22 Search Results

Bottom-up proteomic workflows rely on sequential preprocessing steps, commonly including peptide-to-protein aggregation (“roll-up”), to enhance data reliability and interpretability. While roll-up is effective for protein-centered analyses, it may be suboptimal for applications focused on post-translational modifications (PTMs) or protein structural changes, such as limited proteolysis–mass spectrometry (LiP-MS). Here, we investigate how different roll-up strategies influence site-level quantification in PTM differential analysis. Moreover, we introduce a novel site-centric roll-up approach tailored for LiP-MS, which quantifies proteolytic fragments rather than solely tryptic peptides. We benchmark these methods through simulation studies, comparing their sensitivity and specificity in detecting structural and PTM-driven changes. Wemore » found that the median and mean roll-up methods outperform the sum method in both PTM and LiP proteomics, and site-level quantification in LiP outperforms peptide-level quantification. Our findings offer the first systematic, data-driven guidance for selecting roll-up techniques in site-level proteomic analyses, with implications for both PTM-focused and structural proteomics studies.« less

Covalent conjugation of RNA with synthetic polymers has emerged as a powerful approach for creating bioconjugates with synergistically enhanced properties. However, conventional methods require solid-phase synthesis to preinstall functional groups in RNA, significantly limiting practical applications. Here, we present a novel approach for synthesizing RNA–polymer conjugates via direct incorporation of chain transfer agent (CTA) into RNA through acylation chemistry and reversible addition–fragmentation chain transfer (RAFT) polymerization. A CTA-functionalized acyl imidazole reagent was synthesized to facilitate direct and covalent modification of various RNAs by reacting with their 2′-hydroxyl groups. Subsequent RAFT polymerization using RNA–CTA as a macro-CTA enabled direct grafting-from RNA,more » yielding RNA conjugates with controlled molecular weight and low dispersity. Notably, this postsynthetic modification strategy was successfully extended to modify biomass RNA, yielding thermoresponsive conjugates and biodegradable hydrogels. Overall, this advance allowed for the direct modification of synthetic and biomass RNAs, significantly enhancing the accessibility of functional RNA–polymer materials.« less

Chemically modified plastics have emerged as practical solutions to plastic waste increases. Here, the inherent novelty of decorating polymer chains with chemical functionality results in distinct properties that expand the available application space. Nevertheless, developing designer materials for specific applications beyond compatibilization or mild property enhancement is difficult due to the synergistic effects of both the polar functionality imparted and the parent materials' intrinsic properties. By incorporating perfluoro-alkyl side-chains onto the backbone of dehydrogenated waste HDPE, unique surface properties intermediate between polytetrafluoroethylene (PTFE, the model fluoropolymer) and HDPE become apparent, while the overall material mechanical and thermal properties result inmore » more LLDPE-like materials. This is demonstrated through moderate decreases in the surface free energy of the perfluoroalkylated polyolefin surface (increase in H₂O contact angle of ~ 6°) and increased ordering under shear when blended with PTFE nanoparticles where the crossover point occurred at higher strains. Critically, perfluoroalkylated HDPE possesses improved rheological modification properties at elevated temperatures with PTFE nanoparticles, resulting in more thermally robust and stable composite materials.« less

Surface self-diffusion studies on metals under elevated reaction conditions are limited, as it is inherently challenging to unambiguously follow atomic transport across highly-reactive surfaces. Here, quantitative and mechanistic insight into thermally induced atomic transport processes in bcc α-iron at the sub-nanometer level was achieved using isotopic tracer techniques coupled with in situ atom probe tomography (APT) capabilities. Specifically, using a reactor directly connected to the APT, needle-shaped specimens fabricated from epitaxial thin films with an embedded ⁵⁷Fe tracer layer were annealed in Ar at 500 °C and 350 °C for 1 hour. Furthermore, the tracer was positioned at various depthsmore » in the APT specimen by field evaporation, enabling targeted and simultaneous analysis of lattice and surface diffusion. ⁵⁷Fe concentration profiles reveal lattice self-diffusion occurs at 500 °C on the order of ~7 – 9 monolayers, while lattice diffusion is not resolvable at 350 °C. Considerable surface transport was, however, observed at both conditions, where atomic transport over the specimen surface led to the formation of a thin (≤1 nm), isotopically-intermixed layer at the surface. Further, the observed isotopic redistributions at 500 °C were convoluted by additional processes occurring in the subsurface, such as atomic intermixing in correlation with lattice diffusion. However, surface diffusion was determined to be the primary transport process at 350 °C and was thereby quantified. Ultimately, these results demonstrate the significance of surface self-diffusion as a short circuit pathway. More broadly, this approach has the potential to provide detailed insight into (self-)diffusion mechanisms across various materials while targeting site-specific reactions under elevated reaction conditions.« less

Regardless of their applications, polymers are still considered mechanically weak and functionally insufficient for certain demanding coating and adhesive uses. To address those issues, nanomaterials have been extensively studied as reinforcing fillers, which have been proven to effectively promote the performance of polymer coatings/adhesives. However, conventional nanofillers are expensive and non-biodegradable. Meanwhile, cellulose nanomaterials (CNMs), a class of nanomaterials produced from biomass feedstocks, can circumvent the drawbacks of conventional nanofillers. Here, this review paper first focuses on the multi-functionalities CNMs bring to polymer coatings, including mechanical reinforcement (wear resistance and hardness enhancement), gas barrier, flame resistance, corrosion resistance, self-healing (controlled-release),more » optical regulation, self-cleaning/antifouling, and antimicrobial characteristics. Then we discuss the benefits of CNM addition to polymer adhesives, such as mechanical enhancement, curing promotion, volatile organic compound (VOC) suppression, and electrical conductivity. Finally, we provide insights into future research efforts with CNMs. The goal of this paper is to promote the pilot-scale study and commercial use of CNMs as multifunctional additives in green and sustainable polymer composite coating and adhesive formulations.« less

Conditions affecting biofilm formation differ among bacterial species and this presents a challenge to studying biofilms in the lab. This work leverages functionalized silanes to control surface chemistry in the study of early biofilm propagation, quantified with a semi-automated image processing algorithm. These methods support the study of Pantoea sp. YR343, a gram-negative bacterium isolated from the poplar rhizosphere. We found that Pantoea sp. YR343 does not readily attach to hydrophilic surfaces but will form biofilms with a “honeycomb” morphology on hydrophobic surfaces. Our image processing algorithm described here quantified the evolution of the honeycomb morphology over time, and foundmore » the propagation to display a logarithmic behavior. This methodology was repeated with a flagella-deficient fliR mutant of Pantoea sp. YR343 which resulted in reduced surface attachment. Quantifiable differences between Pantoea WT and ΔfliR biofilm morphologies were captured by the image processing algorithm, further demonstrating the insight gained from these methods.« less

A convenient enzymatic strategy is reported for the modification of cell surfaces. Using a tyrosinase enzyme isolated from Agaricus bisporus, unique tyrosine residues introduced at the C-termini of nanobodies can be site-selectively oxidized to reactive o-quinones. These reactive intermediates undergo rapid modification with nucleophilic thiol, amine, and imidazole residues present on cell surfaces, producing novel nanobody–cell conjugates that display targeted antigen binding. We extend this approach toward the synthesis of nanobody–NK cell conjugates for targeted immunotherapy applications. The resulting NK cell conjugates exhibit targeted cell binding and elicit targeted cell death.

SrTiO ₃ and aluminum-doped SrTiO ₃ are synthesized by calcination of metal salts dissolved in a deep eutectic solvent (DES) without any post-synthesis treatment.