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Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.
Abstract BACKGROUND Peanut allergy is recognized as a major food allergy that triggers severe and even fatal symptoms. Avoidance of peanuts in the diet is the main option for current safety management. Processing techniques reducing peanut allergenicity are required to develop other options. Cold plasma is currently considered as a novel non‐thermal approach to alter protein structure and has the potential to alleviate immunoreactivity of protein allergen. RESULTS The application of a cold argon plasma jet to peanut protein extract could reduce the amount of a 64 kDa protein band corresponding to a major peanut allergen Ara h 1 using sodium dodecyl sulfate–polyacrylamide gel electrophoresis, but the overall protein size distribution did not change significantly. A decrease in peanut protein solubility was a possible cause that led to the loss of protein content in the soluble fraction. Immunoblotting and enzyme‐linked immunosorbent assay elucidated that the immunoreactivity of Ara h 1 was significantly decreased with the time treated with plasma. Ara h 1 antigenicity reduced by 38% after five scans (approximately 3 min) of cold argon plasma jet treatment, and the reduction was up to 66% after approximately 15 min of treatment. CONCLUSION The results indicate that cold argon plasma jet treatment could be a suitable platform for alleviating the immunoreactivity of peanut protein. This work demonstrates an efficient, compact, and rapid platform for mitigating the allergenicity of peanuts, and shows great potential for the plasma platform as a non‐thermal technique in the food industry. © 2023 Society of Chemical Industry.
Ribonucleic acid (RNA) nanotechnology platforms have the potential of harboring therapeutics for in vivo delivery in disease treatment. However, the nonspecific interaction between the harbored hydrophobic drugs and cells or other components before reaching the diseased site has been an obstacle in drug delivery. In this work, we report an encapsulation strategy to prevent such nonspecific hydrophobic interactions in vitro and in vivo based on a self-assembled three-dimensional (3D) RNA nanocage. By placing an RNA three-way junction (3WJ) in the cavity of the nanocage, the conjugated hydrophobic molecules were specifically positioned within the nanocage, preventing their exposure to the biological environment. The assembly of the nanocages was characterized by native polyacrylamide gel electrophoresis (PAGE), atomic force microscopy (AFM), and cryogenic electron microscopy (cryo-EM) imaging. The stealth effect of the nanocage for hydrophobic molecules in vitro was evaluated by gel electrophoresis, flow cytometry, and confocal microscopy. The in vivo sheathing effect of the nanocage for hydrophobic molecules was assessed by biodistribution profiling in mice. The RNA nanocages with hydrophobic biomolecules underwent faster clearance in liver and spleen in comparison to their counterparts. Therefore, this encapsulation strategy holds promise for in vivo delivery of hydrophobic drugs for disease treatment.
Apolipoprotein A-I (APOA1) oligomerization is thought to be essential for high-density lipoprotein (HDL) formation and metabolism. Naturally occurring mutations can disrupt normal APOA1 folding and self-association, leading to dysfunctional HDL formation and cardiovascular disease. The congenital APOA1 variant p.K131del (APOA1 K107del ) has been associated with cardiovascular pathologies such as low HDL-cholesterol levels and aortic amyloidosis, and multiple studies indicate structural changes in APOA1 conformation underlie associated dysfunction. In the current study, we confirmed that APOA1 K107del exhibits no notable defect in lipid-binding. However, using polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC), we found that loss of lysine 107 resulted in a remarkable shift in the distribution of APOA1 oligomers with a much higher proportion of monomers present in APOA1 K107del compared to wild-type APOA1. Further investigation using quantitative cross-linking revealed a major disruption of interactions in helical regions reported to participate in domain swaps necessary for proper self-association. This structural disruption appears to impair N- and C-termini interactions and dynamics that lead to non-specific aggregation. In conclusion, these findings support the hypothesis that lysine 107 is critical for proper folding and self-association of lipid-free APOA1 which could impact HDL biogenesis.
The demand for sustainable and alternative protein sources has been on the rise, driving interest in the valorization of underutilized plants. This study evaluated Calendula officinalis (marigold), a common floral waste, as a sustainable alternative protein source for the food industry. The primary objective of this study was to investigate the physicochemical properties of protein fractions from Calendula officinalis flower to evaluate their potential as a novel protein ingredient. Extraction of the Calendula officinalis flower yielded 92.17% of the crude protein. A sequential extraction of albumin, globulin, glutelin, and prolamin from marigold flower revealed albumin as the dominant fraction (65.47%) and exhibited the highest protein functionality, including water-holding capacity (2.37 g/g), oil-holding capacity (2.49 g/g), and emulsifying capacity (65.22 mL/g). Compared with other protein fractions, glutelin showed a relatively high emulsifying and foaming capacity (EC: 59.13 mL/g; FC: 16.23%). Differential scanning calorimetry revealed high thermal stability for albumin (T p = 105.28 °C) and glutelin (T p = 97.6 °C). Sodium Dodecyl Sulfate–Polyacrylamide Gel Electrophoresis (SDS-PAGE) and Liquid Chromatography–Mass Spectrometry (LC-MS) confirmed the presence of abundant low-molecular-weight polypeptides (<37 kDa), which enhanced emulsification, while scanning electron microscopy revealed porous structures aligned with hydration properties. Antioxidant activity was higher in albumin and glutelin, linked to surface hydrophobicity. LC-MS/MS identified 33 short-chain proteins, including oxidoreductase proteins and lipid-transfer proteins. Findings highlight marigold flower proteins as a sustainable, functional ingredient for a diverse range of food applications.
Kiwifruit canker, caused by Pseudomonas syringae pv. actinidiae (PSA), has led to significant losses in the kiwifruit industry each year. Due to the drug resistance feature of PSA, biological control is currently the most promising method. Developing biocontrol bacteria against PSA could help solve the issue of drug resistance generated during the chemical control of PSA to a certain extent. In this research, a Wq-1 strain that demonstrated excellent inhibitory activity against PSA was isolated from the rhizosphere soil of healthy kiwifruit. Based on the morphological characteristics and phylogenetic analysis of the 16S rRNA gene sequence, the isolated strain was identified as Brevibacillus laterosporus Wq-1. Bacteriostatic proteins were isolated from the cell-free culture filtrate of strain Wq-1 and were found to have a molecular weight of approximately 12 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Liquid chromatography–tandem mass spectrometry (LC–MS/MS) detection revealed that there were several peptides in the target band that were consistent with protein 01021 in the genome. The gene of the 01021 protein was cloned into the plasmid pPICZa, and the recombinant bacteriocin was successfully expressed using the Pichia pastoris X33 expression system. The recombinant protein 01021 effectively inhibited the growth of PSA. This is the first report of the protein’s antimicrobial activity, distinguishing it from previously identified bacteriocins. Therefore, we named this bacteriocin JUQZ-1. In addition, our results showed that the protein JUQZ-1 not only exhibited a broad bacteriostatic spectrum but also high thermal and pH stability suitable for harsh environmental conditions., JUQZ-1, a protein with antimicrobial properties and strong environmental tolerance, may serve as a promising alternative to antibiotics.
The effects of salt stress condition on the growth, morphology, photosynthetic performance, and paramylon content were examined in the mixotrophic, unicellular, flagellate Euglena gracilis. We found that salt stress negatively influenced cell growth, accompanied by a decrease in chlorophyll (Chl) content. Circular dichroism (CD) spectroscopy revealed the changes in the macro-organization of pigment-protein complexes due to salt treatment, while the small-angle neutron scattering (SANS) investigations suggested a reduction in the thylakoid stacking, an effect confirmed by the transmission electron microscopy (TEM). At the same time, the analysis of the thylakoid membrane complexes using native-polyacrylamide gel electrophoresis (PAGE) revealed no significant change in the composition of supercomplexes of the photosynthetic apparatus. Salt stress did not substantially affect the photosynthetic activity, as reflected by the fact that Chl fluorescence yield, electron transport rate (ETR), and energy transfer between the photosystems did not change considerably in the salt-grown cells. We have observed notable increases in the carotenoid-to-Chl ratio and the accumulation of paramylon in the salt-treated cells. We propose that the accumulation of storage polysaccharides and changes in the pigment composition and thylakoid membrane organization help the adaptation of E. gracilis cells to salt stress and contribute to the maintenance of cellular processes under stress conditions.
Protein Engineering is a highly evolved field of engineering aimed at developing proteins for specific industrial, medical, and research applications. Here, we present a practical teaching course to demonstrate fundamental techniques used to express, purify and analyze a recombinant protein produced in Escherichia coli—the enhanced green fluorescent protein (eGFP). The methodologies used for eGFP production were introduced sequentially over six laboratory sessions and included (i) bacterial growth, (ii) sonication (for cell lysis), (iii) affinity chromatography and dialysis (for eGFP purification), (iv) bicinchoninic acid (BCA) and fluorometry assays for total protein and eGFP quantification, respectively, and (v) sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for qualitative analysis. All groups were able to isolate the eGFP from the cell lysate with purity levels up to 72%. Additionally, a mass balance analysis performed by the students showed that eGFP yields up to 46% were achieved at the end of the purification process following the adopted procedures. A sensitivity analysis was performed to pinpoint the most critical steps of the downstream processing.
Hydrogel-embedding is a versatile technique in fluorescence microscopy, offering stabilization, optical clearing, and the physical expansion of biological specimens. DNA-PAINT is a super-resolution microscopy approach based on the diffusion and transient binding of fluorescently labeled oligos, but its feasibility in hydrogels has not yet been explored. In this study, we demonstrate that polyacrylamide hydrogels support sufficient diffusion for effective DNA-PAINT imaging. Using acrydite-anchored oligonucleotides imprinted from patterned DNA origami nanostructures and microtubule filaments in fixed cells, we find that hydrogel embedding preserves docking strand positioning at the nanoscale. Sample clearing via protease treatment had minor structural effects on the microtubule structure and enhanced diffusion and accessibility to hydrogel-imprinted docking strands. Our work demonstrates promising potential for diffusion and binding-based fluorescence imaging applications in hydrogel-embedded samples.
Objectives: Develop and test various diffusive gradient in thin films (DGT) samplers for mercury - SRNL is developing reactive DGTS (rDGTs). Test chemistry to differentiate methylmercury from total and/or inorganic mercury in environmental samples. Fabricate and test rDGT samplers for deployment. Deploy the rDGTs in variable settings. Mercury is a persistent-bioaccumulative-toxic environmental pollutant. Mercury exists in different species such as elemental, inorganic, and methyl. Mercury speciation determine mercury behavior and toxicity. For example, methylmercury strongly accumulates in biota such as fish resulting in potential human health impacts. DGTs are innovative samplers to measure water concentration by diffusion and capture. Types of Hg DGTs used: Total Hg, Inorganic Hg, and Methyl Hg. Deployment Sites: Upper Three Runs, Lower Three Runs, Steele Creek, East Fork Poplar Creek (SRNL Sites), Horizons Creek, NOA Creek, Bruners Creek (ORNL Sites). DGT concentration estimates closely matched alternative measurements for soluble mercury at each Oak Ridge site - DGTs did not respond to particulate mercury. DGTs provide a representative measure for biota uptake since they are left out longer which allows for an average exposure concentration. DMA-80 provided an efficient and quick analysis. Variability in site location made a difference in Hg species. DGT preparations and sampling wasn't as quick and simple as microcolumn technology. Copper reagent degraded agarose gel - more work and cleaner data are needed to assess speciation in rDGTs. Future Work: Use cross-linked polyacrylamide for the collection layer for a stronger plastic. Make a copper diffusion layer without agarose. Test copper separation in lab using realistic stream conditions such as high organic carbon.
The hydraulic conductivity of geosynthetic clay liners (GCLs) containing bentonite–polymer composites (BPCs) is controlled by a pore clogging mechanism related to the swelling of sodium bentonite (NaB) granules and formation of polymer gel in the pore space. Three index testing procedures that are influenced by bentonite swelling and rheology of the polymer gel were evaluated in this study for screening BPC GCLs for hydraulic conductivity: viscosity, liquid limit by fall-cone penetration and active water content. Experiments were conducted using polyacrylamide (PAM) polymer, dry-blended mixtures of PAM and NaB and a BPC from a commercially available GCL. These materials were contacted with inorganic solutions representing leachates from a range of waste containment scenarios. For the BPC that was evaluated, hydraulic conductivities less than 10 -10 m/s were obtained when the viscosity exceeded 220 mPa s and the active water content exceeded 300%. Hydraulic conductivities less than 10 -11 m/s were achieved for viscosity exceeding 350 mPa s, fall-cone liquid limit exceeding 190 and active water content exceeding 300%. Additional testing is needed to assess the generality of these index tests and the identified thresholds when applied to other BPC GCLs and other permeant liquids.
Zinc-air batteries (ZABs) are regarded as one of the most promising candidates for next-generation energy storage systems due to their inherent safety, high energy density, and low cost. In this study, we optimized the composition of gel polymer electrolytes (GPEs), which play a crucial role in enhancing ZAB reversibility due to their water retention capabilities. The GPEs are synthesized using a combination of polyacrylic acid (PAA), polyacrylamide (PAM), and biopolymer kappa-carrageenan (KC), with and without additional additives. Among these, the composite GPE containing KC, PAA, and PAM demonstrated superior ionic conductivity (6.68 mS/cm at 30 °C) and enhanced water retention compared to the PAA–PAM-based GPE. Furthermore, this composite electrolyte operates within a wider electrochemical window of −1.0 V–2.2 V. A bifunctional catalyst, nickel–iron layered double hydroxide (NiFe-LDH), is electrochemically synthesized on a modified activated carbon cloth (CC). The catalyst loading is optimized based on oxygen evolution reaction (OER) performance, showing an overpotential of 555 mV. The oxygen reduction reaction (ORR) occurred at a half-wave potential of 0.620 V, which is lower than that of Pt/C (0.852 V), indicating better catalytic activity. The KC based cell exhibit better cycling stability than PAA–PAM-based GPE. The electrochemical performance of ZAB cells is evaluated under various atmospheres: ambient air and humid conditions and temperatures. Notably, in a humid environment, the cells achieved extended cycling stability, operating for over 500 h—significantly longer than under open-air conditions. Overall, this study highlights the importance of tailored GPE design and efficient bifunctional catalysts to enhance the performance and longevity of zinc-air batteries for long-duration energy storage applications.
Abstract The crystallization of metastable liquid phase change materials releases stored energy as latent heat upon nucleation and may therefore provide a triggerable means of activating downstream processes that respond to changes in temperature. In this work, we describe a strategy for controlling the fast, exothermic crystallization of sodium acetate from a metastable aqueous solution into trihydrate crystals within a polyacrylamide hydrogel whose polymerization state has been patterned using photomasks. A comprehensive experimental study of crystal shapes, crystal growth front velocities and evolving thermal profiles showed that rapid growth of long needle-like crystals through unpolymerized solutions produced peak temperatures of up to 45˚C, while slower-crystallizing polymerized solutions produced polycrystalline composites and peaked at 30˚C due to lower rates of heat release relative to dissipation in these regions. This temperature difference in the propagating heat waves, which we describe using a proposed analytical model, enables the use of this strategy to selectively activate thermoresponsive processes in predefined areas.