De novo identification of CD4+ T cell epitopes.

CD4+ T cells recognize peptide antigens presented on class II major histocompatibility complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of signaling and antigen-presenting bifunctional receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ T cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Furthermore, the SABR-II design is modular in signaling and deployment to T cells and B cells. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery in the context of type 1 diabetes. SABR-II libraries provide a rapid, flexible, scalable and versatile approach for de novo identification of CD4+ T cell ligands from single-cell RNA sequencing data using experimental and computational approaches.

Processing and Characterization of Nanoparticle Coatings for Quartz Crystal Microbalance Measurements.

The quartz-crystal microbalance is a sensitive and versatile tool for measuring adsorption of a variety of compounds (e.g. small molecules, polymers, biomolecules, nanoparticles and cells) to surfaces. While the technique has traditionally been used for measuring adsorption to flat surfaces and thin ridged films, it can also be extended to study adsorption to nanoparticle surfaces when the nanoparticles are fixed to the crystal surface. The sensitivity and accuracy of the measurement depend on the users' ability to reproducibly prepare a thin uniform nanoparticle coating. This study evaluated four coating techniques, including spin coating, spray coating, drop casting, and electrophoretic deposition, for two unique particle chemistries [nanoscale zero valent iron (nZVI) and titanium dioxide (TiO2)] to produce uniform and reproducible nanoparticle coatings for real-time quartz-crystal microbalance measurements. Uniform TiO2 coatings were produced from a 50 mg/mL methanol suspension via spin coating. Nanoscale zero-valent iron was best applied by spray coating a low concentration 1.0 mg/mL suspended in methanol. The application of multiple coatings, rather than an increase in the suspension concentration, was the best method to increase the mass of nanoparticles on the crystal surface while maintaining coating uniformity. An upper mass threshold was determined to be approximately 96 µg/cm(2); above this mass, coatings no longer maintained their uniform rigid characteristic, and a low signal to noise ratio resulted in loss of measurable signal from crystal resonances above the fundamental.

Kinetics of zero valent iron nanoparticle oxidation in oxygenated water.

Zero valent iron (ZVI) nanoparticles are versatile in their ability to remove a wide variety of water contaminants, and ZVI-based bimetallic nanoparticles show increased reactivity above that of ZVI alone. ZVI nanoparticles degrade contaminants through the reactive species (e.g., OH*, H(2(g)), H(2)O(2)) that are produced during iron oxidation. Measurement and modeling of aqueous ZVI nanoparticle oxidation kinetics are therefore necessary to optimize nanoparticle design. Stabilized ZVI and iron-nickel nanoparticles of approximately 150 nm in diameter were synthesized through solution chemistry, and nanoparticle oxidation kinetics were determined via measured mass change using a quartz crystal microbalance (QCM). Under flowing aerated water, ZVI nanoparticles had an initial exponential growth behavior indicating surface-dominated oxidation controlled by migration of species (H(2)O and O(2)) to the surface. A region of logarithmic growth followed the exponential growth which, based on the Mott-Cabrera model of thin oxide film growth, suggests a reaction dominated by movement of species (e.g., iron cations and oxygen anions) through the oxide layer. The presence of ethanol or a nickel shell on the ZVI nanoparticles delayed the onset of iron oxidation and reduced the extent of oxidation. In oxygenated water, ZVI nanoparticles oxidized primarily to the iron oxide-hydroxide lepidocrocite.

Serial and parallel Si, Ge, and SiGe direct-write with scanning probes and conducting stamps.

Precise materials integration in nanostructures is fundamental for future electronic and photonic devices. We demonstrate Si, Ge, and SiGe nanostructure direct-write with deterministic size, geometry, and placement control. The biased probe of an atomic force microscope (AFM) reacts diphenylsilane or diphenylgermane to direct-write carbon-free Si, Ge, and SiGe nano and heterostructures. Parallel direct-write is available on large areas by substituting the AFM probe with conducting microstructured stamps. This facile strategy can be easily expanded to a broad variety of semiconductor materials through precursor selection.

Insights into scanning probe high-field chemistry of diphenylgermane.

Experiments and simulations are used to elucidate a new class of chemical reactions occurring near the tip-sample interface during high field chemistry of diphenylgermane. Current data during writing and bias dependent growth rate are analyzed, supplemented with data from ionization mass spectrometry, and compared with the simulation results.