Search for: All records

Bifunctional molecules such as targeted protein degraders induce proximity to promote gain‐of‐function pharmacology. These powerful approaches have gained broad traction across academia and the pharmaceutical industry, leading to an intensive focus on strategies that can accelerate their identification and optimization. We and others have previously used chemical proteomics to map degradable target space, and these datasets have been used to develop and train multiparameter models to extend degradability predictions across the proteome. In this study, we now turn our attention to develop generalizable chemistry strategies to accelerate the development of new bifunctional degraders. We implement lysine‐targeted reversible‐covalent chemistry to rationally tune the binding kinetics at the protein‐of‐interest across a set of 25 targets. We define an unbiased workflow consisting of global proteomics analysis, IP/MS of ternary complexes and the E‐STUB assay, to mechanistically characterize the effects of ligand residence time on targeted protein degradation and formulate hypotheses about the rate‐limiting step of degradation for each target. Our key finding is that target residence time is a major determinant of degrader activity, and this can be rapidly and rationally tuned through the synthesis of a minimal number of analogues to accelerate early degrader discovery and optimization. 

Abstract We present a search for extreme emission line galaxies (EELGs) atz< 1 in the COSMOS and North Ecliptic Pole (NEP) fields with imaging from Subaru/Hyper Suprime-Cam (HSC) and a combination of new and existing spectroscopy. We select EELGs on the basis of substantial excess flux in thezbroad band, which is sensitive to Hαat 0.3 ≲z≲ 0.42 and [Oiii]λ5007 at 0.7 ≲z≲ 0.86. We identify 10,470 galaxies withzexcesses in the COSMOS data set and 91,385 in the NEP field. We cross-reference the COSMOS EELG sample with the zCOSMOS and DEIMOS 10k spectral catalogs, finding 1395 spectroscopic matches. We made an additional 71 (46 unique) spectroscopic measurements withY< 23 using the HYDRA multiobject spectrograph on the WIYN 3.5 m telescope, and 204 spectroscopic measurements from the DEIMOS spectrograph on the Keck II telescope, providing a total of 1441/10,470 spectroscopic redshifts for the EELG sample in COSMOS (∼14%). We confirm that 1418 (∼98%) are Hαor [Oiii]λ5007 emitters in the above stated redshift ranges. We also identify 240 redshifted Hαand [Oiii]λ5007 emitters in the NEP using spectra taken with WIYN/HYDRA and Keck/DEIMOS. Using broadband-selection techniques in theg−r−icolor space, we distinguish between Hαand [Oiii]λ5007 emitters with 98.6% accuracy. We test our EELG selection by constructing Hαand [Oiii]λ5007 luminosity functions and comparing to recent literature results. We conclude that broadband magnitudes from HSC, the Vera C. Rubin Observatory, and other deep optical multiband surveys can be used to select EELGs in a straightforward manner. 

Abstract The bacterial gut microbiota of many animals is known to be important for many physiological functions including detoxification. The selective pressures imposed on insects by exposure to toxins may also be selective pressures on their symbiotic bacteria, who thus may contribute to the mechanism of toxin tolerance for the insect. Amatoxins are a class of cyclopeptide mushroom toxins that primarily act by binding to RNA polymerase II and inhibiting transcription. Several species of mycophagousDrosophilaare tolerant to amatoxins found in mushrooms of the genusAmanita, despite these toxins being lethal to most other known eukaryotes. These species can tolerate amatoxins in natural concentrations to utilize toxic mushrooms as larval hosts, but the mechanism by which these species are tolerant remains unknown. Previous data have shown that a local population ofD. tripunctataexhibits significant genetic variation in toxin tolerance. This study assesses the potential role of the microbiome in α‐amanitin tolerance in six wild‐derived strains ofDrosophila tripunctata. Normal and antibiotic‐treated samples of six strains were reared on diets with and without α‐amanitin, and then scored for survival from the larval stage to adulthood and for development time to pupation. Our results show that a substantial reduction in bacterial load does not influence toxin tolerance in this system, while confirming genotype and toxin‐specific effects on survival are independent of the microbiome composition. Thus, we conclude that this adaptation to exploit toxic mushrooms as a host is likely intrinsic to the fly's genome and not a property of their microbiome. 

Abstract Understanding plant‐insect interactions is an active area of research in both ecology and evolution. Much attention has been focused on the impact of secondary metabolites in the host plant or fungi on these interactions. Plants and fungi contain a variety of biologically active compounds, and the secondary metabolite profile can vary significantly between individual samples. However, many experiments characterize the biological effects of only a single secondary metabolite or a subset of these compounds.Here, we develop an exhaustive extraction protocol using an accelerated solvent extraction protocol to recover the complete suite of cyclopeptides and other secondary metabolites found inAmanita phalloides(death cap mushrooms) and compare its efficacy to the “Classic” extraction method used in earlier works.We demonstrate that our extraction protocol recovers the full suite of cyclopeptides and other secondary metabolites inA. phalloidesunlike the “Classic” method that favors polar cyclopeptides.Based on these findings, we provide recommendations for how to optimize protocols to ensure exhaustive extracts and also the best practices when using natural extracts in ecological experiments.