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

Decline in an Atlantic Puffin population : evaluation of magnitude and mechanisms

Funding: This study was funded annually by Fair Isle Bird Observatory Trust (www.fairislebirdobs.co.uk) with contributions from the Joint Nature Conservation Committee (jncc.defra.gov.uk). Funding was received from these two sources by Fair Isle Bird Observatory from 1986 to 2013. The Joint Nature Conservation Committee and Fair Isle Bird Observatory Trust supplied guidance on study design, data collection, analyses, preparation of the manuscript and the decision to publish.Peer reviewedPublisher PD

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

Assessing the speed and ease of extracting group and person information from faces

This research was supported by the Australian Research Council (FLFL110100199) and the Canadian Institute for Advanced Research (Social Interactions Identity and Well-Being Program).The human face is a key source of social information. In particular, it communicates a target's personal identity and some of their group memberships. Different models of social perception posit distinct stages at which this group-level and person-level information is extracted from the face, with divergent downstream consequences for cognition and behavior. This paper presents four experiments that explore the time-course of extracting group and person information from faces. In Experiments 1 and 2, we explore the effect of chunked versus unchunked processing on the speed of extracting group versus person information, as well as the impact of familiarity in Experiment 2. In Experiment 3, we examine the effect of the availability of a diagnostic cue on these same judgments. In Experiment 4, we explore the effect of both group-level and person-level prototypicality of face exemplars. Across all four experiments, we find no evidence for the perceptual primacy of either group or person information. Instead, we find that chunked processing, featural processing based on a single diagnostic cue, familiarity, and the prototypicality of face exemplars all result in a processing speed advantage for both group-level and person-level judgments equivalently. These results have important implications for influential models of impression formation and can inform, and be integrated with, an understanding of the process of social categorization more broadly.PostprintPeer reviewe

Sinistral shear during Middle Jurassic emplacement of the Matancilla Plutonic Complex in northern Chile (25.4\u3csup\u3e◦\u3c/sup\u3e S) as evidence of oblique plate convergence during the early Andean orogeny

Arc magmatism in a continental subduction zone facilitates rheological weakening of the rigid upper plate, and can accommodate the partitioned trench-parallel component of oblique subduction into an intra-arc shear zone. We document a shear zone at latitude 25.4◦ S near Taltal, Chile that was associated with intrusion of the Matancilla Plutonic Complex at ~169 Ma to evaluate intra-arc deformation and possible tectonic plate configurations during this time period. Polyphase folding of Paleozoic metasedimentary rocks is overprinted by mylonitic fabrics that are most extensive in a zone up to 1.4 km wide in the thermal aureole of the granodioritic Matancilla pluton, where contact metamorphic andalusite porphyroblasts are synkinematic with fabric development. Mylonite in metasedimentary rocks is overprinted by a ~130 Ma granodiorite (zircon U–Pb) and by ~133 Ma postkinematic monazite (U–Pb). Within the Jurassic Matancilla granodiorite, pervasive ductile shear occurs along the intrusive contact while centimeter-scale discrete high-strain zones throughout the pluton are associated with focused hydrothermal alteration and reaction weakening. Mylonitic foliation in the metasedimentary rocks and within the pluton strikes N- to NE and dips steeply, while stretching lineations are subhorizontal on average. Kinematic indicators record dominantly sinistral shear, though some dextral or symmetric indicators and S \u3e L fabrics suggest a component of coaxial strain and flattening. Sinistral strike-slip kinematics in the Matancilla shear zone may indicate that Middle Jurassic convergence had sinistral obliquity that was locally partitioned into the contemporaneous magmatic arc. Sinistral-oblique convergence would require the Phoenix- Farallon spreading center to be north of ~25◦ S in the Middle Jurassic, providing a constraint to plate reconstructions during the early Andean orogeny

Sinistral shear during Middle Jurassic emplacement of the Matancilla Plutonic Complex in northern Chile (25.4◦ S) as evidence of oblique plate convergence during the early Andean orogeny

component of oblique subduction into an intra-arc shear zone. We document a shear zone at latitude 25.4◦ S near Taltal, Chile that was associated with intrusion of the Matancilla Plutonic Complex at ~169 Ma to evaluate intra-arc deformation and possible tectonic plate configurations during this time period. Polyphase folding of Paleozoic metasedimentary rocks is overprinted by mylonitic fabrics that are most extensive in a zone up to 1.4 km wide in the thermal aureole of the granodioritic Matancilla pluton, where contact metamorphic andalusite porphyroblasts are synkinematic with fabric development. Mylonite in metasedimentary rocks is overprinted by a ~130 Ma granodiorite (zircon U–Pb) and by ~133 Ma postkinematic monazite (U–Pb). Within the Jurassic Matancilla granodiorite, pervasive ductile shear occurs along the intrusive contact while centimeter-scale discrete high-strain zones throughout the pluton are associated with focused hydrothermal alteration and reaction weakening. Mylonitic foliation in the metasedimentary rocks and within the pluton strikes N- to NE and dips steeply, while stretching lineations are subhorizontal on average. Kinematic indicators record dominantly sinistral shear, though some dextral or symmetric indicators and S \u3e L fabrics suggest a component of coaxial strain and flattening. Sinistral strike-slip kinematics in the Matancilla shear zone may indicate that Middle Jurassic convergence had sinistral obliquity that was locally partitioned into the contemporaneous magmatic arc. Sinistral-oblique convergence would require the Phoenix- Farallon spreading center to be north of ~25◦ S in the Middle Jurassic, providing a constraint to plate reconstructions during the early Andean orogeny

Effects of sea temperature and stratification changes on seabird breeding success

As apex predators in marine ecosystems, seabirds may primarily experience climate change impacts indirectly, via changes to their food webs. Observed seabird population declines have been linked to climate-driven oceanographic and food web changes. However, relationships have often been derived from relatively few colonies and consider only sea surface temperature (SST), so important drivers, and spatial variation in drivers, could remain undetected. Further, explicit climate change projections have rarely been made, so longer-term risks remain unclear. Here, we use tracking data to estimate foraging areas for eleven black-legged kittiwake (Rissa tridactyla) colonies in the UK and Ireland, thus reducing reliance on single colonies and allowing calculation of colony-specific oceanographic conditions. We use mixed models to consider how SST, the potential energy anomaly (indicating density stratification strength) and the timing of seasonal stratification influence kittiwake productivity. Across all colonies, higher breeding success was associated with weaker stratification before breeding and lower SSTs during the breeding season. Eight colonies with sufficient data were modelled individually: higher productivity was associated with later stratification at three colonies, weaker stratification at two, and lower SSTs at one, whilst two colonies showed no significant relationships. Hence, key drivers of productivity varied among colonies. Climate change projections, made using fitted models, indicated that breeding success could decline by 21 – 43% between 1961-90 and 2070-99. Climate change therefore poses a longer-term threat to kittiwakes, but as this will be mediated via availability of key prey species, other marine apex predators could also face similar threats

Genetic interaction mapping informs integrative structure determination of protein complexes

Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on similar to 500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations