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"Clark, S"
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The limits of judicial independence
\"This book investigates the causes and consequences of congressional attacks on the U.S. Supreme Court, arguing that the extent of public support for judicial independence constitutes the practical limit of judicial independence. First, the book presents a historical overview of Court-curbing proposals in Congress. Then, building on interviews with Supreme Court justices, members of Congress, and judicial and legislative staffers, as well as existing research, the book theorizes that congressional attacks are driven by public discontent with the Court. From this theoretical model, predictions are derived about the decision to engage in Court-curbing and judicial responsiveness to Court-curbing activity in Congress. The Limits of Judicial Independence draws on illustrative archival evidence, systematic analysis of an original dataset of Court-curbing proposals introduced in Congress from 1877 onward, and judicial decisions. This evidence demonstrates that Court-curbing is driven primarily by public opposition to the Court, and that the Court responds to those proposals by engaging in self-restraint and moderating its decisions\"-- Provided by publisher.
Individuals and the Variation Needed for High Species Diversity in Forest Trees
2010
In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for coexistence of large numbers of competitors. Variation among individuals within populations allows species to differ in their distributions of responses to the environment, despite the fact that the populations to which they belong do not differ, on average. Results are consistent with theory predicting that coexistence depends on competition being stronger within than between species, shown here by analysis of individual-level responses to environmental fluctuation.
Journal Article
Why species tell more about traits than traits about species: predictive analysis
2016
Trait analysis aims to understand relationships between traits, species diversity, and the environment. Current methods could benefit from a model-based probabilistic framework that accommodates covariance between traits and quantifies contributions from inherent trait syndromes, species interactions, and responses to the environment. I develop a model-based approach that separates these effects on trait diversity. Application to USDA Forest Inventory and Analysis (FIA) data in the eastern United States demonstrates an apparent paradox, that the analysis of species better explains and predicts traits than does direct analysis of the traits themselves; trait data contain less, not more, information than species on environmental responses. Whereas variation in some traits is dominated by inherent syndromes (tendency for certain traits to be associated with others within an individual and species), others are strongly controlled by variation in species diversity. There is substantial variation in environmental control on trait patterns, between traits and regionally. In terms of environmental response traits do not aggregate into defined plant functional types, as would be desirable for models.
Journal Article
Quantifying drivers of population dynamics for a migratory bird throughout the annual cycle
by
Marra, Peter P.
,
Ryder, Thomas B.
,
Rushing, Clark S.
in
Animal Migration
,
Animals
,
Climate Change
2016
Worldwide, migratory species are undergoing rapid declines but understanding the factors driving these declines is hindered by missing information about migratory connectivity and the lack of data to quantify environmental processes across the annual cycle. Here, we combined range-wide information about migratory connectivity with global remote-sensing data to quantify the relative importance of breeding and non-breeding environmental processes to persistent long-term population declines of a migratory songbird, the wood thrush (Hylocichla mustelina). Consistent with theoretical predictions about population limitation of migratory birds, our results suggest that habitat loss and climate have contributed to the observed declines in wood thrush breeding abundance, yet the relative importance of breeding versus non-breeding factors is population-specific. For example, high-abundance core breeding populations appear to be more limited by habitat loss, whereas low-abundance, peripheral populations appear to be limited by climate-driven seasonal interactions. Further, our analysis indicates that the relative impact of breeding habitat loss is at least three to six times greater than the impact of equivalent non-breeding habitat loss and therefore the steepest regional declines have likely been driven by the loss of breeding habitat. These results underscore the need for population-specific conservation strategies implemented throughout the annual cycle to reverse long-term declines.
Journal Article
Abiological catalysis by artificial haem proteins containing noble metals in place of iron
2016
Replacing the iron atom in Fe-porphyrin IX proteins with a noble-metal atom enables the creation of enzymes that catalyse reactions not catalysed by native Fe-enzymes or other metalloenzymes; this approach could be used to generate other artificial enzymes that could catalyse a wide range of abiological transformations.
Changing the 'metallo' in metalloenzymes
Naturally occurring metalloenzymes are promising alternatives to transition-metal catalysts and non-metal enzymes for the synthesis of chemicals and biologically active compounds, but they catalyse only a narrow range of reactions. One way of broadening that range is to replace the native catalytic metal with an abiological metal. John Hartwig and colleagues report the effect of substituting the iron atom in Fe-porphyrin IX (Fe-PIX) proteins. Myoglobin variants containing an Ir(Me) site catalyse the functionalization of C–H bonds to form C–C bonds and add carbenes to β-substituted vinylarenes and unactivated aliphatic α-olefins. Directed evolution of the Ir(Me)-myoglobin generates mutants that form either enantiomer of the products of C–H insertion and catalyse the enantio- and diastereoselective cyclopropanation of unactivated olefins. The rich chemistry of free metalloporphyrins and the ease of preparation and evolution of substituted haem proteins using the methods adopted here open the way to the creation of many artificial metalloenzymes.
Enzymes that contain metal ions—that is, metalloenzymes—possess the reactivity of a transition metal centre and the potential of molecular evolution to modulate the reactivity and substrate-selectivity of the system
1
. By exploiting substrate promiscuity and protein engineering, the scope of reactions catalysed by native metalloenzymes has been expanded recently to include abiological transformations
2
,
3
. However, this strategy is limited by the inherent reactivity of metal centres in native metalloenzymes. To overcome this limitation, artificial metalloproteins have been created by incorporating complete, noble-metal complexes within proteins lacking native metal sites
1
,
4
,
5
. The interactions of the substrate with the protein in these systems are, however, distinct from those with the native protein because the metal complex occupies the substrate binding site. At the intersection of these approaches lies a third strategy, in which the native metal of a metalloenzyme is replaced with an abiological metal with reactivity different from that of the metal in a native protein
6
,
7
,
8
. This strategy could create artificial enzymes for abiological catalysis within the natural substrate binding site of an enzyme that can be subjected to directed evolution. Here we report the formal replacement of iron in Fe-porphyrin IX (Fe-PIX) proteins with abiological, noble metals to create enzymes that catalyse reactions not catalysed by native Fe-enzymes or other metalloenzymes
9
,
10
. In particular, we prepared modified myoglobins containing an Ir(Me) site that catalyse the functionalization of C–H bonds to form C–C bonds by carbene insertion and add carbenes to both β-substituted vinylarenes and unactivated aliphatic α-olefins. We conducted directed evolution of the Ir(Me)-myoglobin and generated mutants that form either enantiomer of the products of C–H insertion and catalyse the enantio- and diastereoselective cyclopropanation of unactivated olefins. The presented method of preparing artificial haem proteins containing abiological metal porphyrins sets the stage for the generation of artificial enzymes from innumerable combinations of PIX-protein scaffolds and unnatural metal cofactors to catalyse a wide range of abiological transformations.
Journal Article
A Bivalve Biomineralization Toolbox
by
Yarra, Tejaswi
,
Clark, Melody S
,
Blaxter, Mark
in
Animal Shells - metabolism
,
Animals
,
Biomimetics
2021
Mollusc shells are a result of the deposition of crystalline and amorphous calcite catalyzed by enzymes and shell matrix proteins (SMP). Developing a detailed understanding of bivalve mollusc biomineralization pathways is complicated not only by the multiplicity of shell forms and microstructures in this class, but also by the evolution of associated proteins by domain co-option and domain shuffling. In spite of this, a minimal biomineralization toolbox comprising proteins and protein domains critical for shell production across species has been identified. Using a matched pair design to reduce experimental noise from inter-individual variation, combined with damage-repair experiments and a database of biomineralization SMPs derived from published works, proteins were identified that are likely to be involved in shell calcification. Eighteen new, shared proteins likely to be involved in the processes related to the calcification of shells were identified by the analysis of genes expressed during repair in Crassostrea gigas, Mytilus edulis, and Pecten maximus. Genes involved in ion transport were also identified as potentially involved in calcification either via the maintenance of cell acid–base balance or transport of critical ions to the extrapallial space, the site of shell assembly. These data expand the number of candidate biomineralization proteins in bivalve molluscs for future functional studies and define a minimal functional protein domain set required to produce solid microstructures from soluble calcium carbonate. This is important for understanding molluscan shell evolution, the likely impacts of environmental change on biomineralization processes, materials science, and biomimicry research.
Journal Article