Mapping the T cell repertoire to a complex gut bacterial community.

Certain bacterial strains from the microbiome induce a potent, antigen-specific T cell response1-5. However, the specificity of microbiome-induced T cells has not been explored at the strain level across the gut community. Here, we colonize germ-free mice with complex defined communities (roughly 100 bacterial strains) and profile T cell responses to each strain. The pattern of responses suggests that many T cells in the gut repertoire recognize several bacterial strains from the community. We constructed T cell hybridomas from 92 T cell receptor (TCR) clonotypes; by screening every strain in the community against each hybridoma, we find that nearly all the bacteria-specific TCRs show a one-to-many TCR-to-strain relationship, including 13 abundant TCR clonotypes that each recognize 18 Firmicutes. By screening three pooled bacterial genomic libraries, we discover that these 13 clonotypes share a single target: a conserved substrate-binding protein from an ATP-binding cassette transport system. Peripheral regulatory T cells and T helper 17 cells specific for an epitope from this protein are abundant in community-colonized and specific pathogen-free mice. Our work reveals that T cell recognition of commensals is focused on widely conserved, highly expressed cell-surface antigens, opening the door to new therapeutic strategies in which colonist-specific immune responses are rationally altered or redirected.

Generating experimentally unrelated target molecule-binding highly functionalized nucleic-acid polymers using machine learning.

In vitro selection queries large combinatorial libraries for sequence-defined polymers with target binding and reaction catalysis activity. While the total sequence space of these libraries can extend beyond 1022 sequences, practical considerations limit starting sequences to ≤~1015 distinct molecules. Selection-induced sequence convergence and limited sequencing depth further constrain experimentally observable sequence space. To address these limitations, we integrate experimental and machine learning approaches to explore regions of sequence space unrelated to experimentally derived variants. We perform in vitro selections to discover highly side-chain-functionalized nucleic acid polymers (HFNAPs) with potent affinities for a target small molecule (daunomycin KD = 5-65 nM). We then use the selection data to train a conditional variational autoencoder (CVAE) machine learning model to generate diverse and unique HFNAP sequences with high daunomycin affinities (KD = 9-26 nM), even though they are unrelated in sequence to experimental polymers. Coupling in vitro selection with a machine learning model thus enables direct generation of active variants, demonstrating a new approach to the discovery of functional biopolymers.

Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily.

Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily.

A highly robust approach to fabricate the mass-customizable mold of sharp-tipped biodegradable polymer microneedles for drug delivery.

A skin-perforable dissolving microneedle is a promising mediator for painlessly delivering active pharmaceutical compounds across the skin. All the microneedle manufacturing processes so far, however, are much sensitive to input variation and unfavorable for make-to-order approach. Here, a robust method for fabricating mass-customizable master molds is developed to prepare sharp-tipped biodegradable polymer microneedles. Our approach combines the predrying and chip casting (PCC) of an ultrathick photoresist layer with a substrateless, inclined, and rotational exposure (SIR exposure). The PCC achieves the uniform reduction of solvent across the photoresist thickness which is critically required for the formation of a sharp tip; the SIR exposure creates master molds whose geometry is easily customizable and virtually insensitive to a variation in ultraviolet (UV) exposure dose. A theoretical model for the spatiotemporal distribution of UV dose under SIR exposure is established to show the technological superiority of our method. Next, our method's applicability is proven by fabricating a set of poly(lactic-co-glycolic) acid (PLGA) microneedles and performing both porcine skin penetration test and their in vitro degradation test. Our approach is verified to be robust in manufacturing mass-customizable molds for skin-perforable dissolving microneedles and to have high compatibility with almost all existing biodegradable polymers. The findings of this study lead to both a significant growth of dissolving microneedle-mediated drug delivery and better understanding of drug release kinetics.

Mechanistic Insight Facilitates Discovery of a Mild and Efficient Copper-Catalyzed Dehydration of Primary Amides to Nitriles Using Hydrosilanes.

Metal-catalyzed silylative dehydration of primary amides is an economical approach to the synthesis of nitriles. We report a copper-hydride(CuH)-catalyzed process that avoids a typically challenging 1,2-siloxane elimination step, thereby dramatically increasing the rate of the overall transformation relative to alternative metal-catalyzed systems. This new reaction proceeds at ambient temperature, tolerates a variety of metal-, acid-, or base-sensitive functional groups, and can be performed using a simple ligand, inexpensive siloxanes, and low catalyst loading.

Synthesis of highly functionalized polycyclic quinoxaline derivatives using visible-light photoredox catalysis.

A mild and facile method for preparing highly functionalized pyrrolo[1,2-a]quinoxalines and other nitrogen-rich heterocycles, each containing a quinoxaline core or an analogue thereof, has been developed. The novel method features a visible-light-induced decarboxylative radical coupling of ortho-substituted arylisocyanides and radicals generated from phenyliodine(III) dicarboxylate reagents and exhibits excellent functional group compatibility. A wide range of quinoxaline heterocycles have been prepared. Finally, a telescoped preparation of these polycyclic compounds by integration of the in-line isocyanide formation and photochemical cyclization has been established in a three-step continuous-flow system.