-dependent sediment microbial activity into methylmercury production kinetics modeling
We report in anoxic environments, anaerobic microorganisms carrying the hgcAB gene cluster can mediate the transformation of inorganic mercury (Hg(II)) to monomethylmercury (MMHg). The kinetics of Hg(II) transformation to MMHg in periphyton from East Fork Poplar Creek (EFPC) in Oak Ridge, TN have previously been modeled using a transient availability model (TAM). The TAM for Hg(II) methylation combines methylation/demethylation kinetics with kinetic expressions for processes that decrease Hg(II) and MMHg availability for methylation and demethylation (multisite sorption of Hg(II) and MMHg, Hg(II) reduction/Hg(0) oxidation). In this study, the TAM is used for the first time to describe MMHg production in sediment. We assessed MMHg production in sediment microcosms using two different sediment types from EFPC: a relatively anoxic, carbon-rich sediment with higher microbial activity (higher CO 2 production from sediment) and a relatively oxic, sandy, carbon-poor sediment with lower microbial activity (lower CO 2 production from sediment). Based on 16s rRNA sequencing, the overall microbial community structure in the two sediments was retained during the incubations. However, the hgcA containing methanogenic Euryarchaeota communities differed between sediment types and their growth followed different trajectories over the course of incubations, potentially contributing to the distinct patterns of MMHg production observed. The general TAM paradigm performed well in describing MMHg production in the sediments. However, the MMHg production and ancillary data suggested the need to revise the model structure to incorporate terms for concentration-dependent microbial activity over the course of the incubations. We modified the TAM to include Monod-type kinetics for methylation and demethylation and observed an improved fit for the carbon-rich, microbially active sediment. Overall our work shows that the TAM can be applied to describe Hg(II) methylation in sediments and that including expressions accounting for concentration-dependent microbial activity can improve the accuracy of the model description of the data in some cases.
54 ENVIRONMENTAL SCIENCES↗
The effect of a transducer’s spatial averaging on an elastodynamic guided wave’s wavenumber spectrum
Elastodynamic guided waves propagate in an elastic solid which makes it difficult, if not impractical, to place a receiving transducer in the direct path of the propagating wave (as one would for an acoustic wave in a fluid medium). Thus, to account for this, receiving transducers are often placed on the surface of the solid waveguide such that the transducer surface is parallel to the wave propagation direction. This transducer orientation introduces spatial averaging, which causes the received signal to have an altered signal amplitude and mode bias. We investigate both of these effects and present a simple model from which we derive a scaling-ratio expression that describes the effects of spatial averaging. Furthermore, we then test its performance using finite-element simulations that incorporate “real-world” assumptions (e.g., transient waves, piezoelectric effects, etc.). The results from the simulations demonstrate that the scaling-ratio can characterize the effects resulting from spatial averaging. The scaling-ratio expression will be particularly useful when designing experiments involving high frequency (small wavelength) guided waves. Lastly, the proposed scaling-ratio expression could be applied to other sensing methods, like Laser Doppler Vibrometry (LDV) or piezoelectric waveguides with inter-digitated transducers, because of its generality. However, the authors are careful to note that the scaling-ratio expression is not intended as a replacement of multi-physics analysis or good experimental design, and the effects of spatial averaging should be avoided whenever possible.
2DFFT↗