Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting [preprint]

Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary time scales. Building on our previous work (Mavor et al. 2016), we used deep mutational scanning to determine how twelve new chemicals reveal novel mutational sensitivities of ubiquitin residues. We found sensitization of Lys63 in eight new conditions. In total, our experiments have uncovered a highly sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the Ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance

Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our experiments have identified eight new sensitizing conditions for Lys63 and uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover \u27shared sensitized positions\u27 localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum

Estimating and predicting snakebite risk in the Terai region of Nepal through a high-resolution geospatial and One Health approach

Most efforts to understand snakebite burden in Nepal have been localized to relatively small areas and focused on humans through epidemiological studies. We present the outcomes of a geospatial analysis of the factors influencing snakebite risk in humans and animals, based on both a national-scale multi-cluster random survey and, environmental, climatic, and socio-economic gridded data for the Terai region of Nepal. The resulting Integrated Nested Laplace Approximation models highlight the importance of poverty as a fundamental risk-increasing factor, augmenting the snakebite odds in humans by 63.9 times. For animals, the minimum temperature of the coldest month was the most influential covariate, increasing the snakebite odds 23.4 times. Several risk hotspots were identified along the Terai, helping to visualize at multiple administrative levels the estimated population numbers exposed to different probability risk thresholds in 1 year. These analyses and findings could be replicable in other countries and for other diseases

Perturbative QCD and factorization of coherent pion photoproduction on the deuteron

We analyze the predictions of perturbative QCD for pion photoproduction on the deuteron, gamma D -> pi^0 D, at large momentum transfer using the reduced amplitude formalism. The cluster decomposition of the deuteron wave function at small binding only allows the nuclear coherent process to proceed if each nucleon absorbs an equal fraction of the overall momentum transfer. Furthermore, each nucleon must scatter while remaining close to its mass shell. Thus the nuclear photoproduction amplitude, M_{gamma D -> pi^0 D}(u,t), factorizes as a product of three factors: (1) the nucleon photoproduction amplitude, M_{gamma N_1 -> pi^0 N_1}(u/4,t/4), at half of the overall momentum transfer, (2) a nucleon form factor, F_{N_2}(t/4), at half the overall momentum transfer, and (3) the reduced deuteron form factor, f_d(t), which according to perturbative QCD, has the same monopole falloff as a meson form factor. A comparison with the recent JLAB data for gamma D -> pi^0 D of Meekins et al. [Phys. Rev. C 60, 052201 (1999)] and the available gamma p -> pi^0 p data shows good agreement between the perturbative QCD prediction and experiment over a large range of momentum transfers and center of mass angles. The reduced amplitude prediction is consistent with the constituent counting rule, p^11_T M_{gamma D -> pi^0 D} -> F(theta_cm), at large momentum transfer. This is found to be consistent with measurements for photon lab energies E_gamma > 3 GeV at theta_cm=90 degrees and \elab > 10 GeV at 136 degrees.Comment: RevTeX 3.1, 17 pages, 6 figures; v2: incorporates minor changes as version accepted by Phys Rev